<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1 20151215//EN"  "JATS-archivearticle1.dtd"><article article-type="research-article" dtd-version="1.1" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:xlink="http://www.w3.org/1999/xlink"><front><journal-meta><journal-id journal-id-type="nlm-ta">elife</journal-id><journal-id journal-id-type="publisher-id">eLife</journal-id><journal-title-group><journal-title>eLife</journal-title></journal-title-group><issn pub-type="epub" publication-format="electronic">2050-084X</issn><publisher><publisher-name>eLife Sciences Publications, Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">53986</article-id><article-id pub-id-type="doi">10.7554/eLife.53986</article-id><article-categories><subj-group subj-group-type="display-channel"><subject>Research Article</subject></subj-group><subj-group subj-group-type="heading"><subject>Neuroscience</subject></subj-group></article-categories><title-group><article-title>Slo2 potassium channel function depends on RNA editing-regulated expression of a SCYL1 protein</article-title></title-group><contrib-group><contrib contrib-type="author" id="author-167065"><name><surname>Niu</surname><given-names>Long-Gang</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="fn" rid="con1"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-167066"><name><surname>Liu</surname><given-names>Ping</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="fn" rid="con2"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" id="author-13291"><name><surname>Wang</surname><given-names>Zhao-Wen</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="other" rid="fund2"/><xref ref-type="other" rid="fund3"/><xref ref-type="fn" rid="con3"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-150587"><name><surname>Chen</surname><given-names>Bojun</given-names></name><contrib-id authenticated="true" contrib-id-type="orcid">https://orcid.org/0000-0002-1141-9101</contrib-id><email>bochen@uchc.edu</email><xref ref-type="aff" rid="aff1"/><xref ref-type="other" rid="fund1"/><xref ref-type="fn" rid="con4"/><xref ref-type="fn" rid="conf1"/></contrib><aff id="aff1"><institution>Department of Neuroscience, University of Connecticut Health Center</institution><addr-line><named-content content-type="city">Farmington</named-content></addr-line><country>United States</country></aff></contrib-group><contrib-group content-type="section"><contrib contrib-type="editor"><name><surname>Hobert</surname><given-names>Oliver</given-names></name><role>Reviewing Editor</role><aff><institution>Howard Hughes Medical Institute, Columbia University</institution><country>United States</country></aff></contrib><contrib contrib-type="senior_editor"><name><surname>Aldrich</surname><given-names>Richard W</given-names></name><role>Senior Editor</role><aff><institution>The University of Texas at Austin</institution><country>United States</country></aff></contrib></contrib-group><pub-date date-type="publication" publication-format="electronic"><day>21</day><month>04</month><year>2020</year></pub-date><pub-date pub-type="collection"><year>2020</year></pub-date><volume>9</volume><elocation-id>e53986</elocation-id><history><date date-type="received" iso-8601-date="2019-11-26"><day>26</day><month>11</month><year>2019</year></date><date date-type="accepted" iso-8601-date="2020-04-20"><day>20</day><month>04</month><year>2020</year></date></history><permissions><copyright-statement>© 2020, Niu et al</copyright-statement><copyright-year>2020</copyright-year><copyright-holder>Niu et al</copyright-holder><ali:free_to_read/><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><ali:license_ref>http://creativecommons.org/licenses/by/4.0/</ali:license_ref><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife-53986-v2.pdf"/><abstract><p>Slo2 potassium channels play important roles in neuronal function, and their mutations in humans may cause epilepsies and cognitive defects. However, it is largely unknown how Slo2 is regulated by other proteins. Here we show that the function of <italic>C. elegans</italic> Slo2 (SLO-2) depends on <italic>adr-1</italic>, a gene important to RNA editing. ADR-1 promotes SLO-2 function not by editing the transcripts of <italic>slo-2</italic> but those of <italic>scyl-1</italic>, which encodes an orthologue of mammalian SCYL1. Transcripts of <italic>scyl-1</italic> are greatly decreased in <italic>adr-1</italic> mutants due to deficient RNA editing at a single adenosine in their 3’-UTR. SCYL-1 physically interacts with SLO-2 in neurons. Single-channel open probability (<italic>P<sub>o</sub></italic>) of neuronal SLO-2 is ~50% lower in <italic>scyl-1</italic> knockout mutant than wild type. Moreover, human Slo2.2/Slack <italic>P<sub>o</sub></italic> is doubled by SCYL1 in a heterologous expression system. These results suggest that SCYL-1/SCYL1 is an evolutionarily conserved regulator of Slo2 channels.</p></abstract><kwd-group kwd-group-type="author-keywords"><kwd>slo-2/slo2</kwd><kwd>SCYL-1/SCYL1</kwd><kwd>ADR-1</kwd><kwd>RNA editing</kwd></kwd-group><kwd-group kwd-group-type="research-organism"><title>Research organism</title><kwd><italic>C. elegans</italic></kwd></kwd-group><funding-group><award-group id="fund1"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000057</institution-id><institution>National Institute of General Medical Sciences</institution></institution-wrap></funding-source><award-id>R01GM113004</award-id><principal-award-recipient><name><surname>Chen</surname><given-names>Bojun</given-names></name></principal-award-recipient></award-group><award-group id="fund2"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000025</institution-id><institution>National Institute of Mental Health</institution></institution-wrap></funding-source><award-id>2R01MH085927</award-id><principal-award-recipient><name><surname>Wang</surname><given-names>Zhao-Wen</given-names></name></principal-award-recipient></award-group><award-group id="fund3"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000065</institution-id><institution>National Institute of Neurological Disorders and Stroke</institution></institution-wrap></funding-source><award-id>1R01NS109388</award-id><principal-award-recipient><name><surname>Wang</surname><given-names>Zhao-Wen</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group><custom-meta-group><custom-meta specific-use="meta-only"><meta-name>Author impact statement</meta-name><meta-value>The pseudokinase protein SCYL1 is an evolutionarily conserved enhancer of Slo2 potassium channel activity.</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="s1" sec-type="intro"><title>Introduction</title><p>Slo2 channels are large-conductance potassium channels existing in mammals as well as invertebrates (<xref ref-type="bibr" rid="bib29">Kaczmarek, 2013</xref>; <xref ref-type="bibr" rid="bib62">Yuan et al., 2000</xref>). They are the primary conductor of delayed outward currents in many neurons examined (<xref ref-type="bibr" rid="bib8">Budelli et al., 2009</xref>; <xref ref-type="bibr" rid="bib38">Liu et al., 2014</xref>). Human and mouse each has two Slo2 channels (Slo2.1/Slick and Slo2.2/Slack) (<xref ref-type="bibr" rid="bib29">Kaczmarek, 2013</xref>), whereas the nematode <italic>C. elegans</italic> has only one (SLO-2). These channels are abundantly expressed in the nervous system (<xref ref-type="bibr" rid="bib4">Bhattacharjee et al., 2002</xref>; <xref ref-type="bibr" rid="bib5">Bhattacharjee et al., 2005</xref>; <xref ref-type="bibr" rid="bib28">Joiner et al., 1998</xref>; <xref ref-type="bibr" rid="bib39">Liu et al., 2018</xref>; <xref ref-type="bibr" rid="bib49">Rizzi et al., 2016</xref>), and play major roles in shaping neuronal electrical properties and regulating neurotransmitter release (<xref ref-type="bibr" rid="bib29">Kaczmarek, 2013</xref>; <xref ref-type="bibr" rid="bib38">Liu et al., 2014</xref>). Mutations of Slo2 channels cause epilepsies and severe intellectual disabilities in humans (<xref ref-type="bibr" rid="bib1">Ambrosino et al., 2018</xref>; <xref ref-type="bibr" rid="bib12">Cataldi et al., 2019</xref>; <xref ref-type="bibr" rid="bib18">Evely et al., 2017</xref>; <xref ref-type="bibr" rid="bib22">Gururaj et al., 2017</xref>; <xref ref-type="bibr" rid="bib23">Hansen et al., 2017</xref>; <xref ref-type="bibr" rid="bib30">Kawasaki et al., 2017</xref>; <xref ref-type="bibr" rid="bib35">Lim et al., 2016</xref>; <xref ref-type="bibr" rid="bib42">McTague et al., 2018</xref>; <xref ref-type="bibr" rid="bib50">Rizzo et al., 2016</xref>), and reduced tolerance to hypoxic environment in worms (<xref ref-type="bibr" rid="bib63">Yuan et al., 2003</xref>). Emerging evidence suggests that physiological functions of these channels depend on other proteins. For example, in mice, the fragile mental retardation protein (FMRP), a RNA binding protein, enhances Slack activity by binding to its carboxyl terminus (<xref ref-type="bibr" rid="bib6">Brown et al., 2010</xref>). In worms, HRPU-2, a RNA/DNA binding protein, controls the expression level of SLO-2 through a posttranscriptional effect (<xref ref-type="bibr" rid="bib39">Liu et al., 2018</xref>).</p><p>RNA editing is an evolutionally conserved post-transcriptional process catalyzed by ADARs (<italic>a</italic>denosine <italic>d</italic>eaminases <italic>a</italic>cting on <italic>R</italic>NA) (<xref ref-type="bibr" rid="bib21">Gott and Emeson, 2000</xref>; <xref ref-type="bibr" rid="bib27">Jin et al., 2009</xref>). ADARs convert adenosine (A) to inosine (I) in double-stranded RNA. Since inosine is interpreted as guanosine (G) by cellular machineries (<xref ref-type="bibr" rid="bib2">Basilio et al., 1962</xref>), A-to-I RNA editing may alter the function of a protein by changing its coding potential, or regulate gene expression through altering alternative splicing, microRNA processing, or RNA interference (<xref ref-type="bibr" rid="bib16">Deffit and Hundley, 2016</xref>; <xref ref-type="bibr" rid="bib44">Nishikura, 2016</xref>). Human and mouse each has three ADARs: ADAR1, ADAR2 and ADAR3 (<xref ref-type="bibr" rid="bib14">Chen et al., 2000</xref>; <xref ref-type="bibr" rid="bib31">Kim et al., 1994</xref>; <xref ref-type="bibr" rid="bib43">Melcher et al., 1996</xref>). ADAR1 and ADAR2 possess deaminase activity and catalyze the A-to-I conversion (<xref ref-type="bibr" rid="bib58">Tan et al., 2017</xref>), whereas ADAR3 is catalytically inactive with regulatory roles in RNA editing (<xref ref-type="bibr" rid="bib44">Nishikura, 2016</xref>). Millions of A-to-I editing sites have been detected in the human transcriptome through RNA-seq, with the vast majority of them found in non-coding regions (<xref ref-type="bibr" rid="bib44">Nishikura, 2016</xref>). Biological effects of RNA editing at coding regions have been revealed for a variety of genes, including those encoding ligand- and voltage-gated ion channels and G protein-coupled receptors (<xref ref-type="bibr" rid="bib3">Bhalla et al., 2004</xref>; <xref ref-type="bibr" rid="bib7">Brusa et al., 1995</xref>; <xref ref-type="bibr" rid="bib11">Burns et al., 1997</xref>; <xref ref-type="bibr" rid="bib20">Gonzalez et al., 2011</xref>; <xref ref-type="bibr" rid="bib26">Huang et al., 2012</xref>; <xref ref-type="bibr" rid="bib40">Lomeli et al., 1994</xref>; <xref ref-type="bibr" rid="bib45">Palladino et al., 2000</xref>; <xref ref-type="bibr" rid="bib51">Rula et al., 2008</xref>; <xref ref-type="bibr" rid="bib55">Sommer et al., 1991</xref>; <xref ref-type="bibr" rid="bib57">Streit et al., 2011</xref>). However, little is known about the roles of RNA editing in non-coding regions (<xref ref-type="bibr" rid="bib44">Nishikura, 2016</xref>).</p><p>In a genetic screen for suppressors of a sluggish phenotype caused by expressing a hyperactive SLO-2 in worms, we isolated mutants of several genes, including <italic>adr-1</italic>, which encodes one of two ADARs in <italic>C. elegans</italic> (ADR-1 and ADR-2). While ADR-2 has deaminase activity and plays an indispensable role in the A-to-I conversion, ADR-1 is catalytically inactive but can promote RNA editing by binding to selected target mRNA and tethering ADR-2 to RNA substrates (<xref ref-type="bibr" rid="bib19">Ganem et al., 2019</xref>; <xref ref-type="bibr" rid="bib48">Rajendren et al., 2018</xref>; <xref ref-type="bibr" rid="bib60">Washburn et al., 2014</xref>). We found that loss-of-function (<italic>lf</italic>) mutations of <italic>adr-1</italic> inhibit SLO-2 function through impairing RNA editing of <italic>scyl-1</italic>, which encodes an orthologue of human and mouse SCYL1. In <italic>adr-1(lf)</italic> mutants, a lack of A-to-I conversion at a specific site in <italic>scyl-1</italic> 3’-UTR causes reduced <italic>scyl-1</italic> expression. Knockout of <italic>scyl-1</italic> severely reduces SLO-2 current in worms whereas coexpression of SCYL1 with human Slack in <italic>Xenopus</italic> oocytes greatly augments channel activity. These results suggest that SCYL-1/SCYL1 proteins likely play an evolutionarily conserved role in physiological functions of Slo2 channels. Mutations or knockout mammalian SCYL1 may cause neural degeneration, intellectual disabilities, and liver failure, but the underlying mechanisms are unclear (<xref ref-type="bibr" rid="bib33">Lenz et al., 2018</xref>; <xref ref-type="bibr" rid="bib34">Li et al., 2019</xref>; <xref ref-type="bibr" rid="bib54">Shohet et al., 2019</xref>; <xref ref-type="bibr" rid="bib56">Spagnoli et al., 2019</xref>). The revelation of SCYL-1/SCYL1 as a protein important to Slo2 channels suggests a potential link between diseases caused by SCLY1 mutations and Slo2 channel functions.</p></sec><sec id="s2" sec-type="results"><title>Results</title><sec id="s2-1"><title><italic>adr-1</italic> mutants suppress sluggish phenotype of <italic>slo-2(gf)</italic></title><p>In a genetic screen for mutants that suppressed a sluggish phenotype caused by an engineered hyperactive or gain-of-function (<italic>gf</italic>) SLO-2 (<xref ref-type="bibr" rid="bib39">Liu et al., 2018</xref>), we isolated two mutants (<italic>zw80</italic> and <italic>zw81</italic>) of the <italic>adr-1</italic> gene, as revealed by analyses of whole-genome sequencing data. <italic>zw80</italic> and <italic>zw81</italic> carry nonsense mutations leading to premature stops at tryptophan (W) 366 and W33, respectively (<xref ref-type="fig" rid="fig1">Figure 1A</xref>). <italic>slo-2(gf)</italic> worms showed greatly decreased locomotion speed compared with wild type, and this phenotype was substantially alleviated in <italic>slo-2(gf);adr-1(lf)</italic> double mutants (<xref ref-type="fig" rid="fig1">Figure 1B</xref>). To confirm that the suppression of <italic>slo-2(gf)</italic> phenotype resulted from mutations of <italic>adr-1</italic> rather than that of another gene, we created a new <italic>adr-1</italic> mutant allele (<italic>zw96</italic>) by introducing a premature stop codon at serine (S) 333 (<xref ref-type="fig" rid="fig1">Figure 1A</xref>) using the CRISPR/Cas9 approach. The sluggish phenotype of <italic>slo-2(gf)</italic> was similarly suppressed by <italic>adr-1(zw96)</italic>, which, by itself, did not enhance locomotion speed (<xref ref-type="fig" rid="fig1">Figure 1B</xref>). Expression of wild-type <italic>adr-1</italic> under the control of the pan-neuronal <italic>rab-3</italic> promotor (P<italic>rab-3</italic>) in <italic>slo-2(gf);adr-1(zw96)</italic> unmasked the sluggish phenotype (<xref ref-type="fig" rid="fig1">Figure 1B</xref>). These results indicate that the sluggish phenotype of <italic>slo-2(gf)</italic> is mainly caused by SLO-2 hyperactivity in neurons, and that neuronal function of SLO-2(<italic>gf</italic>) depends on ADR-1.</p><fig id="fig1" position="float"><label>Figure 1.</label><caption><title>Loss-of-function mutations of <italic>adr-1</italic> suppress phenotypes caused by a hyperactive SLO-2.</title><p>(<bold>A</bold>) Diagram of ADR-1 domain structures and locations of the non-sense mutations in the <italic>adr-1</italic> mutants. ADR-1 has two double-stranded RNA-binding motifs (dsRBM) and a pseudodeaminase domain. (<bold>B</bold>) Mutations of <italic>adr-1</italic> mitigated an inhibitory effect of hyperactive or gain-of-function (<italic>gf</italic>) SLO-2 on locomotion through acting in neurons. <italic>adr-1</italic> rescue was achieved by expressing GFP-tagged wild-type ADR-1 in neurons under the control of P<italic>rab-3</italic> (same in <bold>C</bold> and <bold>D</bold>). Sample sizes were 10–12 in each group. (<bold>C</bold>) <italic>adr-1(zw96)</italic> reduced an augmenting effect of <italic>slo-2(gf)</italic> on motor neuron whole-cell outward currents. Pipette solution I and bath solution I were used. Sample sizes were 7 <italic>wild type</italic>, 8 <italic>slo-2(gf)</italic>, 9 <italic>slo-2(gf);adr-1(zw96)</italic>, and 8 <italic>slo-2(gf);adr-1(zw96)</italic> rescue. (<bold>D</bold>) <italic>adr-1(zw96)</italic> mitigated an inhibitory effect of <italic>slo-2(gf)</italic> on postsynaptic current (PSC) bursts at the neuromuscular junction. The vertical dotted lines over the sample traces mark PSC bursts, which are defined as an apparent increase in PSC frequency accompanied by a sustained current (downward baseline shift) lasting &gt;3 s. Pipette solution II and bath solution I were used. Sample sizes were 12 <italic>wild type</italic>, and 7 in each of the remaining groups. All values are shown as mean ± SE. The asterisks indicate statistically significant differences between indicated groups (*p&lt;0.05, ***p&lt;0.001) based on either two-way (<bold>C</bold>) or one-way (<bold>D</bold>) ANOVA with Tukey's post hoc tests.</p><p><supplementary-material id="fig1sdata1"><label>Figure 1—source data 1.</label><caption><title>Raw data and numerical values for data plotted in <xref ref-type="fig" rid="fig1">Figure 1</xref>.</title></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-53986-fig1-data1-v2.xlsx"/></supplementary-material></p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig1-v2.tif"/></fig><p>In <italic>C. elegans</italic>, cholinergic motor neurons control body-wall muscle cells by producing bursts of postsynaptic currents (PSC bursts) (<xref ref-type="bibr" rid="bib38">Liu et al., 2014</xref>). To determine how <italic>adr-1</italic> mutants might alleviate the <italic>slo-2(gf)</italic> locomotion defect, we recorded voltage-activated whole-cell currents from a representative cholinergic motor neuron (VA5) and postsynaptic currents from body-wall muscle cells in wild type, <italic>slo-2(gf)</italic>, <italic>slo-2(gf);adr-1(zw96)</italic>, and <italic>slo-2(gf);adr-1(zw96)</italic> with <italic>adr-1</italic> rescued in neurons. Compared with wild type, the <italic>slo-2(gf)</italic> strain displayed much larger outward currents, and greatly decreased PSC burst frequency, duration and charge transfer (<xref ref-type="fig" rid="fig1">Figure 1C and D</xref>). These phenotypes of <italic>slo-2(gf)</italic> were mostly suppressed in the <italic>slo-2(gf);adr-1(zw96)</italic> strain (<xref ref-type="fig" rid="fig1">Figure 1C and D</xref>), suggesting that <italic>adr-1(lf)</italic> alleviated the sluggish phenotype through inhibiting SLO-2(<italic>gf</italic>). In addition, expression of wild-type <italic>adr-1</italic> in neurons of <italic>slo-2(gf);adr-1(zw96)</italic> unmasked the effects of <italic>slo-2(gf)</italic> on VA5 whole-cell currents and PSC bursts (<xref ref-type="fig" rid="fig1">Figure 1C and D</xref>). These observations suggest that the suppressing effect of <italic>adr-1(lf)</italic> on the <italic>slo-2(gf)</italic> sluggish phenotype was likely due to reduced SLO-2 activities in motor neurons.</p><p>We suspected that the suppression of SLO-2(<italic>gf</italic>) by <italic>adr-1(lf)</italic> resulted from deficient RNA-editing. If so, <italic>adr-2(lf)</italic> might also suppress the sluggish phenotype of <italic>slo-2</italic>(<italic>gf</italic>) because ADR-2 is required for RNA editing. Indeed, the sluggish phenotype of <italic>slo-2(gf)</italic> worms was substantially alleviated in <italic>slo-2(gf);adr-2(lf)</italic> double mutants (<xref ref-type="fig" rid="fig2">Figure 2A</xref>), and the augmenting effect of <italic>slo-2(gf)</italic> on VA5 whole-cell outward currents was mostly eliminated by <italic>adr-2(lf)</italic> (<xref ref-type="fig" rid="fig2">Figure 2B</xref>). Furthermore, <italic>adr-2(lf)</italic> brought VA5 whole-cell currents below the wild-type level (<xref ref-type="fig" rid="fig2">Figure 2B</xref>), which presumably resulted from reduced activities of wild-type SLO-2. These results suggest that RNA editing is important to SLO-2 function in neurons.</p><fig id="fig2" position="float"><label>Figure 2.</label><caption><title>Loss-of-function mutation of <italic>adr-2</italic> suppressed the effects of gain-of-function (<italic>gf</italic>) <italic>slo-</italic>2 on locomotion and motor neuron whole-cell currents.</title><p>(<bold>A</bold>) <italic>adr-2(gv42)</italic> alleviated an inhibitory effect of <italic>slo-2(gf)</italic> on locomotion speed. The sample size was 10–12 in each group. (<bold>B</bold>) <italic>adr-2(gv42)</italic> largely reversed an augmenting effect of <italic>slo-2(gf)</italic> on whole-cell currents in VA5 motor neuron. Sample sizes were 11 <italic>wild type</italic>, 8 <italic>slo-2(gf)</italic>, 11 <italic>slo-2(gf);adr-2(gv42)</italic>, and 10 <italic>adr-2(gv42).</italic> All data are shown as mean ± SE. Pipette solution I and bath solution I were used. The asterisks indicate statistically significant differences (*p&lt;0.05; ***p&lt;0.001) whereas ‘ns’ stands for ‘no significant difference’ between the indicated groups based on either one-way (<bold>A</bold>) or two-way (<bold>B</bold>) ANOVA with Tukey's post hoc tests.</p><p><supplementary-material id="fig2sdata1"><label>Figure 2—source data 1.</label><caption><title>Raw data and numerical values for data plotted in <xref ref-type="fig" rid="fig2">Figure 2</xref>.</title></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-53986-fig2-data1-v2.xlsx"/></supplementary-material></p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig2-v2.tif"/></fig></sec><sec id="s2-2"><title>ADR-1 is expressed in neurons and localized in the nucleus</title><p>The expression pattern of <italic>adr-1</italic> was examined by expressing GFP under the control of <italic>adr-1</italic> promoter (P<italic>adr-1</italic>). In transgenic worms, strong GFP expression was observed in the nervous system, including ventral cord motor neurons and many neurons in the head and tail, while weak GFP expression was observed in the intestine and body-wall muscles (<xref ref-type="fig" rid="fig3">Figure 3A</xref>). We then examined the subcellular localization pattern of ADR-1 by expressing GFP-tagged full-length ADR-1 (ADR-1::GFP) under the control of P<italic>rab-3</italic>. We found that ADR-1::GFP is localized in the nucleus, as indicated by its colocalization with the mStrawberry-tagged nucleus marker HIS-58 (<xref ref-type="bibr" rid="bib39">Liu et al., 2018</xref>) in ventral cord motor neurons (<xref ref-type="fig" rid="fig3">Figure 3B</xref>).</p><fig id="fig3" position="float"><label>Figure 3.</label><caption><title>ADR-1 is coexpressed with SLO-2 in many neurons and localized in the nucleus.</title><p>(<bold>A</bold>) Expression of an <italic>adr-1</italic> promoter (P<italic>adr-1</italic>)::GFP transcriptional fusion in worms resulted in strong GFP signal in many neurons (NR, nerve ring; VNC, ventral nerve cord; TG, tail ganglion) and weak GFP signal in body-wall muscles (BWM) and intestine (Int). (<bold>B</bold>) GFP-tagged ADR-1 (ADR-1::GFP) colocalized with a mStrawberry-tagged HIS-58 nucleus marker, as indicated by fluorescence images of VNC motor neurons. (<bold>C</bold>) <italic>adr-1</italic> and <italic>slo-2</italic> are co-expressed in many neurons but show differential expressions in the pharynx (Phx) and Int. Scale bar = 20 µm in in all panels.</p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig3-v2.tif"/></fig><p>To determine whether <italic>adr-1</italic> is co-expressed with <italic>slo-2</italic>, we crossed the P<italic>adr-1::GFP</italic> transgene into an existing strain expressing P<italic>slo-2::</italic>mStrawberry (<xref ref-type="bibr" rid="bib39">Liu et al., 2018</xref>). We found that the expression patterns of <italic>adr-1</italic> and <italic>slo-2</italic> overlapped extensively in the nervous system (<xref ref-type="fig" rid="fig3">Figure 3C</xref>). For example, the majority of ventral cord motor neurons and numerous head neurons were colabeled by GFP and mStrawberry (<xref ref-type="fig" rid="fig3">Figure 3C</xref>). The occasional non-overlapping expressions of GFP and mStrawberry in ventral cord motor neurons probably resulted from mosaic expression of the transgenes.</p></sec><sec id="s2-3"><title>ADR-1 regulates neurotransmitter release through SLO-2</title><p>SLO-2 is the primary conductor of delayed outward currents in <italic>C. elegans</italic> cholinergic motor neurons (<xref ref-type="bibr" rid="bib38">Liu et al., 2014</xref>). We wondered whether the function of native SLO-2 channels in motor neurons depends on ADR-1. Consistent with our previous report (<xref ref-type="bibr" rid="bib38">Liu et al., 2014</xref>), VA5 delayed outward currents were dramatically smaller and VA5 resting membrane potential was much less hyperpolarized in <italic>slo-2(lf)</italic> than wild type. While <italic>adr-1(lf)</italic> also caused significantly decreased outward currents and less hyperpolarized resting membrane potential in VA5, it did not produce additive effects when combined with <italic>slo-2(lf)</italic> (<xref ref-type="fig" rid="fig4">Figure 4A–C</xref>). These results suggest that <italic>adr-1(lf)</italic> affects motor neuron outward currents and resting membrane potential through SLO-2.</p><fig-group><fig id="fig4" position="float"><label>Figure 4.</label><caption><title>ADR-1 contributes to motor neuron whole-cell currents and regulates postsynaptic current (PSC) bursts through SLO-2.</title><p>(<bold>A</bold>) Representative VA5 whole-cell current traces. (<bold>B</bold>) Current (<bold>I</bold>) - voltage relationships of the whole-cell currents. Sample sizes were 8 <italic>wild type</italic>, 7 <italic>slo-2(lf)</italic>, 9 <italic>adr-1(zw96)</italic>, 7 <italic>slo-2(lf);adr-1(zw96),</italic> and 9 <italic>adr-1(zw96)</italic> rescue. (<bold>C</bold>) Resting membrane potentials of VA5. Sample sizes were 6 <italic>wild type</italic>, and 7 in each of the remaining groups. (<bold>D</bold>) Representative traces of spontaneous PSCs with PSC bursts marked by vertical dotted lines. (<bold>E</bold>) Comparisons of PSC burst properties. Sample sizes were 8 <italic>slo-2(lf);adr-1(zw96),</italic> 6 <italic>adr-1(zw96)</italic> rescue, and 12 in each of the remaining groups. All values are shown as mean ± SE. The asterisks indicate statistically significant differences (*p&lt;0.05, ***p&lt;0.001) compared with <italic>wild type</italic> whereas ‘ns’ stands for no significant difference between the indicated groups based on either two-way (<bold>B</bold>) or one-way (<bold>C and E</bold>) ANOVA with Tukey's post hoc tests. Pipette solution I and bath solution I were used in (<bold>A</bold>) and (<bold>C</bold>). Pipette solution II and bath solution I were used in (<bold>D</bold>).</p><p><supplementary-material id="fig4sdata1"><label>Figure 4—source data 1.</label><caption><title>Raw data and numerical values for data plotted in <xref ref-type="fig" rid="fig4">Figure 4</xref>.</title></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-53986-fig4-data1-v2.xlsx"/></supplementary-material></p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig4-v2.tif"/></fig><fig id="fig4s1" position="float" specific-use="child-fig"><label>Figure 4—figure supplement 1.</label><caption><title>Comparison of <italic>slo-2</italic> transcript level between <italic>wild type</italic> and <italic>adr-1</italic> mutant.</title><p>Shown are mean ± SE of three RNA-seq experiments.</p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig4-figsupp1-v2.tif"/></fig></fig-group><p>We next determined whether <italic>adr-1(lf)</italic> also alters PSC bursts. We found that <italic>adr-1(lf)</italic> caused an increase in the duration and mean charge transfer rate of PSC bursts without altering the burst frequency compared with wild type (<xref ref-type="fig" rid="fig4">Figure 4D and E</xref>). These phenotypes of <italic>adr-1(lf)</italic> were similar to those of <italic>slo-2(lf)</italic> and did not become more severe in the double mutants (<xref ref-type="fig" rid="fig4">Figure 4D and E</xref>), suggesting that ADR-1 modulates neurotransmitter release through SLO-2. The similar effects of <italic>adr-1(lf)</italic> and <italic>slo-2(lf)</italic> on PSC bursts are in contrast to their differential effects on VA5 outward currents and resting membrane potential. This discrepancy suggests that reducing SLO-2 activity beyond a certain threshold may produce similar effects on PSC bursts as does <italic>slo-2(lf)</italic>.</p></sec><sec id="s2-4"><title>ADR-1 regulates SLO-2 function through SCYL-1</title><p>Given that our results suggest that RNA editing is important to SLO-2 function, we determined whether <italic>adr-1(lf)</italic> causes deficient editing or decreased expression of <italic>slo-2</italic> mRNA by comparing RNA-seq data between <italic>adr-1(lf)</italic> and wild type. The <italic>adr-1(zw96)</italic> allele was chosen for these analyses to avoid complications by potential mutations of other genes introduced into the genome during the generation of the other <italic>adr-1</italic> mutants (<italic>zw80</italic> and <italic>zw81</italic>). Unexpectedly, no RNA editing event was detected in <italic>slo-2</italic> transcripts, and <italic>slo-2</italic> mRNA level was similar between wild type and the <italic>adr-1</italic> mutant (<xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1</xref>). These results suggest that ADR-1 might regulate SLO-2 function through RNA editing of another gene.</p><p>A previous study identified 270 high-confidence editing sites in transcripts of 51 genes expressed in <italic>C. elegans</italic> neurons (<xref ref-type="bibr" rid="bib60">Washburn et al., 2014</xref>). We suspected that the putative molecule mediating the effect of ADR-1 on SLO-2 is encoded by one of these genes, and the mRNA level of this gene is reduced in <italic>adr-1(lf)</italic>. Therefore, we compared transcript expression levels of these genes (excluding those encoding transposons) in our RNA-Seq data between wild type and <italic>adr-1(zw96)</italic>. Most of these genes showed either no decrease or only a small decrease in expression, but two of these genes, <italic>rncs-1</italic> and <italic>scyl-1</italic>, were reduced greatly in <italic>adr-1(lf)</italic> compared with wild type (<xref ref-type="fig" rid="fig5">Figure 5</xref>). <italic>rncs-1</italic> is not a conceivable candidate for the putative SLO-2 regulator because it is a non-coding gene expressed in the hypodermis and vulva (<xref ref-type="bibr" rid="bib24">Hellwig and Bass, 2008</xref>). We therefore focused our analyses on <italic>scyl-1</italic>, which encodes an orthologue of mammalian SCYL1 important to neuronal function and survival (<xref ref-type="bibr" rid="bib47">Pelletier, 2016</xref>). Like its mammalian homologs, SCYL-1 has an amino-terminal kinase domain that lacks residues critical to kinase activity, and a central domain containing five HEAT repeats (HEAT for <italic>H</italic>untingtin, <italic>e</italic>longation factor 3, protein phosphatase 2<italic>A</italic>, yeast kinase <italic>T</italic>OR1) (<xref ref-type="bibr" rid="bib47">Pelletier, 2016</xref>). SCYL-1 shares 38% identity and 60% similarity with human SCYL1. Notably, amino acid sequence in the HEAT domain, which is often highly degenerative (<xref ref-type="bibr" rid="bib47">Pelletier, 2016</xref>), shows a very high level of sequence homology (53% identity and 76% similarity) between these two proteins (<xref ref-type="fig" rid="fig5s1">Figure 5—figure supplement 1</xref>).</p><fig-group><fig id="fig5" position="float"><label>Figure 5.</label><caption><title>Normalized transcript expression levels of selected genes in <italic>adr-1(zw96)</italic> mutant.</title><p>The genes were selected based on the detection of ADR-1-dependent RNA editing events in their transcripts reported in an earlier study (<xref ref-type="bibr" rid="bib60">Washburn et al., 2014</xref>). Transcript expression level of each gene in the mutant is normalized by that in the wild type. Shown are mean ± SE from three biological replicates of RNA-seq experiments.</p><p><supplementary-material id="fig5sdata1"><label>Figure 5—source data 1.</label><caption><title>Raw data and numerical values for data plotted in <xref ref-type="fig" rid="fig5">Figure 5</xref>.</title></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-53986-fig5-data1-v2.xlsx"/></supplementary-material></p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig5-v2.tif"/></fig><fig id="fig5s1" position="float" specific-use="child-fig"><label>Figure 5—figure supplement 1.</label><caption><title>Alignment of amino acid sequences between <italic>C. elegans</italic> SCYL-1 (<italic>W07G4.3</italic>, <ext-link ext-link-type="uri" xlink:href="http://www.wormbase.org">www.wormbase.org</ext-link>) and human SCYL1 (hSCYL1, GenBank: NP_065731.3).</title><p>Identical residues are highlighted in black, while similar ones (in size or polarity) in blue. The three residues that are essential for kinase activity in eukaryotic protein kinases are shown in red above the alignment at corresponding locations. Both proteins contain five HEAT repeats (marked by horizontal green lines) in the central portion. The <italic>scyl-1</italic> mutant allele <italic>zw99</italic> was made by introducing a stop codon after the residue I<sup>152</sup> (indicated by an arrow) using the CRISPR/Cas9 approach.</p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig5-figsupp1-v2.tif"/></fig></fig-group><p>We examined the expression pattern of <italic>scyl-1</italic> by expressing GFP under the control of <italic>scyl-1</italic> promoter (P<italic>scyl-1</italic>). Because another gene (<italic>lap-2</italic>) resides ~2 kb upstream of <italic>scyl-1</italic> (<ext-link ext-link-type="uri" xlink:href="http://www.wormbase.org">www.wormbase.org</ext-link>), we first expressed GFP under the control of 2 kb P<italic>scyl-1</italic>. However, no GFP signal was detected in transgenic worms (not shown). We then used an in vivo homologous recombination approach to express a P<italic>scyl-1::GFP</italic> transcriptional fusion that included a much longer sequence upstream of the <italic>scyl-1</italic> initiation site. Specifically, a 0.5 kb genomic fragment upstream of the <italic>scyl-1</italic> initiation site was fused to GFP in a plasmid, which was co-injected with a fosmid covering part of the <italic>scyl-1</italic> coding region and 32 kb sequence upstream of the initiation site into wild type worms. In vivo homologous recombination between the plasmid and the fosmid is expected to result in a <italic>promoter::GFP</italic> transcriptional fusion that includes all the upstream genomic sequence in the fosmid. Transgenic worms from coinjection of the plasmid and the fosmid showed GFP signal in a variety of cells (<xref ref-type="fig" rid="fig6">Figure 6</xref>), suggesting distant upstream sequences are required for <italic>scyl-1</italic> expression. To determine how the expression pattern of <italic>scyl-1</italic> correlates with that of <italic>slo-2</italic>, we crossed the transgene into the P<italic>slo-2</italic>::mStrawberry strain, and examined the expression patterns of GFP and mStrawberry. Co-expression of <italic>scyl-1</italic> and <italic>slo-2</italic> was observed in many ventral cord motor neurons (<xref ref-type="fig" rid="fig6">Figure 6</xref>). However, most other neurons expressing <italic>slo-2</italic> (<italic>e. g.</italic> head and tail neurons) did not appear to express <italic>scyl-1</italic>. In addition, <italic>scyl-1</italic> expression was detected in some cells that did not express <italic>slo-2</italic>, including the excretory cell, spermatheca, uterine ventral cells, and intestinal cells (<xref ref-type="fig" rid="fig6">Figure 6</xref>).</p><fig id="fig6" position="float"><label>Figure 6.</label><caption><title><italic>scyl-1</italic> and <italic>slo-2</italic> are coexpressed in ventral cord motor neurons but differentially expressed in other cells.</title><p>In transgenic worms coexpressing P<italic>scyl-1::GFP</italic> and P<italic>slo-2::mStrawberry</italic> transcriptional fusions, GFP signal was observed in ventral nerve cord (VNC) motor neurons, the large H-shaped excretory (EXC) cell, uterine ventral (UV) cells, and spermatheca (Spe) while mStrawberry signal was detected in VNC motor neurons, body-wall muscles (BMW), and many other neurons. Scale bar = 20 µm.</p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig6-v2.tif"/></fig><p>We next determined whether SCYL-1 is important to SLO-2 function. To this end, we created a mutant, <italic>scyl-1(zw99)</italic>, by introducing a stop codon after isoleucine 152 using the CRISPR/Cas9 approach, and examined the effect of this mutation on VA5 delayed outward currents. <italic>scyl-1(zw99)</italic> showed a substantial decrease in VA5 outward currents compared with wild type; this phenotype could be rescued by expressing wild-type SCYL-1 in neurons, and was non-additive with that of either <italic>slo-2(lf)</italic> or <italic>adr-1(zw96)</italic> (<xref ref-type="fig" rid="fig7">Figure 7A</xref>). These results suggest that SCYL-1 and ADR-1 likely act in a common pathway to contribute to SLO-2 function.</p><fig id="fig7" position="float"><label>Figure 7.</label><caption><title>SCYL-1 contributes to motor neuron outward currents through SLO-2.</title><p>(<bold>A</bold>) Sample whole-cell current traces of VA5 motor neurons and the current-voltage relationships. Sample sizes were 9 <italic>wild type</italic>, 7 <italic>slo-2(lf)</italic>, 10 <italic>scyl-1(zw99),</italic> 7 <italic>slo-2(lf);scyl-1(zw99)</italic>, 7 <italic>adr-1(zw96);scyl-1(zw99)</italic>, and 7 <italic>scyl-1(zw99)</italic> rescue. The rescue strain was created by expressing wild-type <italic>scyl-1</italic> under the control of P<italic>rab-3</italic>. All values are shown as mean ± SE. The asterisks (***) and pound signs (<sup>###</sup>) indicate statistically significant differences (p&lt;0.001) between the indicated groups and from wild type, respectively, whereas ‘ns’ stands for no significant difference between the indicated groups (two-way ANOVA with Tukey's post hoc tests). (<bold>B</bold>) GFP signal in ventral cord motor neurons was indistinguishable between <italic>wild type</italic> and <italic>scyl-1(zw99)</italic> worms expressing GFP-tagged full-length SLO-2 under the control of P<italic>rab-3</italic>. Scale bar = 20 µm.</p><p><supplementary-material id="fig7sdata1"><label>Figure 7—source data 1.</label><caption><title>Raw data and numerical values for data plotted in <xref ref-type="fig" rid="fig7">Figure 7</xref>.</title></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-53986-fig7-data1-v2.xlsx"/></supplementary-material></p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig7-v2.tif"/></fig><p>The decrease of delayed outward currents in <italic>scyl-1(lf)</italic> could have resulted from either reduced expression or reduced function of SLO-2. We first determined whether <italic>scyl-1(lf)</italic> alters SLO-2 expression by crossing a stable (near 100% penetrance) P<italic>rab-3</italic>::SLO-2::GFP transgene from an existing transgenic strain of wild-type genetic background (<xref ref-type="bibr" rid="bib39">Liu et al., 2018</xref>) into <italic>scyl-1(zw99)</italic>, and comparing GFP signal between the two strains. We found that GFP signal in the ventral nerve cord was similar between wild type and the <italic>scyl-1</italic> mutant (<xref ref-type="fig" rid="fig7">Figure 7B</xref>), suggesting that SCYL-1 does not regulate SLO-2 expression. We then determined whether SCYL-1 regulates SLO-2 function by obtaining inside-out patches from VA5 and analyzing SLO-2 single-channel properties. SLO-2 showed &gt;50% decrease in open probability (<italic>P<sub>o</sub></italic>) without a change of single-channel conductance in <italic>scyl-1(zw99)</italic> compared with wild type, and this mutant phenotype was completely rescued by neuronal expression of wild-type SCYL-1 (<xref ref-type="fig" rid="fig8">Figure 8A</xref>). Analyses of single-channel open and closed events revealed that SLO-2 has at least two open states and three closed states, and that the decreased <italic>P<sub>o</sub></italic> of SLO-2 in <italic>scyl-1(lf)</italic> mainly resulted from shorter and fewer long openings (<xref ref-type="fig" rid="fig8">Figure 8B</xref>) and a larger proportion of the longest closings (<xref ref-type="fig" rid="fig8">Figure 8C</xref>).</p><fig id="fig8" position="float"><label>Figure 8.</label><caption><title>Single-channel open probability (<italic>P<sub>o</sub></italic>) of SLO-2 is decreased in <italic>scyl-1</italic> mutant.</title><p>(<bold>A</bold>) Representative SLO-2 single-channel currents from inside-out patches of the VA5 motor neuron, and comparisons of <italic>P<sub>o</sub></italic> and single-channel amplitude between <italic>wild type</italic> (<italic>n</italic> = 14), <italic>scyl-1(zw99)</italic> (<italic>n</italic> = 15), and <italic>scyl-1(zw99)</italic> rescued by expressing wild-type <italic>scyl-1</italic> in neurons under the control of P<italic>rab-3</italic> (<italic>n</italic> = 11). (<bold>B and C</bold>) Fitting of open and closed dwell time histogram to exponentials, and comparisons of τ values and relative areas (<bold>A</bold>) of the fitted components. All the open and closed events of each group were pooled together to plot the dwell time histograms. Statistical comparisons shown below were based on the mean τ values of individual recordings with each dot representing the mean value of one recording. Pipette solution III and bath solution II were used. All values are shown as mean ± SE. The asterisks indicate a significant difference between the indicated groups (*p&lt;0.05, ***p&lt;0.001, one-way ANOVA with Tukey's post hoc tests).</p><p><supplementary-material id="fig8sdata1"><label>Figure 8—source data 1.</label><caption><title>Raw data and numerical values for data plotted in <xref ref-type="fig" rid="fig8">Figure 8</xref>.</title></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-53986-fig8-data1-v2.xlsx"/></supplementary-material></p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig8-v2.tif"/></fig><p>The observed effects of <italic>scyl-1(lf)</italic> on SLO-2 single-channel properties suggest that SCYL-1 may physically interacts with SLO-2. To address this possibility, we performed bimolecular fluorescence complementation (BiFC) (<xref ref-type="bibr" rid="bib25">Hu et al., 2002</xref>) and coimmunoprecipitation assays, which indicate whether these two proteins are physically very close in vivo and whether they coexist in a molecular complex, respectively. In both assays, we determined whether full-length SCYL-1 interacts with either the full-length, the amino-terminal portion (amino acids 1–317), or the carboxyl-terminal portion (amino acids 318–1107) of SLO-2 (<xref ref-type="fig" rid="fig9">Figure 9A</xref>). In the BiFC assay, SCYL-1 and SLO-2 were fused to the N- and C-terminal portions of YFP (YFPa and YFPc), respectively (<xref ref-type="fig" rid="fig9">Figure 9A</xref>). A detection of YFP signal would indicate physical closeness of the two fusion proteins. We observed YFP fluorescence in ventral cord motor neurons when either the full-length or the C-terminal of SLO-2 was used but not when the N-terminal was used in the assays (<xref ref-type="fig" rid="fig9">Figure 9B</xref>). The coimmunoprecipitation assay was performed with homogenates of worms expressing HA-tagged SCYL-1 and GFP-tagged SLO-2. We found that the SCYL-1 immunoprecipitated with either full-length SLO-2 or SLO-2 C-terminal but not SLO-2 N-terminal (<xref ref-type="fig" rid="fig9">Figure 9C</xref>), which is in agreement with the BiFC results. Thus, both the BiFC and coimmunoprecipitation results suggest that SCYL-1 physically interacts with SLO-2, and this interaction is mediated by SLO-2 carboxyl terminal.</p><fig id="fig9" position="float"><label>Figure 9.</label><caption><title>SCYL-1 physically interacts with SLO-2 in neurons.</title><p>(<bold>A</bold>) Diagrams of the various fusion proteins used in the BiFC assays (<italic>left</italic>) and of SLO-2 membrane topology (<italic>right</italic>). The arrow indicates the split site for SLO-2N and SLO-2C fusions. RCK, regulator of conductance for K<sup>+</sup>. (<bold>B</bold>) YFP signal was detected when SCYL-1 was coexpressed with either full-length or the carboxyl terminal portion of SLO-2 but not with the amino terminal portion of SLO-2. Shown are representative fluorescent images of the ventral nerve cord (indicated by arrows) with corresponding DIC images. The bright signals at the top of each fluorescence image was from auto-fluorescence of the intestine. Scale bar = 20 μm. (<bold>C</bold>) SCYL-1 co-immunoprecipitates with full-length SLO-2 and SLO-2C but not SLO-2N. IP, immunoprecipitation; IB, immunoblot. The molecular masses of the protein standard are indicated on the right. Note that multiple bands are seen in the lanes loaded with GFP fusions. The bands that match predicted molecular masses of SLO-2::GFP, SLO-2N::GFP, and SLO-2C::GFP fusions are indicated with arrows, respectively. The other bands likely resulted from cleaved or partially translated GFP fusion proteins.</p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig9-v2.tif"/></fig></sec><sec id="s2-5"><title><italic>scyl-1</italic> expression depends on RNA editing at a specific 3’-UTR site</title><p>Our RNA-Seq data revealed eight high-frequency (&gt;15%) adenosine-to-guanosine editing sites in <italic>scyl-1</italic> transcripts of wild type (<xref ref-type="fig" rid="fig10">Figure 10A</xref>). All these editing sites are located within a predicted 746 bp hair-pin structure in the 3’ end of <italic>scyl-1</italic> pre-mRNA, which contains an inverted repeat with &gt;98% complementary base pairing (<xref ref-type="fig" rid="fig10">Figure 10B</xref>). Interestingly, RNA editing at only one of these sites was significantly deficient (by 74%) in <italic>adr-1(zw96)</italic> compared with wild type (<xref ref-type="fig" rid="fig10">Figure 10A</xref>). Sanger sequencing of <italic>scyl-1</italic> mRNA and the corresponding genomic DNA from wild type, <italic>adr-1(zw96)</italic>, and <italic>adr-2(gv42)</italic> showed that RNA editing at this site was deficient in both the <italic>adr-1</italic> and <italic>adr-2</italic> mutants whereas that at an adjacent site was deficient only in the <italic>adr-2</italic> mutant (<xref ref-type="fig" rid="fig10">Figure 10C</xref>), suggesting that RNA editing at the site impaired by <italic>adr-1(lf)</italic> might be important to <italic>scyl-1</italic> expression. To address this possibility, we created transgenic worms expressing a P<italic>rab-3::GFP</italic> transcriptional fusion (<italic>wp1923</italic>), in which a genomic DNA fragment covering part of the last exon of <italic>scyl-1</italic> and 5 kb downstream sequence was fused in-frame to the 3’-end of GFP coding sequence (<xref ref-type="fig" rid="fig10">Figure 10D</xref>). We also created transgenic worms expressing a modified plasmid (<italic>wp1924</italic>), in which adenosine (A) at the specific ADR-1-dependent editing site was changed to guanosine (G) to mimic the edited nucleotide (<xref ref-type="fig" rid="fig10">Figure 10D</xref>). GFP signal was observed in worms harboring <italic>wp1924</italic> but no GFP signal was detected in worms harboring <italic>wp1923</italic> (<xref ref-type="fig" rid="fig10">Figure 10E</xref>). While observation of GFP signal in the <italic>wp1924</italic> strain was expected, the complete absence of GFP signal in the <italic>wp1923</italic> strain caught us by surprise. To better understand the role of ADR-1 in <italic>scyl-1</italic> mRNA expression, we integrated the <italic>wp1924</italic> transgene into the wild-type genome, crossed it into <italic>adr-1(zw96)</italic>, and compared GFP signal in ventral cord motor neurons between wild type and the mutant. GFP signal was ~50% weaker in the mutant than wild type (<xref ref-type="fig" rid="fig10">Figure 10F and G</xref>). Because the transgene mimicked the edited 3’-UTR sequence of <italic>scyl-1</italic> mRNA, the weaker GFP signal in the mutant than wild type suggests that ADR-1 can also increase <italic>scyl-1</italic> mRNA level through a post-editing effect.</p><fig-group><fig id="fig10" position="float"><label>Figure 10.</label><caption><title>ADR-1 regulates <italic>scyl-1</italic> expression through RNA editing at a specific nucleotide in the 3’-UTR.</title><p>(<bold>A</bold>) RNA editing at one out of eight highly (&gt;15%) edited sites is severely deficient in <italic>adr-1(zw96)</italic> compared <italic>wild type</italic>. The percentage of editing was calculated by diving the number of reads containing A-I conversion by the total number of reads at each site. The <italic>x</italic>-axis indicates the positions of the edited adenosines in chromosome <italic>V</italic> (NC_003283). Shown are results (mean ± SE) of three RNA-seq experiments. The asterisks (***) indicate a statistically significant difference (p&lt;0.001, unpaired <italic>t</italic>-test). (<bold>B</bold>) Diagram showing a predicted hair-pin structure in the 3’ end of <italic>scyl-1</italic> pre-mRNA with 746 complementary base pairs. Nucleotide are numbered from the first nucleotide of the 3’-UTR. (<bold>C</bold>) Chromatograms of <italic>scyl-1</italic> mRNA 3’-UTRs of <italic>wild type</italic>, <italic>adr-1(zw96)</italic>, and <italic>adr-2(gv42)</italic>, and of the corresponding <italic>wild type</italic> genomic DNA. Two editing sites in <italic>wild type</italic> mRNA (indicated by arrows) display a mixture of green (adenosine) and black (guanosine) peaks. While both editing events are non-existent in <italic>adr-2(gv42)</italic>, only one of them is inhibited by <italic>adr-1(zw96)</italic>. (<bold>D</bold>) Diagram of two GFP reporter constructs (<italic>wp1923</italic> and <italic>wp1924</italic>) used to confirm the role of the ADR-1-dependent editing site in gene expression. GFP was placed under the control of P<italic>rab-3</italic> and fused to the last exon (blue) of <italic>scyl-1</italic> followed by 5 kb downstream genomic sequence. The red bars indicate the inverted repeat sequences that form the double-stranded RNA in the hair-pin structure (<bold>B</bold>). <italic>wp1923</italic> contains the intact genomic sequence of <italic>scyl-1</italic> 3’-UTR, whereas <italic>wp1924</italic> differs from it in an A-to-G conversion mimicking the ADR-1-dependent editing. (<bold>E</bold>) Effects of the A-to-G conversion on GFP reporter expression. Shown are fluorescent and corresponding DIC images of transgenic worms harboring either <italic>wp1923</italic> or <italic>wp1924</italic>. GFP expression in the head and ventral nerve cord (VNC) was observed only in worms harboring <italic>wp1924</italic>. The diffused signal below the VNC in fluorescent images was from auto-fluorescence of the intestine (Int). Scale bar = 20 µm. (<bold>F</bold>) GFP expression from <italic>wp1924</italic> was decreased in <italic>adr-1(zw96)</italic> compared with that in wild type. Scale bar = 20 µm. (<bold>G</bold>) Statistical comparison of GFP intensity in the VNC between <italic>wild type</italic> (<italic>n</italic> = 16) and <italic>adr-1(zw96)</italic> (<italic>n</italic> = 19). (***p&lt;0.001, unpaired <italic>t</italic>-test).</p><p><supplementary-material id="fig10sdata1"><label>Figure 10—source data 1.</label><caption><title>Raw data and numerical values for data plotted in <xref ref-type="fig" rid="fig10">Figure 10</xref>.</title></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-53986-fig10-data1-v2.xlsx"/></supplementary-material></p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig10-v2.tif"/></fig><fig id="fig10s1" position="float" specific-use="child-fig"><label>Figure 10—figure supplement 1.</label><caption><title>Expression of P<italic>rab-3::GFP::scyl-1 3’-UTR</italic> (A–to–G) was greatly decreased in isolated mutants.</title><p>(<bold>A</bold>) Images from wild type and two representative mutants, <italic>zw103</italic> and <italic>zw105</italic>, expressing P<italic>rab-3::GFP::scyl-1 3’-UTR</italic> (A–to–G). The GFP signals in the head and the ventral nerve cord (VNC) are almost invisible in the two mutants. The fluorescent signals at the bottom of the right panels were from auto-fluorescence of the intestine (Int). (<bold>B</bold>) GFP expression levels from P<italic>rab-3::GFP::unc-10 3’-UTR</italic> are comparable between wild type and the mutants. Scale bars = 20 µm.</p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig10-figsupp1-v2.tif"/></fig></fig-group><p>If ADR-1 does enhance <italic>scyl-1</italic> mRNA level through a post-editing mechanism in addition to RNA editing, it likely perform this function through interacting with some other proteins, and such proteins might be identified by screening for mutants showing decreased GFP signal from the <italic>wp1924</italic> transgene. Indeed, eleven mutants with reduced GFP expression were isolated from ~5000 mutagenized haploid genomes in a pilot genetic screen, as shown by two examples (<xref ref-type="fig" rid="fig10s1">Figure 10—figure supplement 1</xref>). The deficiency of GFP expression in these mutants was related to the function of <italic>scyl-1</italic> 3’-UTR because GFP expression from a control transgene with <italic>unc-10</italic> 3’-UTR was not compromised in these mutants (<xref ref-type="fig" rid="fig10s1">Figure 10—figure supplement 1</xref>). These results favor the notion that ADR-1 may also interact with other molecules after RNA editing to promote <italic>scyl-1</italic> expression.</p></sec><sec id="s2-6"><title>Human Slo2.2/Slack is regulated by SCYL1</title><p>The HEAT domain of SCYL proteins is important to protein-protein interactions but generally varies considerably in amino acid sequence for interactions with specific protein partners (<xref ref-type="bibr" rid="bib61">Yoshimura and Hirano, 2016</xref>). The high level of sequence homology of the HEAT domain between mammalian SCYL1 and worm SCYL-1 (<xref ref-type="fig" rid="fig5s1">Figure 5—figure supplement 1</xref>) promoted us to test whether mammalian Slo2.2/Slack is also regulated by SCYL1. We expressed human Slo2.2 (hSlo2.2) either alone or together with mouse SCYL1 in <italic>Xenopus</italic> oocytes, and analyzed hSlo2.2 single-channel properties in inside-out patches. SCYL1 increased hSlo2.2 <italic>P<sub>o</sub></italic> greatly without altering the single-channel conductance (<xref ref-type="fig" rid="fig11">Figure 11A</xref>). The channel has at least two open states and three closed states (<xref ref-type="fig" rid="fig11">Figure 11B–D</xref>). While events of both the open states and the two shorter closed states were numerous, those of the longest closed state were infrequent. Nevertheless, the longest closed state had a major impact on <italic>P<sub>o</sub></italic> because of its rather long duration. Dwell time analyses indicate that SCYL1 increased hSlo2.2 <italic>P<sub>o</sub></italic> mainly by increasing the duration and proportion of the longer open state, and shortening the duration of the longest closed state (<xref ref-type="fig" rid="fig11">Figure 11B–D</xref>). The overall effect of SCYL1 on hSlo2.2 <italic>P<sub>o</sub></italic> is similar to that of SCYL-1 on SLO-2 <italic>P<sub>o</sub></italic> in wild-type worms (<xref ref-type="fig" rid="fig8">Figure 8</xref>). Taken together, these results suggest that a physiological function of both mammalian SCYL1 and worm SCYL-1 is to enhance Slo2 channel activities.</p><fig id="fig11" position="float"><label>Figure 11.</label><caption><title>Single-channel open probability (<italic>P<sub>o</sub></italic>) of human Slo2.2/Slack is augmented by SCYL1 in <italic>Xenopus</italic> oocyte expression system.</title><p>(<bold>A</bold>) Representative traces of single-channel currents from inside-out patches and comparisons of <italic>P<sub>o</sub></italic> and single-channel amplitude between patches with and without mouse SCYL1. (<bold>B and C</bold>) Dwell time histograms and statistical comparisons of open and closed (≤30 ms in duration) events. The histograms were constructed and the τ values were quantified as described in <xref ref-type="fig" rid="fig8">Figure 8</xref> legend. (<bold>D</bold>) Dwell time histograms and statistical comparisons of the long closed events. Closed events that were &gt;30 ms in duration of all recordings in each group were pooled together to construct the dwell time histogram. The average duration and frequency of these events were compared between the two groups. Each dot represents the mean value of one recording. Sample sizes were 13 in both groups. All values are shown as mean ± SE. The asterisks indicate a significant difference compared between the indicated groups (*p&lt;0.05, ***p&lt;0.001, unpaired <italic>t</italic>-test).</p><p><supplementary-material id="fig11sdata1"><label>Figure 11—source data 1.</label><caption><title>Raw data and numerical values for data plotted in <xref ref-type="fig" rid="fig11">Figure 11</xref>.</title></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife-53986-fig11-data1-v2.xlsx"/></supplementary-material></p></caption><graphic mime-subtype="tiff" mimetype="image" xlink:href="elife-53986-fig11-v2.tif"/></fig></sec></sec><sec id="s3" sec-type="discussion"><title>Discussion</title><p>This study shows that both ADR-1 and SCYL-1 are critical to SLO-2 physiological function in neurons. While ADR-1 enhances SLO-2 function indirectly through promoting SCYL-1 expression, SCYL-1 regulates SLO-2 through physical interactions. These conclusions are supported by multiple lines of evidence, including the isolation of <italic>adr-1(lf)</italic> mutants as suppressors of SLO-2(<italic>gf</italic>), the inhibition of SLO-2 activities by either <italic>adr-1(lf)</italic> or <italic>scyl-1(lf)</italic>, the reduction of <italic>scyl-1</italic> transcript expression in <italic>adr-1(lf)</italic>, the correlation between <italic>scyl-1</italic> mRNA level and RNA editing at its 3’-UTR, the evidence of physical interactions between SCYL-1 and SLO-2, and the reduction of SLO-2 <italic>P<sub>o</sub></italic> due to changes in the dwell times of open and closed events in <italic>scyl-1(lf)</italic>. Importantly, we found that the human Slo2.2/Slack is also regulated by SCYL1.</p><p>The biological significance of RNA editing at non-coding regions is only beginning to be appreciated. A recent study with <italic>C. elegans</italic> identified many neuron-specific A-to-I editing sites in the 3’-UTR of <italic>clec-41</italic>, and showed that elimination of these editing events by <italic>adr-2</italic> knockout compromises <italic>clec-41</italic> expression and impairs a chemotaxis behavior (<xref ref-type="bibr" rid="bib15">Deffit et al., 2017</xref>). However, it remains to be determined how <italic>clec-41</italic> expression is controlled by these editing events, and whether the chemotaxis defect of <italic>adr-2(lf)</italic> mutant is caused by decreased <italic>clec-41</italic> expression. In the present study, we demonstrate that an A-to-I RNA editing event at the 3’UTR of <italic>scyl-1</italic> controls its expression, and that SCYL-1 contributes to neuronal whole-cell currents through a direct effect on SLO-2. The results of these two studies have provided a glimpse of the biological roles of 3’-UTR RNA editing in gene expression and neuronal function.</p><p>Our results demonstrate that RNA editing at a single site in the 3’-UTR could have a profound effect on gene expression. The A-to-I conversion at the ADR-1-regulated editing site increases base pairing in the putative double-stranded structure of <italic>scyl-1</italic> 3’-UTR (<xref ref-type="fig" rid="fig10">Figure 10B</xref>). Increased base paring in a double-stranded RNA generally facilitates RNA degradation. It is therefore intriguing how such an editing event may cause increased gene expression. One possibility is that editing at this site helps maintain mRNA stability through recruiting other regulatory proteins to the 3’-UTR. The isolation of mutants exhibiting diminished GFP expression from a reporter construct containing the edited <italic>scyl-1</italic> 3’-UTR but not the <italic>unc-10</italic> 3’-UTR (<xref ref-type="fig" rid="fig10s1">Figure 10—figure supplement 1</xref>) indicates potential existence of such regulatory proteins. In combination with the observation that GFP signal was undetectable in transgenic worms expressing a reporter construct containing the non-edited <italic>scyl-1</italic> 3’-UTR, this result suggests that RNA editing at the ADR-1-dependent site in <italic>scyl-1</italic> 3’-UTR is likely important to recruiting the putative regulatory proteins to increase mRNA stability.</p><p><italic>scyl-1</italic> has four different transcripts with identical 5’-UTR and coding sequence but different 3’-UTRs of variable lengths (ranging from 167 to 1862 nucleotides) and sequences (<ext-link ext-link-type="uri" xlink:href="http://www.wormbase.org">www.wormbase.org</ext-link>). The ADR-1-dependent editing site exists only in the transcript with the longest 3’-UTR. The presence of an ADR-1-regulated editing site in this but not the other transcripts suggests that ADR-1 may regulate <italic>scyl-1</italic> expression in a cell-specific manner depending on where the specific transcript is expressed. Interestingly, the 3’-UTR of human <italic>SCYL1</italic> transcripts (NM_020680.4) also has a high probability of forming hair-pin structures based on software prediction (<ext-link ext-link-type="uri" xlink:href="https://rna.urmc.rochester.edu/RNAstructureWeb/Servers">https://rna.urmc.rochester.edu/RNAstructureWeb/Servers</ext-link>). It remains to be determined whether human <italic>SCYL1</italic> transcripts are also edited in the 3’-UTR, and if so, whether the editing regulates their expression.</p><p>SCYL1 proteins are evolutionarily conserved proteins that share an N-terminal pseudokinase domain (<xref ref-type="bibr" rid="bib41">Manning et al., 2002</xref>; <xref ref-type="bibr" rid="bib47">Pelletier, 2016</xref>). Results of previous studies with cultured cells suggest that SCYL1 may regulate intracellular trafficking between the Golgi apparatus and the ER (<xref ref-type="bibr" rid="bib9">Burman et al., 2008</xref>; <xref ref-type="bibr" rid="bib10">Burman et al., 2010</xref>), and facilitate nuclear tRNA export by acting at the nuclear pore complex (<xref ref-type="bibr" rid="bib13">Chafe and Mangroo, 2010</xref>). Mutations of SCYL1 in humans are associated with a variety of disorders, including neurodegeneration, intellectual disabilities, and liver failure (<xref ref-type="bibr" rid="bib33">Lenz et al., 2018</xref>; <xref ref-type="bibr" rid="bib34">Li et al., 2019</xref>; <xref ref-type="bibr" rid="bib53">Schmidt et al., 2015</xref>; <xref ref-type="bibr" rid="bib54">Shohet et al., 2019</xref>; <xref ref-type="bibr" rid="bib56">Spagnoli et al., 2019</xref>). Mice with SCYL1 deficiency develop an early onset and progressive neurodegenerative disorder (<xref ref-type="bibr" rid="bib46">Pelletier et al., 2012</xref>). However, it is unclear whether the documented mutant phenotypes of SCYL1 are related to its roles in intracellular trafficking and nuclear tRNA export (<xref ref-type="bibr" rid="bib47">Pelletier, 2016</xref>). This study brings into view a new potential mechanism for SCYL1 mutation-associated disorders: impairing Slo2 channel function. What might be the molecular mechanism through which SCYL-1 enhances SLO-2 activity? Since SCYL-1 physically associates with SLO-2, and enhances SLO-2 single-channel <italic>P<sub>o</sub></italic> by altering the open and closed states, it likely regulates channel function either directly or through a closely associated protein. Although the exact mechanism remains to be determined, the similar effects of SCYL-1 and SCYL1 on Slo2 channels suggest that they likely play an important role in Slo2 physiological functions across animal species.</p><p>The expression patterns of <italic>scyl-1</italic> and <italic>slo-2</italic> largely do not overlap. Although they are coexpressed in ventral cord motor neurons, most other neurons expressing <italic>slo-2</italic> do not express <italic>scyl-1</italic>, suggesting that the regulatory effect of SCYL-1 on SLO-2 is cell- and tissue-specific. The expression of <italic>scyl-1</italic> in cells not expressing <italic>slo-2</italic> suggests that SCYL-1 physiological functions are not limited to regulating SLO-2. In mouse, SCYL1 and Slo2.2 are both expressed in the hippocampus and cerebellum but their expression patterns do not completely overlap (<xref ref-type="bibr" rid="bib28">Joiner et al., 1998</xref>; <xref ref-type="bibr" rid="bib52">Schmidt et al., 2007</xref>). Conceivably, the regulation of hSlo2.2 by SCYL1 might also occur in a cell- and tissue-specific manner, and SCYL1 likely performs other physiological functions. The latter possibility is supported by the pleiotropic phenotypes observed in patients and mice with SCYL1 mutations (<xref ref-type="bibr" rid="bib33">Lenz et al., 2018</xref>; <xref ref-type="bibr" rid="bib34">Li et al., 2019</xref>; <xref ref-type="bibr" rid="bib46">Pelletier et al., 2012</xref>; <xref ref-type="bibr" rid="bib53">Schmidt et al., 2015</xref>; <xref ref-type="bibr" rid="bib54">Shohet et al., 2019</xref>; <xref ref-type="bibr" rid="bib56">Spagnoli et al., 2019</xref>).</p><p>In summary, this study demonstrates that ADAR-mediated RNA editing controls the expression of SCYL-1, which interacts with SLO-2 to allow SLO-2 perform its physiological functions. Moreover, this study shows that this regulatory mechanism is conserved with mammalian SCYL1 and Slo2. Our findings reveal a new molecular mechanism of Slo2 channel regulation, and provide the bases for investigating how physiological functions of human Slo2 are regulated by SCYL1, and whether the neurodegeneration and intellectual disability phenotypes of SCYL1 mutations are related to Slo2 channel dysfunction.</p></sec><sec id="s4" sec-type="materials|methods"><title>Materials and methods</title><table-wrap id="keyresource" position="anchor"><label>Key resources table</label><table frame="hsides" rules="groups"><thead><tr><th valign="top">Reagent type (species) or resource</th><th valign="top">Designation</th><th valign="top">Source or reference</th><th valign="top">Identifiers</th><th valign="top">Additional information</th></tr></thead><tbody><tr><td valign="top">Strain, strain background(<italic>C. elegans</italic>)</td><td valign="top">N2</td><td valign="top">Caenorhabditis <break/>Genetics Center</td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/WB-STRAIN:WBStrain00000001">WB-STRAIN:WBStrain00000001</ext-link></td><td valign="top">Laboratory reference strain (wild type).</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">LY101</td><td valign="top">Caenorhabditis <break/>Genetics Center</td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/WB-STRAIN:WBStrain00026423">WB-STRAIN:WBStrain00026423</ext-link></td><td valign="top">Genotype: <italic>slo-2(nf101).</italic></td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">BB3</td><td valign="top">Caenorhabditis <break/>Genetics Center</td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/WB-STRAIN:WBStrain00000435">WB-STRAIN:WBStrain00000435</ext-link></td><td valign="top">Genotype: <italic>adr-2(gv42).</italic></td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW860</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs139[Pslo-1::slo-2(gf)(wp1311), Pmyo-2::YFP(wp214)]</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW876</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs139[Pslo-1::slo-2(gf)(wp1311), Pmyo-2::YFP(wp214)]; adr-1(zw80)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW877</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs139[Pslo-1::slo-2(gf)(wp1311), Pmyo-2::YFP(wp214)]; adr-1(zw81)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW983</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs139[Pslo-1::slo-2(gf)(wp1311), Pmyo-2::YFP(wp214)]; adr-2(gv42)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1049</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx221[Prab-3::slo-2::GFP]</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1388</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx260[Prab-3::His-58::mStrawberry(p1749), Prab-3::adr-1::GFP(p1374)]</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1394</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>adr-1(zw96).</italic></td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1401</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx261[Padr-1::GFP(wp1872), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1407</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs139[Pslo-1::slo-2(gf)(wp1311), Pmyo-2::YFP(wp214)]; adr-1(zw96)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1408</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs139[Pslo-1::slo-2(gf)(wp1311), Pmyo-2::YFP(wp214)]; zwEx262[Prab-3::adr-1::GFP(p1374);Pmyo-2::mStrawberry (wp1613)]; adr-1(zw96)</italic>.</td></tr><tr><td valign="top">Strain, strain <break/>background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1409</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>scyl-1(zw99).</italic> ZW1410: <italic>slo-2(nf101); scyl-1(zw99).</italic></td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1415</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype:: <italic>zwEx221[Prab-3::slo-2::GFP]; scyl-1(zw99)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1416</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx247[Pslo-2::mStrawberry(wp1776), lin-15(+)]; zwEx263[Pscyl-1::GFP(wp1901+wp1902), lin-15(+)]; lin-15(n765).</italic></td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1417</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx264[Prab-3::scyl-1(wp1912), Pmyo-2::mStrawberry (wp1613)]</italic>; <italic>scyl-1(zw99)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1418</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx247[Pslo-2::mStrawberry(wp1776), lin-15(+)]; zwEx261[Padr-1::GFP(wp1872), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1419</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx265[Prab-3::GFP::scyl-1 3-UTR(wp1923), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1420</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx266[Prab-3::GFP::scyl-1 3’-UTR(A-to-G)(wp1924), lin-15(+)]; lin-15(n765).</italic></td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1428</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>slo-2(nf101); adr-1(zw96)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1505</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx273[Prab-3::scyl-1::YFPc(wp1952), Prab-3::slo-2::YFPa(wp1783), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1506</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx274[Prab-3::scyl-1::YFPc(wp1952), Prab-3::slo-2N::YFPa(wp1784), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1507</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx275[Prab-3::scyl-1::YFPc(wp1952), Prab-3::slo-2C::YFPa(wp1785), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1537</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>adr-1(zw96);scyl-1(zw99)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1538</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx280[Prab-3::scyl-1::HA(wp1998), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1539</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx281[Prab-3::scyl-1::HA(wp1998), Prab-3::slo-2::GFP(wp1318), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1540</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx282[Prab-3::scyl-1::HA(wp1998), Prab-3::slo-2N::GFP(wp1999), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1541</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx283[Prab-3::scyl-1::HA(wp1998), Prab-3::slo-2C::GFP(wp2000), lin-15(+)]; lin-15(n765)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1544</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs146[Prab-3::GFP::scyl-1 3’-UTR(A-to-G)(wp1924)].</italic></td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1545</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs146[Prab-3::GFP::scyl-1 3’-UTR(A-to-G)(wp1924)]; adr-1(zw96)</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1549</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs146[Prab-3::GFP::scyl-1 3’-UTR(A-to-G)(wp1924)]; zw103.</italic></td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1552</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwIs146[Prab-3::GFP::scyl-1 3’UTR(A-to-G)(wp1924)]; zw105.</italic></td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1562</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx284[Prab-3::GFP::unc-10 3’-UTR(wp70)]</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1563</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx284[Prab-3::GFP::unc-10 3’-UTR(wp70)]; zw103</italic>.</td></tr><tr><td valign="top">Strain, strain background <break/>(<italic>C. elegans</italic>)</td><td valign="top">ZW1564</td><td valign="top">This paper</td><td valign="top"/><td valign="top">Genotype: <italic>zwEx284[Prab-3::GFP::unc-10 3’-UTR(wp70)]; zw105</italic>.</td></tr><tr><td valign="top">Antibody</td><td valign="top">Mouse monoclonal anti-HA</td><td valign="top">Santa Cruz Biotechnology</td><td valign="top">Cat# sc-7392, RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/AB_627809">AB_627809</ext-link></td><td valign="top">WB: 1:500</td></tr><tr><td valign="top">Antibody</td><td valign="top">Mouse monoclonal anti-GFP</td><td valign="top">Santa Cruz Biotechnology</td><td valign="top">Cat# sc-9996, RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/AB_627695">AB_627695</ext-link></td><td valign="top">WB: 1:500</td></tr><tr><td valign="top">Antibody</td><td valign="top">Donkey anti-Mouse IgG</td><td valign="top">Thermo Fisher Scientific</td><td valign="top">Cat# A16011, RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/AB_2534685">AB_2534685</ext-link></td><td valign="top">WB: 1:10000</td></tr><tr><td valign="top">Antibody</td><td valign="top">GFP-Trap_MA</td><td valign="top">ChromoTek</td><td valign="top">Cat# gtma-20, RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/AB_2631358">AB_2631358</ext-link></td><td valign="top"/></tr><tr><td valign="top">Commercial assay or kit</td><td valign="top">ECL Substrate</td><td valign="top">Bio-Rad</td><td valign="top">Cat# 1705060</td><td valign="top"/></tr><tr><td valign="top">Commercial assay or kit</td><td valign="top">mMESSAGE mMACHINE</td><td valign="top">Ambion</td><td valign="top">Cat# AM1348</td><td valign="top"/></tr><tr><td valign="top">Software, algorithm</td><td valign="top">Photoshop CS5</td><td valign="top">Adobe</td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/SCR_014199">SCR_014199</ext-link></td><td valign="top"><ext-link ext-link-type="uri" xlink:href="https://www.adobe.com/products/photoshop.html">https://www.adobe.com/products/photoshop.html</ext-link></td></tr><tr><td valign="top">Software, algorithm</td><td valign="top">Origin</td><td valign="top">OriginLab</td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/SCR_014212">SCR_014212</ext-link></td><td valign="top"><ext-link ext-link-type="uri" xlink:href="http://www.originlab.com/index.aspx?go=PRODUCTS/Origin">http://www.originlab.com/index.aspx?go=PRODUCTS/Origin</ext-link></td></tr><tr><td valign="top">Software, algorithm</td><td valign="top">ImageJ</td><td valign="top">NIH</td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/SCR_003070">SCR_003070</ext-link></td><td valign="top"><ext-link ext-link-type="uri" xlink:href="https://imagej.nih.gov/ij/">https://imagej.nih.gov/ij/</ext-link></td></tr><tr><td valign="top">Software, algorithm</td><td valign="top">pClamp</td><td valign="top">Molecular Devices</td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/SCR_011323">SCR_011323</ext-link></td><td valign="top"><ext-link ext-link-type="uri" xlink:href="http://www.moleculardevices.com/products/software/pclamp.html">http://www.moleculardevices.com/products/software/pclamp.html</ext-link></td></tr><tr><td valign="top">Software, algorithm</td><td valign="top">MATLAB</td><td valign="top">MathWorks</td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/SCR_001622">SCR_001622</ext-link></td><td valign="top"><ext-link ext-link-type="uri" xlink:href="http://www.mathworks.com/products/matlab/">http://www.mathworks.com/products/matlab/</ext-link></td></tr><tr><td valign="top">Software, algorithm</td><td valign="top">TopHat</td><td valign="top">PMID:<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/pubmed/23618408">23618408</ext-link></td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/SCR_013035">SCR_013035</ext-link></td><td valign="top"><ext-link ext-link-type="uri" xlink:href="http://ccb.jhu.edu/software/tophat/index.shtml">http://ccb.jhu.edu/software/tophat/index.shtml</ext-link></td></tr><tr><td valign="top">Software, algorithm</td><td valign="top">Trim Galore</td><td valign="top">Babraham Bioinformatics</td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/SCR_011847">SCR_011847</ext-link></td><td valign="top"><ext-link ext-link-type="uri" xlink:href="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/">http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/</ext-link></td></tr><tr><td valign="top">Software, algorithm</td><td valign="top">Track-A-Worm</td><td valign="top">PMID:<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/pubmed/23922769">23922769</ext-link></td><td valign="top">RRID:<ext-link ext-link-type="uri" xlink:href="https://scicrunch.org/resolver/SCR_018299">SCR_018299</ext-link></td><td valign="top"><ext-link ext-link-type="uri" xlink:href="https://health.uconn.edu/worm-lab/track-a-worm/">https://health.uconn.edu/worm-lab/track-a-worm/</ext-link></td></tr></tbody></table></table-wrap><sec id="s4-1"><title><italic>C. elegans</italic> culture and strains</title><p><italic>C. elegans</italic> hermaphrodites were grown on nematode growth medium (NGM) plates spotted with a layer of OP50 <italic>Escherichia coli</italic> at 22°C inside an environmental chamber. All the strains used in this study are listed in the Key Resource Table (plasmids used in making the transgenic strains are indicated by numbers with a ‘<italic>wp</italic>’ prefix).</p></sec><sec id="s4-2"><title>Mutant screening and mapping</title><p>An integrated transgenic strain expressing P<italic>slo-1</italic>::SLO-2(<italic>gf</italic>) and P<italic>myo-2</italic>::YFP (transgenic marker) in the wild-type genetic background was used for mutant screen. L4-stage <italic>slo-2(gf)</italic> worms were treated with the chemical mutagen ethyl methanesulfonate (50 mM) for 4 hr at room temperature. F2 progeny from the mutagenized worms were screened under stereomicroscope for animals that moved better than the original <italic>slo-2(gf)</italic> worms. 17 suppressors were isolated in the screen and were subjected to whole-genome sequencing. Analysis of the whole-genome sequencing data showed that 2 mutants have mutations in the <italic>adr-1 gene</italic> (<ext-link ext-link-type="uri" xlink:href="http://www.wormbase.com">www.wormbase.com</ext-link>). Identification of <italic>adr-1</italic> mutants was confirmed by the recovery of the sluggish phenotype when a wild-type cDNA of <italic>adr-1</italic> under the control of P<italic>rab-3</italic> was expressed in <italic>slo-2(gf);adr-1(zw81)</italic> double mutants.</p></sec><sec id="s4-3"><title>Generation of <italic>adr-1</italic> and <italic>scyl-1</italic> knockout mutants</title><p>The CRISPR/Cas9 approach (<xref ref-type="bibr" rid="bib17">Dickinson et al., 2013</xref>) was used to create <italic>adr-1</italic> and <italic>scyl-1</italic> knockouts. The guide RNA sequences for <italic>adr-1</italic> and <italic>scyl-1</italic> are 5’- <named-content content-type="sequence">CCAGTTTTCGAAGCTTCGG</named-content> and 5’- <named-content content-type="sequence">GAGGAGATTGGAAAATTGG</named-content>, which were inserted into pDD162 (P<italic>eft-3::Cas9</italic> + Empty <italic>sgRNA</italic>; Addgene #47549), respectively. The resultant plasmids (<italic>wp1645</italic> for <italic>adr-1</italic> and <italic>wp1887</italic> for <italic>scyl-1</italic>) were injected into wild type worms, respectively, along with a repair primer (5’-<named-content content-type="sequence">GAGAAGTATTCACCAGTTTTCGAAGCTTAATGAGTTCCAAAAGATCCAGAGATTCCCGAA</named-content> for <italic>adr-1</italic>, and 5’-<named-content content-type="sequence">TTGTAACAGCCGGAGGAGATTGGAAAATCTAGCTGGTGGACTTCATTTGGTCACTGGATT</named-content> for <italic>scyl-1</italic>) and P<italic>myo-2::mStrawberry</italic> (<italic>wp1613</italic>) as the transgenic marker. The <italic>adr-1</italic> knockout worms were identified by PCR using primers 5’-<named-content content-type="sequence">TCACCAGTTTTCGAAGCTTAATGA</named-content> (forward) and 5’-<named-content content-type="sequence">TCTTCTGCTGGCTCACATTCA</named-content> (reverse). The <italic>scyl-1</italic> knockout worms were identified by PCR using primers 5’- <named-content content-type="sequence">CCGAAGTCCCAATTCCCAT</named-content> (forward) and 5’- <named-content content-type="sequence">CCAAATGAAGTCCACCAGCTAG</named-content> (reverse). The knockout worms were confirmed by Sanger sequencing.</p></sec><sec id="s4-4"><title>Analysis of expression pattern and subcellular localization</title><p>The expression pattern of <italic>adr-1</italic> was assessed by expressing GFP under the control of 1.8 kb <italic>adr-1</italic> promoter (P<italic>adr-1::GFP</italic>, <italic>wp1872</italic>). Primers for cloning P<italic>adr-1</italic> are 5’- <named-content content-type="sequence">TAAGGTACCAAGGACACGTTGCATATGAAT</named-content> (forward) and 5’- <named-content content-type="sequence">TTTACCGGTTGGCTGACATATTGTGGGA</named-content> (reverse). Subcellular localization of ADR-1 was determined by fusing GFP to its carboxyl terminus and expressing the fusion protein under the control of P<italic>rab-3</italic> (P<italic>rab-3::adr-1::GFP</italic>, <italic>wp1374</italic>). Primers for cloning <italic>adr-1</italic> cDNA are 5’- <named-content content-type="sequence">AAAGCGGCCGCATGGATCAAAATCCTAACTACAA</named-content> (forward) and 5’- <named-content content-type="sequence">TTTACCGGTCCATCGAAAGCAGCAAGAGTGAAG</named-content> (reverse). A plasmid (<italic>wp1749</italic>) harboring P<italic>rab-3::his-58::mStrawberry</italic> serves as a nucleus marker. The expression pattern of <italic>scyl-1</italic> was assessed by an in vivo recombination approach. Specifically, a 0.5 kb fragment immediately upstream of <italic>scyl-1</italic> initiation site was cloned and fused to GFP using the primers 5’- <named-content content-type="sequence">AATCTGCAGCATCGGCACGAGAAGTACA</named-content> (forward) and 5’- <named-content content-type="sequence">TTAGGATCCCTAAAAGTGATCGAAATTTA</named-content> (reverse). The resultant plasmid (P<italic>scyl-1::GFP</italic>, <italic>wp1902</italic>) was linearized and co-injected with a linearized (fosmid WRM068bA03), which contains 32 kb of <italic>scyl-1</italic> upstream sequence and part of its coding region, into the <italic>lin-15(n765)</italic> strain along with a <italic>lin-15</italic> rescue plasmid to serve as a transformation marker. To assay the effect of the identified adenosine site at the 3’UTR of <italic>scyl-1</italic> on gene expression, a 5.1 kb genomic DNA fragment covering part of the <italic>scyl-1</italic> last exon and subsequent sequence was cloned and fused in-frame to GFP using the primers 5’- <named-content content-type="sequence">AATGCTAGCATGCAGGCTAGAAATGAAGCTCG</named-content> (forward) and 5’- <named-content content-type="sequence">TATGGGCCCGAAATCAGCATCTTTGACGAA</named-content> (reverse). To mimic the A-to-I editing at the identified specific site, a second plasmid was made by mutating the specific adenosine to guanosine in the above plasmid. The two resultant plasmids were injected into <italic>lin-15(n765)</italic>, respectively, with a <italic>lin-15</italic> rescue plasmid as the transgenic marker. Images of transgenic worms were taken with a digital CMOS camera (Hamamatsu, C11440-22CU) mounted on a Nikon TE2000-U inverted microscope equipped with EGFP/FITC and mCherry/Texas Red filter sets (49002 and 49008, Chroma Technology Corporation, Rockingham, VT, USA).</p></sec><sec id="s4-5"><title>Behavioral assay</title><p>Locomotion velocity was determined using an automated locomotion tracking system as described previously (<xref ref-type="bibr" rid="bib59">Wang and Wang, 2013</xref>). Briefly, a single adult hermaphrodite was transferred to an NGM plate without food. After allowing ~30 s for recovery from the transfer, snapshots of the worm were taken at 15 frames per second for 30 s using a IMAGINGSOURCE camera (DMK37BUX273) mounted on a stereomicroscope (LEICA M165FC). The worm was constantly kept in the center of the view field with a motorized microscope stage (OptiScanTM ES111, Prior Scientific, Inc, Rockland, MA, USA). Both the camera and the motorized stage were controlled by a custom program (<xref ref-type="supplementary-material" rid="scode1">Source code 1</xref>) running in MATLAB (The MathWorks, Inc, Natick, MA).</p></sec><sec id="s4-6"><title>RNA-seq and data analysis</title><p>Total RNA was extracted from young adult-stage worms using TRIzol Reagent (Invitrogen) and treated with TURBO DNase (Ambion). RNA-seq was performed by Novogene Corp. Sacramento, CA.</p><p>Raw reads ware filtered using Trim Galore software (<ext-link ext-link-type="uri" xlink:href="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/">http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/</ext-link>) to remove reads containing adapters or reads of low quality. The filtered reads were mapped to <italic>C. elegans</italic> genome (<italic>ce</italic>11) using TopHat2 (<xref ref-type="bibr" rid="bib32">Kim et al., 2013</xref>). The gene expression level is estimated by counting the reads that map to exons.</p></sec><sec id="s4-7"><title>Bimolecular fluorescence complementation (BiFC) assay</title><p>BiFC assays were performed by coexpressing SLO-2 and SCYL-1 tagged with the amino and carboxyl terminal portions of YFP (YFPa and YFPc), respectively, in neurons under the control of <italic>rab-3</italic> promoter (P<italic>rab-3</italic>). To assay which portion of SLO-2 may interact with SCYL-1, the full-length, N-terminal, and C-terminal portion of SLO-2 were fused with YFPa, respectively. The resultant plasmids (<italic>wp1783</italic>, P<italic>rab-3</italic>::SLO-2::YFPa; <italic>wp1784</italic>, P<italic>rab-3</italic>::SLO-2N::YFPa, and <italic>wp1785</italic>, P<italic>rab-3</italic>::SLO-2C::YFPa) were coinjected with P<italic>rab-3</italic>::SCYL-1::YFPc (<italic>wp1952</italic>), respectively, into <italic>lin-15(n765)</italic> strain. A <italic>lin-15</italic> rescue plasmid was also coinjected to serve as a transformation marker. Epifluorescence of the transgenic worms was visualized and imaged as described above.</p></sec><sec id="s4-8"><title>Co-immunoprecipitation</title><p>Mixed stage transgenic worms expressing either SCYL-1::HA alone or SCYL-1::HA with one of the GFP fusions (full-length SLO-2, SLO-2 amino-terminal, and SLO-2 carboxyl-terminal) were homogenized in lysis buffer containing 150 mM NaCl, 0.5 mM EDTA, 0.5 % P40, and 10 mM Tris/Cl pH 7.5. Immunoprecipitation was performed with a GFP-Trap Magnetic Agarose Kit (gtmak-20, ChromoTek Inc) according to the manufacturer’s manual. The immune complexes and the worm lysates were separated on 4–20% Novex Tris-Glysine gels (XP04202BOX, Thermo Fisher Scientific) and probed with HA or GFP antibodies (sc-7392, sc-9996, Santa Cruz Biotechnology, Inc).</p></sec><sec id="s4-9"><title><italic>C. elegans</italic> electrophysiology</title><p>Adult hermaphrodites were used in all electrophysiological experiments. Worms were immobilized and dissected as described previously (<xref ref-type="bibr" rid="bib36">Liu et al., 2007</xref>). Borosilicate glass pipettes were used as electrodes for recording whole-cell currents. Pipette tip resistance for recording muscle cell currents was 3–5 MΩ whereas that for recording motor neuron currents was ~20 MΩ. The dissected worm preparation was treated briefly with collagenase and perfused with the extracellular solution for 5 to 10-fold of bath volume. Classical whole-cell configuration was obtained by applying a negative pressure to the recording pipette. Current- and voltage-clamp experiments were performed with a Multiclamp 700B amplifier (Molecular Devices, Sunnyvale, CA, USA) and the Clampex software (version 10, Molecular Devices). Data were sampled at a rate of 10 kHz after filtering at 2 kHz. Spontaneous membrane potential changes were recorded using the current-clamp technique without current injection. Motor neuron whole-cell outward currents were recorded by applying a series of voltage steps (−60 to +70 mV at 10 mV intervals, 600 ms pulse duration) from a holding potential of −60 mV. Spontaneous PSCs were recorded from body-wall muscle cells at a holding potential of −60 mV. Two bath solutions and three pipette solutions were used in electrophysiological experiments as specified in figure legends. Bath solution I contained (in mM) 140 NaCl, 5 KCl, 5 CaCl<sub>2</sub>, 5 MgCl<sub>2</sub>, 11 dextrose and 5 HEPES (pH 7.2). Bath solution II contained (in mM) 100 K<sup>+</sup> gluconate, 50 KCl, 1 Mg<sup>2+</sup> gluconate, 0.1 Ca<sup>2+</sup> gluconate and 10 HEPES (pH 7.2). Pipette solution I contained (in mM) 120 KCl, 20 KOH, 5 Tris, 0.25 CaCl<sub>2</sub>, 4 MgCl<sub>2</sub>, 36 sucrose, 5 EGTA, and 4 Na<sub>2</sub>ATP (pH 7.2). Pipette solution II differed from pipette solution I in that 120 KCl was substituted by K<sup>+</sup> gluconate. Pipette solution III contained (in mM) 150 K<sup>+</sup> gluconate, 1 Mg<sup>2+</sup> gluconate and 10 HEPES (pH 7.2).</p></sec><sec id="s4-10"><title><italic>Xenopus</italic> oocytes expression and electrophysiology</title><p>A construct containing human <italic>Slack</italic> cDNA (pOX + <italic>hSlo2.2</italic>, a gift from Dr. Salkoff) was linearized with Pvu I. The mouse <italic>Scyl1</italic> cDNA was amplified from a construct (MR210762, Origene) and cloned into an existing vector downstream of the T3 promoter. The resultant plasmid (<italic>wp</italic>1982) was linearized with NgoM4. Capped cRNAs were synthesized using the mMessage mMachine Kit (Ambion). Approximately 50 nl cRNA of either <italic>Slack</italic> alone (0.5 ng/nl) or <italic>Slack</italic> (0.5 ng/nl) plus <italic>Scyl1</italic> (0.5 ng/nl) was injected into each oocyte using a Drummond Nanoject II injector (Drummond Scientific). Injected oocytes were incubated at 18°C in ND96 medium (in mM): 96 NaCl, 2 KCl, 1.8 CaCl<sub>2</sub>, 1 MgCl<sub>2</sub>, 5 HEPES (pH 7.5). 2 to 3 days after cRNA injection, single channel recordings were made in inside-out patches with a Multiclamp 700B amplifier (Molecular Devices, Sunnyvale, CA, USA) and the Clampex software (version 10, Molecular Devices). Data were sampled at 10 kHz after filtering at 2 kHz. Bath solution contained (in mM) 60 NaCl, 40 KCl, 50 K<sup>+</sup> gluconate, 10 KOH, 5 EGTA, and 5 HEPES (pH 7.2). Pipette solution contained (in mM) 100 K<sup>+</sup> gluconate, 60 Na<sup>+</sup> gluconate, 2 MgCl<sub>2</sub>, and 5 HEPES (pH 7.2).</p></sec><sec id="s4-11"><title>Data analyses for electrophysiology</title><p>Amplitudes of whole-cell currents in response to voltage steps were determined from the mean current during the last 100 ms of the 1200 ms voltage pulses using the Clampfit software. The duration and charge transfer of PSC bursts were quantified with Clampfit software (version 10, Molecular Devices) as previously described (<xref ref-type="bibr" rid="bib37">Liu et al., 2013</xref>). The frequency of PSC bursts was counted manually. For single channel analysis, the QuB software (<ext-link ext-link-type="uri" xlink:href="https://qub.mandelics.com/">https://qub.mandelics.com/</ext-link>) was used to fit open and closed times to exponentials, and to quantify the τ values and relative areas of the fitted components, which were automatically determined by the software. Single-channel conductance was calculated by dividing the single-channel current amplitude (determined from a Gaussian fit to the amplitude histogram) by the holding voltage. The first 30 s recording of each experiment was used for such analyses. Statistical comparisons were made with Origin Pro 2019 (OriginLab Corporation, Northampton, MA) using either <italic>ANOVA</italic> or unpaired <italic>t</italic>-test as specified in figure legends. p&lt;0.05 is considered to be statistically significant. The sample size (<italic>n</italic>) equals the number of cells or membrane patches analyzed. All values are shown as mean ± SE and data graphing was done with Origin Pro 2019.</p></sec></sec></body><back><ack id="ack"><title>Acknowledgements</title><p>This work was supported by National Institute of Health (R01GM113004 to BC, and 2R01MH085927 and 1R01NS109388 to Z-WW). We thank Dr. Laurence Salkoff for the human <italic>Slo2.2/Slack</italic> construct. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440).</p></ack><sec id="s5" sec-type="additional-information"><title>Additional information</title><fn-group content-type="competing-interest"><title>Competing interests</title><fn fn-type="COI-statement" id="conf1"><p>No competing interests declared</p></fn></fn-group><fn-group content-type="author-contribution"><title>Author contributions</title><fn fn-type="con" id="con1"><p>Data curation, Formal analysis, Investigation, Writing - review and editing</p></fn><fn fn-type="con" id="con2"><p>Data curation, Formal analysis, Investigation, Writing - review and editing</p></fn><fn fn-type="con" id="con3"><p>Conceptualization, Resources, Supervision, Funding acquisition, Writing - review and editing</p></fn><fn fn-type="con" id="con4"><p>Conceptualization, Supervision, Funding acquisition, Writing - original draft, Project administration, Writing - review and editing</p></fn></fn-group></sec><sec id="s6" sec-type="supplementary-material"><title>Additional files</title><supplementary-material id="scode1"><label>Source code 1.</label><caption><title>Track-A-Worm software.</title></caption><media mime-subtype="octet-stream" mimetype="application" xlink:href="elife-53986-code1-v2.rar"/></supplementary-material><supplementary-material id="transrepform"><label>Transparent reporting form</label><media mime-subtype="pdf" mimetype="application" xlink:href="elife-53986-transrepform-v2.pdf"/></supplementary-material></sec><sec id="s7" sec-type="data-availability"><title>Data availability</title><p>All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 1, 2, 4, 5, 7, 8, 10,and 11. Sequencing data have been deposited in GEO under accession code GSE141316.</p><p>The following dataset was generated:</p><p><element-citation id="dataset1" publication-type="data" specific-use="isSupplementedBy"><person-group person-group-type="author"><name><surname>Niu</surname><given-names>L</given-names></name><name><surname>Liu</surname><given-names>P</given-names></name><name><surname>Wang</surname><given-names>Z</given-names></name><name><surname>Chen</surname><given-names>B</given-names></name></person-group><year iso-8601-date="2019">2019</year><data-title>Slo2 potassium channel function depends on a SCYL1 protein</data-title><source>NCBI Gene Expression Omnibus</source><pub-id assigning-authority="NCBI" pub-id-type="accession" xlink:href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141316">GSE141316</pub-id></element-citation></p></sec><ref-list><title>References</title><ref id="bib1"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ambrosino</surname> <given-names>P</given-names></name><name><surname>Soldovieri</surname> <given-names>MV</given-names></name><name><surname>Bast</surname> <given-names>T</given-names></name><name><surname>Turnpenny</surname> <given-names>PD</given-names></name><name><surname>Uhrig</surname> <given-names>S</given-names></name><name><surname>Biskup</surname> <given-names>S</given-names></name><name><surname>Döcker</surname> <given-names>M</given-names></name><name><surname>Fleck</surname> <given-names>T</given-names></name><name><surname>Mosca</surname> <given-names>I</given-names></name><name><surname>Manocchio</surname> <given-names>L</given-names></name><name><surname>Iraci</surname> <given-names>N</given-names></name><name><surname>Taglialatela</surname> <given-names>M</given-names></name><name><surname>Lemke</surname> <given-names>JR</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>De novo gain‐of‐function variants in <italic>KCNT2</italic> as a novel cause of developmental and epileptic encephalopathy</article-title><source>Annals of Neurology</source><volume>83</volume><fpage>1198</fpage><lpage>1204</lpage><pub-id pub-id-type="doi">10.1002/ana.25248</pub-id></element-citation></ref><ref id="bib2"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Basilio</surname> <given-names>C</given-names></name><name><surname>Wahba</surname> <given-names>AJ</given-names></name><name><surname>Lengyel</surname> <given-names>P</given-names></name><name><surname>Speyer</surname> <given-names>JF</given-names></name><name><surname>Ochoa</surname> <given-names>S</given-names></name></person-group><year iso-8601-date="1962">1962</year><article-title>Synthetic polynucleotides and the amino acid code V</article-title><source>PNAS</source><volume>48</volume><fpage>613</fpage><lpage>616</lpage><pub-id pub-id-type="doi">10.1073/pnas.48.4.613</pub-id><pub-id pub-id-type="pmid">13865603</pub-id></element-citation></ref><ref id="bib3"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bhalla</surname> <given-names>T</given-names></name><name><surname>Rosenthal</surname> <given-names>JJ</given-names></name><name><surname>Holmgren</surname> <given-names>M</given-names></name><name><surname>Reenan</surname> <given-names>R</given-names></name></person-group><year iso-8601-date="2004">2004</year><article-title>Control of human potassium channel inactivation by editing of a small mRNA hairpin</article-title><source>Nature Structural &amp; Molecular Biology</source><volume>11</volume><fpage>950</fpage><lpage>956</lpage><pub-id pub-id-type="doi">10.1038/nsmb825</pub-id><pub-id pub-id-type="pmid">15361858</pub-id></element-citation></ref><ref id="bib4"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bhattacharjee</surname> <given-names>A</given-names></name><name><surname>Gan</surname> <given-names>L</given-names></name><name><surname>Kaczmarek</surname> <given-names>LK</given-names></name></person-group><year iso-8601-date="2002">2002</year><article-title>Localization of the slack potassium channel in the rat central nervous system</article-title><source>The Journal of Comparative Neurology</source><volume>454</volume><fpage>241</fpage><lpage>254</lpage><pub-id pub-id-type="doi">10.1002/cne.10439</pub-id><pub-id pub-id-type="pmid">12442315</pub-id></element-citation></ref><ref id="bib5"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Bhattacharjee</surname> <given-names>A</given-names></name><name><surname>von Hehn</surname> <given-names>CA</given-names></name><name><surname>Mei</surname> <given-names>X</given-names></name><name><surname>Kaczmarek</surname> <given-names>LK</given-names></name></person-group><year iso-8601-date="2005">2005</year><article-title>Localization of the na+-activated K+ channel slick in the rat central nervous system</article-title><source>The Journal of Comparative Neurology</source><volume>484</volume><fpage>80</fpage><lpage>92</lpage><pub-id pub-id-type="doi">10.1002/cne.20462</pub-id><pub-id pub-id-type="pmid">15717307</pub-id></element-citation></ref><ref id="bib6"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Brown</surname> <given-names>MR</given-names></name><name><surname>Kronengold</surname> <given-names>J</given-names></name><name><surname>Gazula</surname> <given-names>VR</given-names></name><name><surname>Chen</surname> <given-names>Y</given-names></name><name><surname>Strumbos</surname> <given-names>JG</given-names></name><name><surname>Sigworth</surname> <given-names>FJ</given-names></name><name><surname>Navaratnam</surname> <given-names>D</given-names></name><name><surname>Kaczmarek</surname> <given-names>LK</given-names></name></person-group><year iso-8601-date="2010">2010</year><article-title>Fragile X mental retardation protein controls gating of the sodium-activated potassium channel slack</article-title><source>Nature Neuroscience</source><volume>13</volume><fpage>819</fpage><lpage>821</lpage><pub-id pub-id-type="doi">10.1038/nn.2563</pub-id><pub-id pub-id-type="pmid">20512134</pub-id></element-citation></ref><ref id="bib7"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Brusa</surname> <given-names>R</given-names></name><name><surname>Zimmermann</surname> <given-names>F</given-names></name><name><surname>Koh</surname> <given-names>DS</given-names></name><name><surname>Feldmeyer</surname> <given-names>D</given-names></name><name><surname>Gass</surname> <given-names>P</given-names></name><name><surname>Seeburg</surname> <given-names>PH</given-names></name><name><surname>Sprengel</surname> <given-names>R</given-names></name></person-group><year iso-8601-date="1995">1995</year><article-title>Early-onset epilepsy and postnatal lethality associated with an editing-deficient GluR-B allele in mice</article-title><source>Science</source><volume>270</volume><fpage>1677</fpage><lpage>1680</lpage><pub-id pub-id-type="doi">10.1126/science.270.5242.1677</pub-id><pub-id pub-id-type="pmid">7502080</pub-id></element-citation></ref><ref id="bib8"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Budelli</surname> <given-names>G</given-names></name><name><surname>Hage</surname> <given-names>TA</given-names></name><name><surname>Wei</surname> <given-names>A</given-names></name><name><surname>Rojas</surname> <given-names>P</given-names></name><name><surname>Jong</surname> <given-names>YJ</given-names></name><name><surname>O'Malley</surname> <given-names>K</given-names></name><name><surname>Salkoff</surname> <given-names>L</given-names></name></person-group><year iso-8601-date="2009">2009</year><article-title>Na+-activated K+ channels express a large delayed outward current in neurons during normal physiology</article-title><source>Nature Neuroscience</source><volume>12</volume><fpage>745</fpage><lpage>750</lpage><pub-id pub-id-type="doi">10.1038/nn.2313</pub-id><pub-id pub-id-type="pmid">19412167</pub-id></element-citation></ref><ref id="bib9"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Burman</surname> <given-names>JL</given-names></name><name><surname>Bourbonniere</surname> <given-names>L</given-names></name><name><surname>Philie</surname> <given-names>J</given-names></name><name><surname>Stroh</surname> <given-names>T</given-names></name><name><surname>Dejgaard</surname> <given-names>SY</given-names></name><name><surname>Presley</surname> <given-names>JF</given-names></name><name><surname>McPherson</surname> <given-names>PS</given-names></name></person-group><year iso-8601-date="2008">2008</year><article-title>Scyl1, mutated in a recessive form of spinocerebellar neurodegeneration, regulates COPI-mediated retrograde traffic</article-title><source>Journal of Biological Chemistry</source><volume>283</volume><fpage>22774</fpage><lpage>22786</lpage><pub-id pub-id-type="doi">10.1074/jbc.M801869200</pub-id><pub-id pub-id-type="pmid">18556652</pub-id></element-citation></ref><ref id="bib10"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Burman</surname> <given-names>JL</given-names></name><name><surname>Hamlin</surname> <given-names>JN</given-names></name><name><surname>McPherson</surname> <given-names>PS</given-names></name></person-group><year iso-8601-date="2010">2010</year><article-title>Scyl1 regulates golgi morphology</article-title><source>PLOS ONE</source><volume>5</volume><elocation-id>e9537</elocation-id><pub-id pub-id-type="doi">10.1371/journal.pone.0009537</pub-id><pub-id pub-id-type="pmid">20209057</pub-id></element-citation></ref><ref id="bib11"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Burns</surname> <given-names>CM</given-names></name><name><surname>Chu</surname> <given-names>H</given-names></name><name><surname>Rueter</surname> <given-names>SM</given-names></name><name><surname>Hutchinson</surname> <given-names>LK</given-names></name><name><surname>Canton</surname> <given-names>H</given-names></name><name><surname>Sanders-Bush</surname> <given-names>E</given-names></name><name><surname>Emeson</surname> <given-names>RB</given-names></name></person-group><year iso-8601-date="1997">1997</year><article-title>Regulation of serotonin-2C receptor G-protein coupling by RNA editing</article-title><source>Nature</source><volume>387</volume><fpage>303</fpage><lpage>308</lpage><pub-id pub-id-type="doi">10.1038/387303a0</pub-id><pub-id pub-id-type="pmid">9153397</pub-id></element-citation></ref><ref id="bib12"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Cataldi</surname> <given-names>M</given-names></name><name><surname>Nobili</surname> <given-names>L</given-names></name><name><surname>Zara</surname> <given-names>F</given-names></name><name><surname>Combi</surname> <given-names>R</given-names></name><name><surname>Prato</surname> <given-names>G</given-names></name><name><surname>Giacomini</surname> <given-names>T</given-names></name><name><surname>Capra</surname> <given-names>V</given-names></name><name><surname>De Marco</surname> <given-names>P</given-names></name><name><surname>Ferini-Strambi</surname> <given-names>L</given-names></name><name><surname>Mancardi</surname> <given-names>MM</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Migrating focal seizures in autosomal dominant Sleep-related hypermotor epilepsy with KCNT1 mutation</article-title><source>Seizure</source><volume>67</volume><fpage>57</fpage><lpage>60</lpage><pub-id pub-id-type="doi">10.1016/j.seizure.2019.02.019</pub-id><pub-id pub-id-type="pmid">30903923</pub-id></element-citation></ref><ref id="bib13"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chafe</surname> <given-names>SC</given-names></name><name><surname>Mangroo</surname> <given-names>D</given-names></name></person-group><year iso-8601-date="2010">2010</year><article-title>Scyl1 facilitates nuclear tRNA export in mammalian cells by acting at the nuclear pore complex</article-title><source>Molecular Biology of the Cell</source><volume>21</volume><fpage>2483</fpage><lpage>2499</lpage><pub-id pub-id-type="doi">10.1091/mbc.e10-03-0176</pub-id><pub-id pub-id-type="pmid">20505071</pub-id></element-citation></ref><ref id="bib14"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Chen</surname> <given-names>CX</given-names></name><name><surname>Cho</surname> <given-names>DS</given-names></name><name><surname>Wang</surname> <given-names>Q</given-names></name><name><surname>Lai</surname> <given-names>F</given-names></name><name><surname>Carter</surname> <given-names>KC</given-names></name><name><surname>Nishikura</surname> <given-names>K</given-names></name></person-group><year iso-8601-date="2000">2000</year><article-title>A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains</article-title><source>RNA</source><volume>6</volume><fpage>755</fpage><lpage>767</lpage><pub-id pub-id-type="doi">10.1017/S1355838200000170</pub-id><pub-id pub-id-type="pmid">10836796</pub-id></element-citation></ref><ref id="bib15"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Deffit</surname> <given-names>SN</given-names></name><name><surname>Yee</surname> <given-names>BA</given-names></name><name><surname>Manning</surname> <given-names>AC</given-names></name><name><surname>Rajendren</surname> <given-names>S</given-names></name><name><surname>Vadlamani</surname> <given-names>P</given-names></name><name><surname>Wheeler</surname> <given-names>EC</given-names></name><name><surname>Domissy</surname> <given-names>A</given-names></name><name><surname>Washburn</surname> <given-names>MC</given-names></name><name><surname>Yeo</surname> <given-names>GW</given-names></name><name><surname>Hundley</surname> <given-names>HA</given-names></name></person-group><year iso-8601-date="2017">2017</year><article-title>The <italic>C. elegans</italic> neural editome reveals an ADAR target mRNA required for proper chemotaxis</article-title><source>eLife</source><volume>6</volume><elocation-id>e28625</elocation-id><pub-id pub-id-type="doi">10.7554/eLife.28625</pub-id><pub-id pub-id-type="pmid">28925356</pub-id></element-citation></ref><ref id="bib16"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Deffit</surname> <given-names>SN</given-names></name><name><surname>Hundley</surname> <given-names>HA</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>To edit or not to edit: regulation of ADAR editing specificity and efficiency</article-title><source>Wiley Interdisciplinary Reviews: RNA</source><volume>7</volume><fpage>113</fpage><lpage>127</lpage><pub-id pub-id-type="doi">10.1002/wrna.1319</pub-id><pub-id pub-id-type="pmid">26612708</pub-id></element-citation></ref><ref id="bib17"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Dickinson</surname> <given-names>DJ</given-names></name><name><surname>Ward</surname> <given-names>JD</given-names></name><name><surname>Reiner</surname> <given-names>DJ</given-names></name><name><surname>Goldstein</surname> <given-names>B</given-names></name></person-group><year iso-8601-date="2013">2013</year><article-title>Engineering the <italic>Caenorhabditis elegans</italic> genome using Cas9-triggered homologous recombination</article-title><source>Nature Methods</source><volume>10</volume><fpage>1028</fpage><lpage>1034</lpage><pub-id pub-id-type="doi">10.1038/nmeth.2641</pub-id><pub-id pub-id-type="pmid">23995389</pub-id></element-citation></ref><ref id="bib18"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Evely</surname> <given-names>KM</given-names></name><name><surname>Pryce</surname> <given-names>KD</given-names></name><name><surname>Bhattacharjee</surname> <given-names>A</given-names></name></person-group><year iso-8601-date="2017">2017</year><article-title>The Phe932Ile mutation in KCNT1 channels associated with severe epilepsy, delayed myelination and leukoencephalopathy produces a loss-of-function channel phenotype</article-title><source>Neuroscience</source><volume>351</volume><fpage>65</fpage><lpage>70</lpage><pub-id pub-id-type="doi">10.1016/j.neuroscience.2017.03.035</pub-id><pub-id pub-id-type="pmid">28366665</pub-id></element-citation></ref><ref id="bib19"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ganem</surname> <given-names>NS</given-names></name><name><surname>Ben-Asher</surname> <given-names>N</given-names></name><name><surname>Manning</surname> <given-names>AC</given-names></name><name><surname>Deffit</surname> <given-names>SN</given-names></name><name><surname>Washburn</surname> <given-names>MC</given-names></name><name><surname>Wheeler</surname> <given-names>EC</given-names></name><name><surname>Yeo</surname> <given-names>GW</given-names></name><name><surname>Zgayer</surname> <given-names>OB</given-names></name><name><surname>Mantsur</surname> <given-names>E</given-names></name><name><surname>Hundley</surname> <given-names>HA</given-names></name><name><surname>Lamm</surname> <given-names>AT</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Disruption in A-to-I editing levels affects <italic>C. elegans</italic> Development More Than a Complete Lack of Editing</article-title><source>Cell Reports</source><volume>27</volume><fpage>1244</fpage><lpage>1253</lpage><pub-id pub-id-type="doi">10.1016/j.celrep.2019.03.095</pub-id><pub-id pub-id-type="pmid">31018137</pub-id></element-citation></ref><ref id="bib20"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gonzalez</surname> <given-names>C</given-names></name><name><surname>Lopez-Rodriguez</surname> <given-names>A</given-names></name><name><surname>Srikumar</surname> <given-names>D</given-names></name><name><surname>Rosenthal</surname> <given-names>JJ</given-names></name><name><surname>Holmgren</surname> <given-names>M</given-names></name></person-group><year iso-8601-date="2011">2011</year><article-title>Editing of human K(V)1.1 channel mRNAs disrupts binding of the N-terminus tip at the intracellular cavity</article-title><source>Nature Communications</source><volume>2</volume><elocation-id>436</elocation-id><pub-id pub-id-type="doi">10.1038/ncomms1446</pub-id><pub-id pub-id-type="pmid">21847110</pub-id></element-citation></ref><ref id="bib21"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gott</surname> <given-names>JM</given-names></name><name><surname>Emeson</surname> <given-names>RB</given-names></name></person-group><year iso-8601-date="2000">2000</year><article-title>Functions and mechanisms of RNA editing</article-title><source>Annual Review of Genetics</source><volume>34</volume><fpage>499</fpage><lpage>531</lpage><pub-id pub-id-type="doi">10.1146/annurev.genet.34.1.499</pub-id><pub-id pub-id-type="pmid">11092837</pub-id></element-citation></ref><ref id="bib22"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Gururaj</surname> <given-names>S</given-names></name><name><surname>Palmer</surname> <given-names>EE</given-names></name><name><surname>Sheehan</surname> <given-names>GD</given-names></name><name><surname>Kandula</surname> <given-names>T</given-names></name><name><surname>Macintosh</surname> <given-names>R</given-names></name><name><surname>Ying</surname> <given-names>K</given-names></name><name><surname>Morris</surname> <given-names>P</given-names></name><name><surname>Tao</surname> <given-names>J</given-names></name><name><surname>Dias</surname> <given-names>K-R</given-names></name><name><surname>Zhu</surname> <given-names>Y</given-names></name><name><surname>Dinger</surname> <given-names>ME</given-names></name><name><surname>Cowley</surname> <given-names>MJ</given-names></name><name><surname>Kirk</surname> <given-names>EP</given-names></name><name><surname>Roscioli</surname> <given-names>T</given-names></name><name><surname>Sachdev</surname> <given-names>R</given-names></name><name><surname>Duffey</surname> <given-names>ME</given-names></name><name><surname>Bye</surname> <given-names>A</given-names></name><name><surname>Bhattacharjee</surname> <given-names>A</given-names></name></person-group><year iso-8601-date="2017">2017</year><article-title>A de novo mutation in the Sodium-Activated potassium channel KCNT2 alters ion selectivity and causes epileptic encephalopathy</article-title><source>Cell Reports</source><volume>21</volume><fpage>926</fpage><lpage>933</lpage><pub-id pub-id-type="doi">10.1016/j.celrep.2017.09.088</pub-id></element-citation></ref><ref id="bib23"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hansen</surname> <given-names>N</given-names></name><name><surname>Widman</surname> <given-names>G</given-names></name><name><surname>Hattingen</surname> <given-names>E</given-names></name><name><surname>Elger</surname> <given-names>CE</given-names></name><name><surname>Kunz</surname> <given-names>WS</given-names></name></person-group><year iso-8601-date="2017">2017</year><article-title>Mesial temporal lobe epilepsy associated with KCNT1 mutation</article-title><source>Seizure</source><volume>45</volume><fpage>181</fpage><lpage>183</lpage><pub-id pub-id-type="doi">10.1016/j.seizure.2016.12.018</pub-id><pub-id pub-id-type="pmid">28081520</pub-id></element-citation></ref><ref id="bib24"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hellwig</surname> <given-names>S</given-names></name><name><surname>Bass</surname> <given-names>BL</given-names></name></person-group><year iso-8601-date="2008">2008</year><article-title>A starvation-induced noncoding RNA modulates expression of Dicer-regulated genes</article-title><source>PNAS</source><volume>105</volume><fpage>12897</fpage><lpage>12902</lpage><pub-id pub-id-type="doi">10.1073/pnas.0805118105</pub-id><pub-id pub-id-type="pmid">18723671</pub-id></element-citation></ref><ref id="bib25"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Hu</surname> <given-names>CD</given-names></name><name><surname>Chinenov</surname> <given-names>Y</given-names></name><name><surname>Kerppola</surname> <given-names>TK</given-names></name></person-group><year iso-8601-date="2002">2002</year><article-title>Visualization of interactions among bZIP and rel family proteins in living cells using bimolecular fluorescence complementation</article-title><source>Molecular Cell</source><volume>9</volume><fpage>789</fpage><lpage>798</lpage><pub-id pub-id-type="doi">10.1016/s1097-2765(02)00496-3</pub-id><pub-id pub-id-type="pmid">11983170</pub-id></element-citation></ref><ref id="bib26"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Huang</surname> <given-names>H</given-names></name><name><surname>Tan</surname> <given-names>BZ</given-names></name><name><surname>Shen</surname> <given-names>Y</given-names></name><name><surname>Tao</surname> <given-names>J</given-names></name><name><surname>Jiang</surname> <given-names>F</given-names></name><name><surname>Sung</surname> <given-names>YY</given-names></name><name><surname>Ng</surname> <given-names>CK</given-names></name><name><surname>Raida</surname> <given-names>M</given-names></name><name><surname>Köhr</surname> <given-names>G</given-names></name><name><surname>Higuchi</surname> <given-names>M</given-names></name><name><surname>Fatemi-Shariatpanahi</surname> <given-names>H</given-names></name><name><surname>Harden</surname> <given-names>B</given-names></name><name><surname>Yue</surname> <given-names>DT</given-names></name><name><surname>Soong</surname> <given-names>TW</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>RNA editing of the IQ domain in ca(v)1.3 channels modulates their Ca²⁺-dependent inactivation</article-title><source>Neuron</source><volume>73</volume><fpage>304</fpage><lpage>316</lpage><pub-id pub-id-type="doi">10.1016/j.neuron.2011.11.022</pub-id><pub-id pub-id-type="pmid">22284185</pub-id></element-citation></ref><ref id="bib27"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jin</surname> <given-names>Y</given-names></name><name><surname>Zhang</surname> <given-names>W</given-names></name><name><surname>Li</surname> <given-names>Q</given-names></name></person-group><year iso-8601-date="2009">2009</year><article-title>Origins and evolution of ADAR-mediated RNA editing</article-title><source>IUBMB Life</source><volume>61</volume><fpage>572</fpage><lpage>578</lpage><pub-id pub-id-type="doi">10.1002/iub.207</pub-id><pub-id pub-id-type="pmid">19472181</pub-id></element-citation></ref><ref id="bib28"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Joiner</surname> <given-names>WJ</given-names></name><name><surname>Tang</surname> <given-names>MD</given-names></name><name><surname>Wang</surname> <given-names>LY</given-names></name><name><surname>Dworetzky</surname> <given-names>SI</given-names></name><name><surname>Boissard</surname> <given-names>CG</given-names></name><name><surname>Gan</surname> <given-names>L</given-names></name><name><surname>Gribkoff</surname> <given-names>VK</given-names></name><name><surname>Kaczmarek</surname> <given-names>LK</given-names></name></person-group><year iso-8601-date="1998">1998</year><article-title>Formation of intermediate-conductance calcium-activated potassium channels by interaction of slack and slo subunits</article-title><source>Nature Neuroscience</source><volume>1</volume><fpage>462</fpage><lpage>469</lpage><pub-id pub-id-type="doi">10.1038/2176</pub-id><pub-id pub-id-type="pmid">10196543</pub-id></element-citation></ref><ref id="bib29"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kaczmarek</surname> <given-names>LK</given-names></name></person-group><year iso-8601-date="2013">2013</year><article-title>Slack, slick, and Sodium-Activated potassium channels</article-title><source>ISRN Neuroscience</source><volume>2013</volume><fpage>1</fpage><lpage>14</lpage><pub-id pub-id-type="doi">10.1155/2013/354262</pub-id></element-citation></ref><ref id="bib30"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kawasaki</surname> <given-names>Y</given-names></name><name><surname>Kuki</surname> <given-names>I</given-names></name><name><surname>Ehara</surname> <given-names>E</given-names></name><name><surname>Murakami</surname> <given-names>Y</given-names></name><name><surname>Okazaki</surname> <given-names>S</given-names></name><name><surname>Kawawaki</surname> <given-names>H</given-names></name><name><surname>Hara</surname> <given-names>M</given-names></name><name><surname>Watanabe</surname> <given-names>Y</given-names></name><name><surname>Kishimoto</surname> <given-names>S</given-names></name><name><surname>Suda</surname> <given-names>K</given-names></name><name><surname>Saitsu</surname> <given-names>H</given-names></name><name><surname>Matsumoto</surname> <given-names>N</given-names></name></person-group><year iso-8601-date="2017">2017</year><article-title>Three cases of KCNT1 mutations: malignant migrating partial seizures in infancy with massive systemic to pulmonary collateral arteries</article-title><source>The Journal of Pediatrics</source><volume>191</volume><fpage>270</fpage><lpage>274</lpage><pub-id pub-id-type="doi">10.1016/j.jpeds.2017.08.057</pub-id></element-citation></ref><ref id="bib31"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kim</surname> <given-names>U</given-names></name><name><surname>Wang</surname> <given-names>Y</given-names></name><name><surname>Sanford</surname> <given-names>T</given-names></name><name><surname>Zeng</surname> <given-names>Y</given-names></name><name><surname>Nishikura</surname> <given-names>K</given-names></name></person-group><year iso-8601-date="1994">1994</year><article-title>Molecular cloning of cDNA for double-stranded RNA Adenosine Deaminase, a candidate enzyme for nuclear RNA editing</article-title><source>PNAS</source><volume>91</volume><fpage>11457</fpage><lpage>11461</lpage><pub-id pub-id-type="doi">10.1073/pnas.91.24.11457</pub-id></element-citation></ref><ref id="bib32"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Kim</surname> <given-names>D</given-names></name><name><surname>Pertea</surname> <given-names>G</given-names></name><name><surname>Trapnell</surname> <given-names>C</given-names></name><name><surname>Pimentel</surname> <given-names>H</given-names></name><name><surname>Kelley</surname> <given-names>R</given-names></name><name><surname>Salzberg</surname> <given-names>SL</given-names></name></person-group><year iso-8601-date="2013">2013</year><article-title>TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions</article-title><source>Genome Biology</source><volume>14</volume><elocation-id>R36</elocation-id><pub-id pub-id-type="doi">10.1186/gb-2013-14-4-r36</pub-id><pub-id pub-id-type="pmid">23618408</pub-id></element-citation></ref><ref id="bib33"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lenz</surname> <given-names>D</given-names></name><name><surname>McClean</surname> <given-names>P</given-names></name><name><surname>Kansu</surname> <given-names>A</given-names></name><name><surname>Bonnen</surname> <given-names>PE</given-names></name><name><surname>Ranucci</surname> <given-names>G</given-names></name><name><surname>Thiel</surname> <given-names>C</given-names></name><name><surname>Straub</surname> <given-names>BK</given-names></name><name><surname>Harting</surname> <given-names>I</given-names></name><name><surname>Alhaddad</surname> <given-names>B</given-names></name><name><surname>Dimitrov</surname> <given-names>B</given-names></name><name><surname>Kotzaeridou</surname> <given-names>U</given-names></name><name><surname>Wenning</surname> <given-names>D</given-names></name><name><surname>Iorio</surname> <given-names>R</given-names></name><name><surname>Himes</surname> <given-names>RW</given-names></name><name><surname>Kuloğlu</surname> <given-names>Z</given-names></name><name><surname>Blakely</surname> <given-names>EL</given-names></name><name><surname>Taylor</surname> <given-names>RW</given-names></name><name><surname>Meitinger</surname> <given-names>T</given-names></name><name><surname>Kölker</surname> <given-names>S</given-names></name><name><surname>Prokisch</surname> <given-names>H</given-names></name><name><surname>Hoffmann</surname> <given-names>GF</given-names></name><name><surname>Haack</surname> <given-names>TB</given-names></name><name><surname>Staufner</surname> <given-names>C</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>SCYL1 variants cause a syndrome with low γ-glutamyl-transferase cholestasis, acute liver failure, and neurodegeneration (CALFAN)</article-title><source>Genetics in Medicine</source><volume>20</volume><fpage>1255</fpage><lpage>1265</lpage><pub-id pub-id-type="doi">10.1038/gim.2017.260</pub-id></element-citation></ref><ref id="bib34"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Li</surname> <given-names>JQ</given-names></name><name><surname>Gong</surname> <given-names>JY</given-names></name><name><surname>Knisely</surname> <given-names>AS</given-names></name><name><surname>Zhang</surname> <given-names>MH</given-names></name><name><surname>Wang</surname> <given-names>JS</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Recurrent acute liver failure associated with novel <italic>SCYL1</italic> mutation: a case report</article-title><source>World Journal of Clinical Cases</source><volume>7</volume><fpage>494</fpage><lpage>499</lpage><pub-id pub-id-type="doi">10.12998/wjcc.v7.i4.494</pub-id><pub-id pub-id-type="pmid">30842961</pub-id></element-citation></ref><ref id="bib35"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lim</surname> <given-names>CX</given-names></name><name><surname>Ricos</surname> <given-names>MG</given-names></name><name><surname>Dibbens</surname> <given-names>LM</given-names></name><name><surname>Heron</surname> <given-names>SE</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title><italic>KCNT1</italic> mutations in seizure disorders: the phenotypic spectrum and functional effects</article-title><source>Journal of Medical Genetics</source><volume>53</volume><fpage>217</fpage><lpage>225</lpage><pub-id pub-id-type="doi">10.1136/jmedgenet-2015-103508</pub-id><pub-id pub-id-type="pmid">26740507</pub-id></element-citation></ref><ref id="bib36"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>Q</given-names></name><name><surname>Chen</surname> <given-names>B</given-names></name><name><surname>Ge</surname> <given-names>Q</given-names></name><name><surname>Wang</surname> <given-names>ZW</given-names></name></person-group><year iso-8601-date="2007">2007</year><article-title>Presynaptic Ca2+/calmodulin-dependent protein kinase II modulates neurotransmitter release by activating BK channels at <italic>Caenorhabditis elegans</italic> neuromuscular junction</article-title><source>Journal of Neuroscience</source><volume>27</volume><fpage>10404</fpage><lpage>10413</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.5634-06.2007</pub-id><pub-id pub-id-type="pmid">17898212</pub-id></element-citation></ref><ref id="bib37"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>P</given-names></name><name><surname>Chen</surname> <given-names>B</given-names></name><name><surname>Wang</surname> <given-names>ZW</given-names></name></person-group><year iso-8601-date="2013">2013</year><article-title>Postsynaptic current bursts instruct action potential firing at a graded synapse</article-title><source>Nature Communications</source><volume>4</volume><elocation-id>1911</elocation-id><pub-id pub-id-type="doi">10.1038/ncomms2925</pub-id><pub-id pub-id-type="pmid">23715270</pub-id></element-citation></ref><ref id="bib38"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>P</given-names></name><name><surname>Chen</surname> <given-names>B</given-names></name><name><surname>Wang</surname> <given-names>ZW</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>SLO-2 potassium channel is an important regulator of neurotransmitter release in <italic>Caenorhabditis elegans</italic></article-title><source>Nature Communications</source><volume>5</volume><elocation-id>5155</elocation-id><pub-id pub-id-type="doi">10.1038/ncomms6155</pub-id><pub-id pub-id-type="pmid">25300429</pub-id></element-citation></ref><ref id="bib39"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Liu</surname> <given-names>P</given-names></name><name><surname>Wang</surname> <given-names>SJ</given-names></name><name><surname>Wang</surname> <given-names>ZW</given-names></name><name><surname>Chen</surname> <given-names>B</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>HRPU-2, a homolog of mammalian hnRNP U, regulates synaptic transmission by controlling the expression of SLO-2 potassium channel in <italic>Caenorhabditis elegans</italic></article-title><source>The Journal of Neuroscience</source><volume>38</volume><fpage>1073</fpage><lpage>1084</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.1991-17.2017</pub-id><pub-id pub-id-type="pmid">29217678</pub-id></element-citation></ref><ref id="bib40"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Lomeli</surname> <given-names>H</given-names></name><name><surname>Mosbacher</surname> <given-names>J</given-names></name><name><surname>Melcher</surname> <given-names>T</given-names></name><name><surname>Höger</surname> <given-names>T</given-names></name><name><surname>Geiger</surname> <given-names>JR</given-names></name><name><surname>Kuner</surname> <given-names>T</given-names></name><name><surname>Monyer</surname> <given-names>H</given-names></name><name><surname>Higuchi</surname> <given-names>M</given-names></name><name><surname>Bach</surname> <given-names>A</given-names></name><name><surname>Seeburg</surname> <given-names>PH</given-names></name></person-group><year iso-8601-date="1994">1994</year><article-title>Control of kinetic properties of AMPA receptor channels by nuclear RNA editing</article-title><source>Science</source><volume>266</volume><fpage>1709</fpage><lpage>1713</lpage><pub-id pub-id-type="doi">10.1126/science.7992055</pub-id><pub-id pub-id-type="pmid">7992055</pub-id></element-citation></ref><ref id="bib41"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Manning</surname> <given-names>G</given-names></name><name><surname>Whyte</surname> <given-names>DB</given-names></name><name><surname>Martinez</surname> <given-names>R</given-names></name><name><surname>Hunter</surname> <given-names>T</given-names></name><name><surname>Sudarsanam</surname> <given-names>S</given-names></name></person-group><year iso-8601-date="2002">2002</year><article-title>The protein kinase complement of the human genome</article-title><source>Science</source><volume>298</volume><fpage>1912</fpage><lpage>1934</lpage><pub-id pub-id-type="doi">10.1126/science.1075762</pub-id><pub-id pub-id-type="pmid">12471243</pub-id></element-citation></ref><ref id="bib42"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>McTague</surname> <given-names>A</given-names></name><name><surname>Nair</surname> <given-names>U</given-names></name><name><surname>Malhotra</surname> <given-names>S</given-names></name><name><surname>Meyer</surname> <given-names>E</given-names></name><name><surname>Trump</surname> <given-names>N</given-names></name><name><surname>Gazina</surname> <given-names>EV</given-names></name><name><surname>Papandreou</surname> <given-names>A</given-names></name><name><surname>Ngoh</surname> <given-names>A</given-names></name><name><surname>Ackermann</surname> <given-names>S</given-names></name><name><surname>Ambegaonkar</surname> <given-names>G</given-names></name><name><surname>Appleton</surname> <given-names>R</given-names></name><name><surname>Desurkar</surname> <given-names>A</given-names></name><name><surname>Eltze</surname> <given-names>C</given-names></name><name><surname>Kneen</surname> <given-names>R</given-names></name><name><surname>Kumar</surname> <given-names>AV</given-names></name><name><surname>Lascelles</surname> <given-names>K</given-names></name><name><surname>Montgomery</surname> <given-names>T</given-names></name><name><surname>Ramesh</surname> <given-names>V</given-names></name><name><surname>Samanta</surname> <given-names>R</given-names></name><name><surname>Scott</surname> <given-names>RH</given-names></name><name><surname>Tan</surname> <given-names>J</given-names></name><name><surname>Whitehouse</surname> <given-names>W</given-names></name><name><surname>Poduri</surname> <given-names>A</given-names></name><name><surname>Scheffer</surname> <given-names>IE</given-names></name><name><surname>Chong</surname> <given-names>WKK</given-names></name><name><surname>Cross</surname> <given-names>JH</given-names></name><name><surname>Topf</surname> <given-names>M</given-names></name><name><surname>Petrou</surname> <given-names>S</given-names></name><name><surname>Kurian</surname> <given-names>MA</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>Clinical and molecular characterization of <italic>KCNT1</italic>-related severe early-onset epilepsy</article-title><source>Neurology</source><volume>90</volume><fpage>e55</fpage><lpage>e66</lpage><pub-id pub-id-type="doi">10.1212/WNL.0000000000004762</pub-id><pub-id pub-id-type="pmid">29196579</pub-id></element-citation></ref><ref id="bib43"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Melcher</surname> <given-names>T</given-names></name><name><surname>Maas</surname> <given-names>S</given-names></name><name><surname>Herb</surname> <given-names>A</given-names></name><name><surname>Sprengel</surname> <given-names>R</given-names></name><name><surname>Seeburg</surname> <given-names>PH</given-names></name><name><surname>Higuchi</surname> <given-names>M</given-names></name></person-group><year iso-8601-date="1996">1996</year><article-title>A mammalian RNA editing enzyme</article-title><source>Nature</source><volume>379</volume><fpage>460</fpage><lpage>464</lpage><pub-id pub-id-type="doi">10.1038/379460a0</pub-id><pub-id pub-id-type="pmid">8559253</pub-id></element-citation></ref><ref id="bib44"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Nishikura</surname> <given-names>K</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>A-to-I editing of coding and non-coding RNAs by ADARs</article-title><source>Nature Reviews Molecular Cell Biology</source><volume>17</volume><fpage>83</fpage><lpage>96</lpage><pub-id pub-id-type="doi">10.1038/nrm.2015.4</pub-id></element-citation></ref><ref id="bib45"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Palladino</surname> <given-names>MJ</given-names></name><name><surname>Keegan</surname> <given-names>LP</given-names></name><name><surname>O'Connell</surname> <given-names>MA</given-names></name><name><surname>Reenan</surname> <given-names>RA</given-names></name></person-group><year iso-8601-date="2000">2000</year><article-title>A-to-I pre-mRNA editing in <italic>Drosophila</italic> is primarily involved in adult nervous system function and integrity</article-title><source>Cell</source><volume>102</volume><fpage>437</fpage><lpage>449</lpage><pub-id pub-id-type="doi">10.1016/S0092-8674(00)00049-0</pub-id><pub-id pub-id-type="pmid">10966106</pub-id></element-citation></ref><ref id="bib46"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pelletier</surname> <given-names>S</given-names></name><name><surname>Gingras</surname> <given-names>S</given-names></name><name><surname>Howell</surname> <given-names>S</given-names></name><name><surname>Vogel</surname> <given-names>P</given-names></name><name><surname>Ihle</surname> <given-names>JN</given-names></name></person-group><year iso-8601-date="2012">2012</year><article-title>An early onset progressive motor neuron disorder in Scyl1-deficient mice is associated with mislocalization of TDP-43</article-title><source>Journal of Neuroscience</source><volume>32</volume><fpage>16560</fpage><lpage>16573</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.1787-12.2012</pub-id><pub-id pub-id-type="pmid">23175812</pub-id></element-citation></ref><ref id="bib47"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Pelletier</surname> <given-names>S</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>SCYL pseudokinases in neuronal function and survival</article-title><source>Neural Regeneration Research</source><volume>11</volume><fpage>42</fpage><lpage>44</lpage><pub-id pub-id-type="doi">10.4103/1673-5374.175040</pub-id></element-citation></ref><ref id="bib48"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rajendren</surname> <given-names>S</given-names></name><name><surname>Manning</surname> <given-names>AC</given-names></name><name><surname>Al-Awadi</surname> <given-names>H</given-names></name><name><surname>Yamada</surname> <given-names>K</given-names></name><name><surname>Takagi</surname> <given-names>Y</given-names></name><name><surname>Hundley</surname> <given-names>HA</given-names></name></person-group><year iso-8601-date="2018">2018</year><article-title>A protein-protein interaction underlies the molecular basis for substrate recognition by an adenosine-to-inosine RNA-editing enzyme</article-title><source>Nucleic Acids Research</source><volume>46</volume><fpage>9647</fpage><lpage>9659</lpage><pub-id pub-id-type="doi">10.1093/nar/gky800</pub-id><pub-id pub-id-type="pmid">30202880</pub-id></element-citation></ref><ref id="bib49"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rizzi</surname> <given-names>S</given-names></name><name><surname>Knaus</surname> <given-names>H-G</given-names></name><name><surname>Schwarzer</surname> <given-names>C</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Differential distribution of the sodium-activated potassium channels slick and slack in mouse brain</article-title><source>Journal of Comparative Neurology</source><volume>524</volume><fpage>2093</fpage><lpage>2116</lpage><pub-id pub-id-type="doi">10.1002/cne.23934</pub-id></element-citation></ref><ref id="bib50"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rizzo</surname> <given-names>F</given-names></name><name><surname>Ambrosino</surname> <given-names>P</given-names></name><name><surname>Guacci</surname> <given-names>A</given-names></name><name><surname>Chetta</surname> <given-names>M</given-names></name><name><surname>Marchese</surname> <given-names>G</given-names></name><name><surname>Rocco</surname> <given-names>T</given-names></name><name><surname>Soldovieri</surname> <given-names>MV</given-names></name><name><surname>Manocchio</surname> <given-names>L</given-names></name><name><surname>Mosca</surname> <given-names>I</given-names></name><name><surname>Casara</surname> <given-names>G</given-names></name><name><surname>Vecchi</surname> <given-names>M</given-names></name><name><surname>Taglialatela</surname> <given-names>M</given-names></name><name><surname>Coppola</surname> <given-names>G</given-names></name><name><surname>Weisz</surname> <given-names>A</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>Characterization of two de novoKCNT1 mutations in children with malignant migrating partial seizures in infancy</article-title><source>Molecular and Cellular Neuroscience</source><volume>72</volume><fpage>54</fpage><lpage>63</lpage><pub-id pub-id-type="doi">10.1016/j.mcn.2016.01.004</pub-id><pub-id pub-id-type="pmid">26784557</pub-id></element-citation></ref><ref id="bib51"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Rula</surname> <given-names>EY</given-names></name><name><surname>Lagrange</surname> <given-names>AH</given-names></name><name><surname>Jacobs</surname> <given-names>MM</given-names></name><name><surname>Hu</surname> <given-names>N</given-names></name><name><surname>Macdonald</surname> <given-names>RL</given-names></name><name><surname>Emeson</surname> <given-names>RB</given-names></name></person-group><year iso-8601-date="2008">2008</year><article-title>Developmental modulation of GABA(A) receptor function by RNA editing</article-title><source>Journal of Neuroscience</source><volume>28</volume><fpage>6196</fpage><lpage>6201</lpage><pub-id pub-id-type="doi">10.1523/JNEUROSCI.0443-08.2008</pub-id><pub-id pub-id-type="pmid">18550761</pub-id></element-citation></ref><ref id="bib52"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schmidt</surname> <given-names>WM</given-names></name><name><surname>Kraus</surname> <given-names>C</given-names></name><name><surname>Höger</surname> <given-names>H</given-names></name><name><surname>Hochmeister</surname> <given-names>S</given-names></name><name><surname>Oberndorfer</surname> <given-names>F</given-names></name><name><surname>Branka</surname> <given-names>M</given-names></name><name><surname>Bingemann</surname> <given-names>S</given-names></name><name><surname>Lassmann</surname> <given-names>H</given-names></name><name><surname>Müller</surname> <given-names>M</given-names></name><name><surname>Macedo-Souza</surname> <given-names>LI</given-names></name><name><surname>Vainzof</surname> <given-names>M</given-names></name><name><surname>Zatz</surname> <given-names>M</given-names></name><name><surname>Reis</surname> <given-names>A</given-names></name><name><surname>Bittner</surname> <given-names>RE</given-names></name></person-group><year iso-8601-date="2007">2007</year><article-title>Mutation in the <italic>Scyl1</italic> gene encoding amino-terminal kinase-like protein causes a recessive form of spinocerebellar neurodegeneration</article-title><source>EMBO Reports</source><volume>8</volume><fpage>691</fpage><lpage>697</lpage><pub-id pub-id-type="doi">10.1038/sj.embor.7401001</pub-id><pub-id pub-id-type="pmid">17571074</pub-id></element-citation></ref><ref id="bib53"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Schmidt</surname> <given-names>WM</given-names></name><name><surname>Rutledge</surname> <given-names>SL</given-names></name><name><surname>Schüle</surname> <given-names>R</given-names></name><name><surname>Mayerhofer</surname> <given-names>B</given-names></name><name><surname>Züchner</surname> <given-names>S</given-names></name><name><surname>Boltshauser</surname> <given-names>E</given-names></name><name><surname>Bittner</surname> <given-names>RE</given-names></name></person-group><year iso-8601-date="2015">2015</year><article-title>Disruptive SCYL1 mutations underlie a syndrome characterized by recurrent episodes of liver failure, peripheral neuropathy, cerebellar atrophy, and ataxia</article-title><source>The American Journal of Human Genetics</source><volume>97</volume><fpage>855</fpage><lpage>861</lpage><pub-id pub-id-type="doi">10.1016/j.ajhg.2015.10.011</pub-id><pub-id pub-id-type="pmid">26581903</pub-id></element-citation></ref><ref id="bib54"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Shohet</surname> <given-names>A</given-names></name><name><surname>Cohen</surname> <given-names>L</given-names></name><name><surname>Haguel</surname> <given-names>D</given-names></name><name><surname>Mozer</surname> <given-names>Y</given-names></name><name><surname>Shomron</surname> <given-names>N</given-names></name><name><surname>Tzur</surname> <given-names>S</given-names></name><name><surname>Bazak</surname> <given-names>L</given-names></name><name><surname>Basel Salmon</surname> <given-names>L</given-names></name><name><surname>Krause</surname> <given-names>I</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>Variant in SCYL1 gene causes aberrant splicing in a family with cerebellar ataxia, recurrent episodes of liver failure, and growth retardation</article-title><source>European Journal of Human Genetics</source><volume>27</volume><fpage>263</fpage><lpage>268</lpage><pub-id pub-id-type="doi">10.1038/s41431-018-0268-2</pub-id><pub-id pub-id-type="pmid">30258122</pub-id></element-citation></ref><ref id="bib55"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Sommer</surname> <given-names>B</given-names></name><name><surname>Köhler</surname> <given-names>M</given-names></name><name><surname>Sprengel</surname> <given-names>R</given-names></name><name><surname>Seeburg</surname> <given-names>PH</given-names></name></person-group><year iso-8601-date="1991">1991</year><article-title>RNA editing in brain controls a determinant of ion flow in glutamate-gated channels</article-title><source>Cell</source><volume>67</volume><fpage>11</fpage><lpage>19</lpage><pub-id pub-id-type="doi">10.1016/0092-8674(91)90568-J</pub-id><pub-id pub-id-type="pmid">1717158</pub-id></element-citation></ref><ref id="bib56"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Spagnoli</surname> <given-names>C</given-names></name><name><surname>Frattini</surname> <given-names>D</given-names></name><name><surname>Salerno</surname> <given-names>GG</given-names></name><name><surname>Fusco</surname> <given-names>C</given-names></name></person-group><year iso-8601-date="2019">2019</year><article-title>On CALFAN syndrome: report of a patient with a novel variant in SCYL1 gene and recurrent respiratory failure</article-title><source>Genetics in Medicine</source><volume>21</volume><fpage>1663</fpage><lpage>1664</lpage><pub-id pub-id-type="doi">10.1038/s41436-018-0389-6</pub-id><pub-id pub-id-type="pmid">30531813</pub-id></element-citation></ref><ref id="bib57"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Streit</surname> <given-names>AK</given-names></name><name><surname>Derst</surname> <given-names>C</given-names></name><name><surname>Wegner</surname> <given-names>S</given-names></name><name><surname>Heinemann</surname> <given-names>U</given-names></name><name><surname>Zahn</surname> <given-names>RK</given-names></name><name><surname>Decher</surname> <given-names>N</given-names></name></person-group><year iso-8601-date="2011">2011</year><article-title>RNA editing of Kv1.1 channels may account for reduced ictogenic potential of 4-aminopyridine in chronic epileptic rats</article-title><source>Epilepsia</source><volume>52</volume><fpage>645</fpage><lpage>648</lpage><pub-id pub-id-type="doi">10.1111/j.1528-1167.2011.02986.x</pub-id></element-citation></ref><ref id="bib58"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Tan</surname> <given-names>MH</given-names></name><name><surname>Li</surname> <given-names>Q</given-names></name><name><surname>Shanmugam</surname> <given-names>R</given-names></name><name><surname>Piskol</surname> <given-names>R</given-names></name><name><surname>Kohler</surname> <given-names>J</given-names></name><name><surname>Young</surname> <given-names>AN</given-names></name><name><surname>Liu</surname> <given-names>KI</given-names></name><name><surname>Zhang</surname> <given-names>R</given-names></name><name><surname>Ramaswami</surname> <given-names>G</given-names></name><name><surname>Ariyoshi</surname> <given-names>K</given-names></name><name><surname>Gupte</surname> <given-names>A</given-names></name><name><surname>Keegan</surname> <given-names>LP</given-names></name><name><surname>George</surname> <given-names>CX</given-names></name><name><surname>Ramu</surname> <given-names>A</given-names></name><name><surname>Huang</surname> <given-names>N</given-names></name><name><surname>Pollina</surname> <given-names>EA</given-names></name><name><surname>Leeman</surname> <given-names>DS</given-names></name><name><surname>Rustighi</surname> <given-names>A</given-names></name><name><surname>Goh</surname> <given-names>YPS</given-names></name><name><surname>Chawla</surname> <given-names>A</given-names></name><name><surname>Del Sal</surname> <given-names>G</given-names></name><name><surname>Peltz</surname> <given-names>G</given-names></name><name><surname>Brunet</surname> <given-names>A</given-names></name><name><surname>Conrad</surname> <given-names>DF</given-names></name><name><surname>Samuel</surname> <given-names>CE</given-names></name><name><surname>O’Connell</surname> <given-names>MA</given-names></name><name><surname>Walkley</surname> <given-names>CR</given-names></name><name><surname>Nishikura</surname> <given-names>K</given-names></name><name><surname>Li</surname> <given-names>JB</given-names></name></person-group><year iso-8601-date="2017">2017</year><article-title>Dynamic landscape and regulation of RNA editing in mammals</article-title><source>Nature</source><volume>550</volume><fpage>249</fpage><lpage>254</lpage><pub-id pub-id-type="doi">10.1038/nature24041</pub-id></element-citation></ref><ref id="bib59"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Wang</surname> <given-names>SJ</given-names></name><name><surname>Wang</surname> <given-names>ZW</given-names></name></person-group><year iso-8601-date="2013">2013</year><article-title>Track-a-worm, an open-source system for quantitative assessment of <italic>C. elegans</italic> locomotory and bending behavior</article-title><source>PLOS ONE</source><volume>8</volume><elocation-id>e69653</elocation-id><pub-id pub-id-type="doi">10.1371/journal.pone.0069653</pub-id><pub-id pub-id-type="pmid">23922769</pub-id></element-citation></ref><ref id="bib60"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Washburn</surname> <given-names>MC</given-names></name><name><surname>Kakaradov</surname> <given-names>B</given-names></name><name><surname>Sundararaman</surname> <given-names>B</given-names></name><name><surname>Wheeler</surname> <given-names>E</given-names></name><name><surname>Hoon</surname> <given-names>S</given-names></name><name><surname>Yeo</surname> <given-names>GW</given-names></name><name><surname>Hundley</surname> <given-names>HA</given-names></name></person-group><year iso-8601-date="2014">2014</year><article-title>The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the <italic>C. elegans</italic> transcriptome</article-title><source>Cell Reports</source><volume>6</volume><fpage>599</fpage><lpage>607</lpage><pub-id pub-id-type="doi">10.1016/j.celrep.2014.01.011</pub-id><pub-id pub-id-type="pmid">24508457</pub-id></element-citation></ref><ref id="bib61"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yoshimura</surname> <given-names>SH</given-names></name><name><surname>Hirano</surname> <given-names>T</given-names></name></person-group><year iso-8601-date="2016">2016</year><article-title>HEAT repeats – versatile arrays of amphiphilic helices working in crowded environments?</article-title><source>Journal of Cell Science</source><volume>129</volume><elocation-id>jcs.185710</elocation-id><pub-id pub-id-type="doi">10.1242/jcs.185710</pub-id></element-citation></ref><ref id="bib62"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yuan</surname> <given-names>A</given-names></name><name><surname>Dourado</surname> <given-names>M</given-names></name><name><surname>Butler</surname> <given-names>A</given-names></name><name><surname>Walton</surname> <given-names>N</given-names></name><name><surname>Wei</surname> <given-names>A</given-names></name><name><surname>Salkoff</surname> <given-names>L</given-names></name></person-group><year iso-8601-date="2000">2000</year><article-title>SLO-2, a K+ channel with an unusual cl− dependence</article-title><source>Nature Neuroscience</source><volume>3</volume><fpage>771</fpage><lpage>779</lpage><pub-id pub-id-type="doi">10.1038/77670</pub-id></element-citation></ref><ref id="bib63"><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Yuan</surname> <given-names>A</given-names></name><name><surname>Santi</surname> <given-names>CM</given-names></name><name><surname>Wei</surname> <given-names>A</given-names></name><name><surname>Wang</surname> <given-names>ZW</given-names></name><name><surname>Pollak</surname> <given-names>K</given-names></name><name><surname>Nonet</surname> <given-names>M</given-names></name><name><surname>Kaczmarek</surname> <given-names>L</given-names></name><name><surname>Crowder</surname> <given-names>CM</given-names></name><name><surname>Salkoff</surname> <given-names>L</given-names></name></person-group><year iso-8601-date="2003">2003</year><article-title>The sodium-activated potassium channel is encoded by a member of the slo gene family</article-title><source>Neuron</source><volume>37</volume><fpage>765</fpage><lpage>773</lpage><pub-id pub-id-type="doi">10.1016/S0896-6273(03)00096-5</pub-id><pub-id pub-id-type="pmid">12628167</pub-id></element-citation></ref></ref-list></back><sub-article article-type="decision-letter" id="sa1"><front-stub><article-id pub-id-type="doi">10.7554/eLife.53986.sa1</article-id><title-group><article-title>Decision letter</article-title></title-group><contrib-group><contrib contrib-type="editor"><name><surname>Hobert</surname><given-names>Oliver</given-names></name><role>Reviewing Editor</role><aff><institution>Howard Hughes Medical Institute, Columbia University</institution><country>United States</country></aff></contrib></contrib-group><contrib-group><contrib contrib-type="reviewer"><name><surname>Kaczmarek</surname><given-names>Leonard</given-names> </name><role>Reviewer</role><aff><institution>Yale University</institution><country>United States</country></aff></contrib><contrib contrib-type="reviewer"><name><surname>Boulin</surname><given-names>Thomas</given-names> </name><role>Reviewer</role><aff><institution>University of Lyon - INSERM - CNRS</institution><country>France</country></aff></contrib></contrib-group></front-stub><body><boxed-text><p>In the interests of transparency, eLife publishes the most substantive revision requests and the accompanying author responses.</p></boxed-text><p>Thank you for submitting your article &quot;Slo2 potassium channel function depends on a SCYL1 protein&quot; for consideration by <italic>eLife</italic>. Your article has been reviewed by Richard Aldrich as the Senior Editor, a Reviewing Editor (Oliver Hobert), and two reviewers. The following individuals involved in review of your submission have agreed to reveal their identity: Leonard Kaczmarek (Reviewer #1); Thomas Boulin (Reviewer #2).</p><p>The reviewers have discussed the reviews with one another and the Reviewing Editor has drafted this decision to help you prepare a revised submission. As you will see in the reviews below, there is general agreement about the general interest and importance of the study. However, a set of important clarifications and experiments need to be conducted to make this paper become acceptable for publication in <italic>eLife</italic>.</p><p>In brief, the requested experiments are:</p><p>1) Independent validation of interactions (reviewer #1, comment 2)</p><p>2) Engineering the A&gt;G mutation into the genome (reviewer #2)</p><p>3) Improved expression pattern analysis (reviewer #2)(the in vivo recombineering technique has by now been shown to be inadequate).</p><p>There are also a number of very important clarifications that are required (e.g. reviewer #1, comment 1)</p><p><italic>Reviewer #1:</italic> </p><p>This manuscript presents some very interesting work demonstrating that Slo2 channels in C-elegans interact with SYCL<sup>-</sup>1 to alter open probability of these channels. The effects of SYCL<sup>-</sup>1 on the channels is, in turn, influenced by ADR-2, which is required for A-to-I RNA editing of a site in the 3' UTR of the scyl-1 gene. The work is provocative and points the way to future work to unravel how this potential interaction affects the biology of neurons in the nematode and in mammalian systems.</p><p>1) My major comment is on the work that extrapolates the nematode findings to the human Slack channel. The latter has previously been shows to differ from the C-elegans channel in several ways. This interaction with the human channel is an important aspect of the presented work. Examination of the data in Figure 11, however, suggest that the gating of the human channel is quite different from the Slo2 channel records shown in Figure 8. Specifically (if the time bars shown in Figure 11A are correct, the overall open probability of the human channel is dominated by the presence of very long closed states (lasting many seconds). Examination of the X-axis scale bars in Figure 11B and C suggest these may have been excluded from the analyses. The conclusions on the effects of SCYL1 on open probability stated in the last paragraph of the Results section may not be completely valid until these are taken into account.</p><p>2) The bimolecular fluorescence complementation assay presented does make a case that there may be a physical interaction of SCLY-1 with SLO-2 but is not completely definitive. It would be good to have some other indicator of physical interaction to support this claim. A more conventional coimmunoprecipitation experiments would be a good addition, one that could perhaps be carried out using the co-expression <italic>Xenopus</italic> oocyte heterologous expression system.</p><p><italic>Reviewer #2:</italic> </p><p>In this study Niu et al., describe a striking and entirely unsuspected regulatory cascade that controls SLO-2/Slo2 potassium channel activity. They report the role of SYCL<sup>-</sup>1, a novel physical interactor of the SLO-2 potassium channel, and describe how syCl<sup>-</sup>1 expression is controled by ADAR-dependent RNA editing in the non-coding sequence this gene. After dissecting this mechanism in worms, they proceed to directly demonstrate the conservation of this novel regulatory interaction with the human SLO-2 ortholog. Given the importance of this class of potassium channel in health and disease, identifying this modulatory mechanism is a very important finding in my opinion.</p><p>Essentiaol revisions:</p><p>- Please clarify the functional relationship between adr-1 and adr-2. Indeed, in the Introduction the authors seem to indicate that ADAR proteins could compete (&quot;altering the accessibility&quot;) for certain binding sites. In this model, wouldn't one expect that adr-1(lf) would &quot;free&quot; access to the scyl-1 site, which would be inconsistent with the similarity of adr-1 and adr-2 mutant phenotypes?</p><p>Do the authors think that ADR-1 promotes the recruitement of ADR-2 to the scyl-1 3'UTR?</p><p>- I was very intrigued by the results described in Figure 10, and specifically Figure 10D/E. The result is not what I had intuitively expected. Since it was performed in an adr-1/2 wild-type background as far as I could determine from the Materials and methods section, I would have thought that ADAR activity would have edited the wild-type sequence and I would have expected to see GFP in both cases.</p><p>I would have performed this experiment in an adr-1(lf) background. Have the authors attempted this experiment in this background? How many independent lines were tested with the wp1923 construct? Is expression seen anywhere else in the nervous system (outside de VNC) to make sure that GFP can indeed be expressed from this transgene?</p><p>- Following on this previous point, a direct way to demonstrate the functional importance of this editing site would be to generate the following genotype by engineering the A&gt;G mutation by CRISPR/Cas9 gene editing:slo-2(gf); adr-1(0); scyl-1(A&gt;G)</p><p>My prediction would be that the mutation in scyl-1 would restore the slo-2 gain-of-function locomotor impairement, by bypassing the adr-1 requirement. To me this experiment would very strongly support this new and exciting functional regulation and I would encourage the authors to perform this rather simple experiment.</p><p>- In wormbase, the annotation of the scyl-1 locus shows a rather sizable 3'UTR. I was curious whether the authors have any comments on that point, and whether this is a common feature of ADAR-edited 3'UTRs.</p><p>Does the human SCYL1 3'UTR have a similar hair-pin structure, which could suggest a similar regulation mechanism?</p><p>- I was a bit surprised about the strategy used to generate the scyl-1 expression pattern. Why was the in vivo recombination approach used? What happens when the 0.5kb promoter-GFP construct is injected alone?</p><p>The previous gene is only approx 2kb upstream and there is significant sequence conservation to C. remanei and C. briggsae DNA less than 1kb upstream of the ATG (see UCSC genome browser for example). Did the authors test such a 2kb promoter fragment?</p><p>- Figure 6: I'm not convinced that scyl-1::GFP labels vm1 or vm2 muscles based on this image. I could be wrong, but higher magnification images would need to be checked.</p></body></sub-article><sub-article article-type="reply" id="sa2"><front-stub><article-id pub-id-type="doi">10.7554/eLife.53986.sa2</article-id><title-group><article-title>Author response</article-title></title-group></front-stub><body><disp-quote content-type="editor-comment"><p>Reviewer #1:</p><p>1) My major comment is on the work that extrapolates the nematode findings to the human Slack channel. The latter has previously been shows to differ from the C-elegans channel in several ways. This interaction with the human channel is an important aspect of the presented work. Examination of the data in Figure 11, however, suggest that the gating of the human channel is quite different from the Slo2 channel records shown in Figure 8. Specifically (if the time bars shown in Figure 11A are correct, the overall open probability of the human channel is dominated by the presence of very long closed states (lasting many seconds). Examination of the X-axis scale bars in Figure 11B and C suggest these may have been excluded from the analyses. The conclusions on the effects of SCYL1 on open probability stated in the last paragraph of the Results section may not be completely valid until these are taken into account.</p></disp-quote><p>We thank the reviewer for the comment. The open probability in the original Figure 11 was calculated from all the open and closed events. As the reviewer pointed out, events of the very long closed state had a major impact on the open probability. However, they had little contribution to the dwell time histograms in the original figure because these events account for a tiny (nearly negligible) portion of the total event counts and the majority of them fell outside of the <italic>x</italic>-axis displayed in the figure. In the revised manuscript, we added a new panel (panel D) to Figure 11 to show dwell time histograms of the very long closed events (&gt;30 ms, chosen arbitrarily as the threshold) for both groups. Because these events were scarce, our approach used for comparing τ and A values in panels B and C of this figure and of Figure 8 could not be applied to them. Therefore, we compared the average duration and frequency of these very long closed events between hSlo2.2 and hSlo2.2+SCYL1 (Figure 11D, bottom). We also have replaced the traces in Figure 11A with longer and more representative ones. In addition, the dwell time histograms in panels B and C of both Figures 8 and Figure 11, which were based on a single sample recording trace in the original figures, have been revised to include events from all the recordings to be consistent with the histogram in the new panel D. In the revised manuscript, we describe the presence of the very long closed state and its impact on the open probability (–subsection “scyl-1 expression depends on RNA editing at a specific 3’-UTR site”). The legends of Figure 8 and Figure 11 have also been updated accordingly.</p><disp-quote content-type="editor-comment"><p>2) The bimolecular fluorescence complementation assay presented does make a case that there may be a physical interaction of SCLY-1 with SLO-2 but is not completely definitive. It would be good to have some other indicator of physical interaction to support this claim. A more conventional coimmunoprecipitation experiments would be a good addition, one that could perhaps be carried out using the co-expression Xenopus oocyte heterologous expression system.</p></disp-quote><p>We performed coimmunoprecipitation assays with transgenic worms expressing HA-tagged SCYL-1 and GFP-tagged SLO-2. Worms instead of a heterologous expression system were used for this experiment because SLO-2 is poorly expressed in both <italic>Xenopus oocytes</italic> and HEK293 cells even with a codon-optimized version (our unpublished observation). Our results of the co-IP assays were in agreement with those of the BiFC assays (Figure 9), which provides further evidence for physical interactions between SLO-2 and SCYL-1.</p><disp-quote content-type="editor-comment"><p>Reviewer #2:</p><p>Comments</p><p>1) Please clarify the functional relationship between adr-1 and adr-2. Indeed, in the Introducution the authors seem to indicate that ADAR proteins could compete (&quot;altering the accessibility&quot;) for certain binding sites. In this model, wouldn't one expect that adr-1(lf) would &quot;free&quot; access to the scyl-1 site, which would be inconsistent with the similarity of adr-1 and adr-2 mutant phenotypes?</p><p>Do the authors think that ADR-1 promotes the recruitement of ADR-2 to the scyl-1 3'UTR?</p></disp-quote><p>We thank the reviewer for the comment. Indeed, our description about the functional relationship between ADR-1 and ADR-2 in the Introduction was inaccurate. ADR-1 promotes RNA editing by binding to target mRNAs and recruiting ADR-2 to some specific editing sites. Our results with <italic>adr-1(lf)</italic> and <italic>adr-2(lf)</italic> mutants are compatible with this knowledge. In the revised manuscript, a sentence in the Introduction has been changed to “ADR-1 is catalytically inactive but can promote RNA editing by binding to selected target mRNA and tethering ADR-2 to RNA substrates (Ganem et al., 2019; Rajendren et al., 2018; Washburn et al., 2014).” (Introduction)</p><disp-quote content-type="editor-comment"><p>2) I was very intrigued by the results described in Figure 10, and specifically Figure 10D/E. The result is not what I had intuitively expected. Since it was performed in an adr-1/2 wild-type background as far as I could determine from the Materials and methods section, I would have thought that ADAR activity would have edited the wild-type sequence and I would have expected to see GFP in both cases.</p><p>I would have performed this experiment in an adr-1(lf) background. Have the authors attempted this experiment in this background? How many independent lines were tested with the wp1923 construct? Is expression seen anywhere else in the nervous system (outside de VNC) to make sure that GFP can indeed be expressed from this transgene?</p></disp-quote><p>We obtained five <italic>wp1923</italic> lines and three <italic>wp1924</italic> lines. While GFP signal was observed in all the <italic>wp1924</italic> lines, no GFP signal was detected anywhere in any of the <italic>wp1923</italic> lines. We were also surprised by the lack of GFP expression in the <italic>wp1923</italic> lines. As suggested, we performed the same experiments as those in Figure 10E with the <italic>adr-1(zw96)</italic> mutant. Specifically, <italic>adr-1(zw96)</italic> mutant strains expressing the <italic>wp1923</italic> transgene were made by injecting the <italic>wp1923</italic> plasmid into the mutant whereas that expressing the <italic>wp1924</italic> transgene by first integrating the <italic>wp1924</italic> transgene into the wild-type genome and then crossing it into <italic>adr-1(zw96)</italic>. As expected, GFP signal was not detected in the <italic>adr-1(zw96)</italic> mutant worms harboring the <italic>wp1923</italic> transgene (not shown). Interestingly, GFP signal from the <italic>wp1924</italic> transgene was much weaker (by ~50%) in the mutant strain than the wild-type strain (Figure 10 F and G). Because <italic>scyl-1</italic> 3’-UTR had already been “edited” at the ADR-1-dependent editing site in the <italic>wp1924</italic> transgene, the difference in GFP signal between wild-type and <italic>adr-1(zw96)</italic> strains suggests that ADR-1 can also regulate <italic>scyl-1</italic> mRNA level through a post-editing effect, perhaps through interacting with some other proteins. In agreement with this possibility, we were able to isolate several mutants showing decreased GFP signal from the <italic>wp1924</italic> transgene in a pilot genetic screen (Figure 10—figure supplement 1).</p><disp-quote content-type="editor-comment"><p>3) Following on this previous point, a direct way to demonstrate the functional importance of this editing site would be to generate the following genotype by engineering the A&gt;G mutation by CRISPR/Cas9 gene editing:slo-2(gf); adr-1(0); scyl-1(A&gt;G)</p><p>My prediction would be that the mutation in scyl-1 would restore the slo-2 gain-of-function locomotor impairement, by bypassing the adr-1 requirement. To me this experiment would very strongly support this new and exciting functional regulation and I would encourage the authors to perform this rather simple experiment.</p></disp-quote><p>As suggested by the reviewer, we tried to engineer the A&gt;G mutation at the ADR-1-dependent editing site in <italic>scyl-1</italic> 3’-UTR in the worm genome by CRISPR/Cas9. Unfortunately, our attempt was unsuccessful, probably because this editing site is located within an inverted sequence (Figure 10D). We then tried to address the reviewer’s comment by expressing P<italic>rab-3::scyl-1::unc-10 3’-UTR</italic> in <italic>slo-2(gf);adr-1(lf)</italic> double mutant and wild type (as a control) in the hope that expression of this transgene in the double mutant would restore the <italic>slo-2(gf)</italic> sluggish locomotion by bypassing the ADR-1 requirement. However, expression of the transgene caused larval arrest in the double mutant and a sluggish phenotype in wildtype worms, which prevented us from performing further analysis. Finally, we built a <italic>scyl-1(zw99);adr1(zw96)</italic> double mutant, and recorded whole-cell currents from VA5 motor neuron. We observed similar VA5 outward currents between the double mutant and the <italic>scyl-1(zw99)</italic> single mutant (Figure 7A), suggesting that SCYL-1 and ADR-1 likely contribute to SLO-2 function through a common pathway. This result provides further evidence for the putative role of ADR-1 in regulating SCYL-1 expression.</p><disp-quote content-type="editor-comment"><p>4) – In wormbase, the annotation of the scyl-1 locus shows a rather sizable 3'UTR. I was curious whether the authors have any comments on that point, and whether this is a common feature of ADAR-edited 3'UTRs.</p><p>Does the human SCYL1 3'UTR have a similar hair-pin structure, which could suggest a similar regulation mechanism?</p></disp-quote><p>In Wormbase, there are four different <italic>scyl-1</italic> transcripts that differ only in the 3’-UTR sequence and length (167 nt, 169 nt, 564 nt, and 1862 nt). The identified ADR-1-dependent editing site exists only in the variant with the longest 3’UTR, which we speculate could be a mechanism for cell-specific expression of <italic>scyl-1</italic>. It is difficult to comment on whether RNA editing by ADARs at 3’-UTRs is a common mechanism of regulating mRNA expression based on the rather limited literatures. The 3’-UTR of human SCYL1 transcripts (NM_020680.4) also has a high probability of forming hair-pin structures based on software prediction (https://rna.urmc.rochester.edu/RNAstructureWeb/Servers). It remains to be determined whether human SCYL1 transcripts are also edited at the 3’-UTR, and if so, whether the editing regulates SCYL1 transcript expression. We added these comments to the Discussion section in the revised manuscript –.</p><disp-quote content-type="editor-comment"><p> <italic>5) I was a bit surprised about the strategy used to generate the scyl-1 expression pattern. Why was the</italic> in vivo recombination approach used? What happens when the 0.5kb promoter-GFP construct is injected alone?</p><p>The previous gene is only approx 2kb upstream and there is significant sequence conservation to C. remanei and C. briggsae DNA less than 1kb upstream of the ATG (see UCSC genome browser for example). Did the authors test such a 2kb promoter fragment?</p></disp-quote><p>We initially tried to examine <italic>scyl-1</italic> expression pattern using a 2-kb P<italic>scyl-1</italic> because, as the reviewer pointed out, another gene (<italic>lap-2</italic>) resides approximately 2 kb upstream of <italic>scyl-1</italic>. However, GFP signal was not detected in transgenic worms expressing the P<italic>scyl-1(2 kb)::gfp</italic> transcriptional fusion. We therefore resorted to the commonly used in vivo homologous recombination approach to include potential distant upstream regulatory elements in the P<italic>scyl-1::gfp</italic> transcriptional fusion. A description about the unsuccessful experiment with the 2-kb P<italic>scyl-1</italic> has been added to the manuscript (–subsection “ADR-1 regulates SLO-2 function through SCYL-1”). As suggested by the reviewer, we also created transgenic worms expressing only the P<italic>scyl-1(0.5 kb)::gfp</italic> transcriptional fusion but were unable to detect any GFP signal from them (not shown).</p><disp-quote content-type="editor-comment"><p>6) Figure 6: I'm not convinced that scyl-1::GFP labels vm1 or vm2 muscles based on this image. I could be wrong, but higher magnification images would need to be checked.</p></disp-quote><p>We thank the reviewer for pointing out our mistake. In Figure 6, P<italic>scyl-1::GFP</italic> labels uterine ventral cells rather than vulval muscle cells.</p></body></sub-article></article>