RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.
Identifieur interne : 001A90 ( Ncbi/Merge ); précédent : 001A89; suivant : 001A91RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.
Auteurs : Kate B. Cook [Canada] ; Shankar Vembu [Canada] ; Kevin C H. Ha [Canada] ; Hong Zheng [Canada] ; Kaitlin U. Laverty [Canada] ; Timothy R. Hughes [Canada] ; Debashish Ray [Canada] ; Quaid D. Morris [Canada]Source :
- Methods (San Diego, Calif.) [ 1095-9130 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : RNA-Binding Proteins.
- genetics : Base Sequence, RNA-Binding Proteins.
- methods : High-Throughput Nucleotide Sequencing, Sequence Analysis, RNA.
- Humans.
Abstract
RNA-binding proteins recognize RNA sequences and structures, but there is currently no systematic and accurate method to derive large (>12base) motifs de novo that reflect a combination of intrinsic preference to both sequence and structure. To address this absence, we introduce RNAcompete-S, which couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models). RNAcompete-S confirms that HuR, QKI, and SRSF1 prefer binding sites that are single stranded, and recapitulates known 8-10bp sequence and structure preferences for Vts1p and RBMY. We also derive an 18-base long SSM for Drosophila SLBP, which to our knowledge has not been previously determined by selections from pure random sequence, and accurately discriminates human replication-dependent histone mRNAs. Thus, RNAcompete-S enables accurate identification of large, intrinsic sequence-structure specificities with a uniform assay.
DOI: 10.1016/j.ymeth.2017.06.024
PubMed: 28651966
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Electronic address: quaid.morris@utoronto.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28651966</idno><idno type="pmid">28651966</idno><idno type="doi">10.1016/j.ymeth.2017.06.024</idno><idno type="wicri:Area/PubMed/Corpus">000C45</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000C45</idno><idno type="wicri:Area/PubMed/Curation">000C45</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000C45</idno><idno type="wicri:Area/PubMed/Checkpoint">000B55</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000B55</idno><idno type="wicri:Area/Ncbi/Merge">001A90</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.</title><author><name sortKey="Cook, Kate B" sort="Cook, Kate B" uniqKey="Cook K" first="Kate B" last="Cook">Kate B. Cook</name><affiliation wicri:level="4"><nlm:affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Vembu, Shankar" sort="Vembu, Shankar" uniqKey="Vembu S" first="Shankar" last="Vembu">Shankar Vembu</name><affiliation wicri:level="4"><nlm:affiliation>Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Donnelly Centre, University of Toronto, Toronto M5S 3E1</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Ha, Kevin C H" sort="Ha, Kevin C H" uniqKey="Ha K" first="Kevin C H" last="Ha">Kevin C H. Ha</name><affiliation wicri:level="4"><nlm:affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Zheng, Hong" sort="Zheng, Hong" uniqKey="Zheng H" first="Hong" last="Zheng">Hong Zheng</name><affiliation wicri:level="4"><nlm:affiliation>Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Donnelly Centre, University of Toronto, Toronto M5S 3E1</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Laverty, Kaitlin U" sort="Laverty, Kaitlin U" uniqKey="Laverty K" first="Kaitlin U" last="Laverty">Kaitlin U. Laverty</name><affiliation wicri:level="4"><nlm:affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R" last="Hughes">Timothy R. Hughes</name><affiliation wicri:level="4"><nlm:affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada. Electronic address: t.hughes@utoronto.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Ray, Debashish" sort="Ray, Debashish" uniqKey="Ray D" first="Debashish" last="Ray">Debashish Ray</name><affiliation wicri:level="4"><nlm:affiliation>Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada. Electronic address: d.ray@utoronto.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Donnelly Centre, University of Toronto, Toronto M5S 3E1</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Morris, Quaid D" sort="Morris, Quaid D" uniqKey="Morris Q" first="Quaid D" last="Morris">Quaid D. Morris</name><affiliation wicri:level="4"><nlm:affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada. Electronic address: quaid.morris@utoronto.ca.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author></analytic><series><title level="j">Methods (San Diego, Calif.)</title><idno type="eISSN">1095-9130</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (genetics)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Humans</term><term>RNA-Binding Proteins (chemistry)</term><term>RNA-Binding Proteins (genetics)</term><term>Sequence Analysis, RNA (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ARN ()</term><term>Humains</term><term>Protéines de liaison à l'ARN ()</term><term>Protéines de liaison à l'ARN (génétique)</term><term>Séquence nucléotidique (génétique)</term><term>Séquençage nucléotidique à haut débit ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Base Sequence</term><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéines de liaison à l'ARN</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ARN</term><term>Humains</term><term>Protéines de liaison à l'ARN</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">RNA-binding proteins recognize RNA sequences and structures, but there is currently no systematic and accurate method to derive large (>12base) motifs de novo that reflect a combination of intrinsic preference to both sequence and structure. To address this absence, we introduce RNAcompete-S, which couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models). RNAcompete-S confirms that HuR, QKI, and SRSF1 prefer binding sites that are single stranded, and recapitulates known 8-10bp sequence and structure preferences for Vts1p and RBMY. We also derive an 18-base long SSM for Drosophila SLBP, which to our knowledge has not been previously determined by selections from pure random sequence, and accurately discriminates human replication-dependent histone mRNAs. Thus, RNAcompete-S enables accurate identification of large, intrinsic sequence-structure specificities with a uniform assay.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28651966</PMID><DateCompleted><Year>2018</Year><Month>05</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>06</Month><Day>04</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1095-9130</ISSN><JournalIssue CitedMedium="Internet"><Volume>126</Volume><PubDate><Year>2017</Year><Month>08</Month><Day>15</Day></PubDate></JournalIssue><Title>Methods (San Diego, Calif.)</Title><ISOAbbreviation>Methods</ISOAbbreviation></Journal><ArticleTitle>RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.</ArticleTitle><Pagination><MedlinePgn>18-28</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1046-2023(17)30031-2</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ymeth.2017.06.024</ELocationID><Abstract><AbstractText>RNA-binding proteins recognize RNA sequences and structures, but there is currently no systematic and accurate method to derive large (>12base) motifs de novo that reflect a combination of intrinsic preference to both sequence and structure. To address this absence, we introduce RNAcompete-S, which couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models). RNAcompete-S confirms that HuR, QKI, and SRSF1 prefer binding sites that are single stranded, and recapitulates known 8-10bp sequence and structure preferences for Vts1p and RBMY. We also derive an 18-base long SSM for Drosophila SLBP, which to our knowledge has not been previously determined by selections from pure random sequence, and accurately discriminates human replication-dependent histone mRNAs. Thus, RNAcompete-S enables accurate identification of large, intrinsic sequence-structure specificities with a uniform assay.</AbstractText><CopyrightInformation>Copyright © 2017. Published by Elsevier Inc.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cook</LastName><ForeName>Kate B</ForeName><Initials>KB</Initials><AffiliationInfo><Affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vembu</LastName><ForeName>Shankar</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ha</LastName><ForeName>Kevin C H</ForeName><Initials>KCH</Initials><AffiliationInfo><Affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Hong</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Laverty</LastName><ForeName>Kaitlin U</ForeName><Initials>KU</Initials><AffiliationInfo><Affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hughes</LastName><ForeName>Timothy R</ForeName><Initials>TR</Initials><AffiliationInfo><Affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada. Electronic address: t.hughes@utoronto.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ray</LastName><ForeName>Debashish</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada. Electronic address: d.ray@utoronto.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Morris</LastName><ForeName>Quaid D</ForeName><Initials>QD</Initials><AffiliationInfo><Affiliation>Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada. Electronic address: quaid.morris@utoronto.ca.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>MOP-49451</GrantID><Agency>CIHR</Agency><Country>Canada</Country></Grant><Grant><GrantID>MOP-125894 </GrantID><Agency>CIHR</Agency><Country>Canada</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>06</Month><Day>24</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Methods</MedlineTA><NlmUniqueID>9426302</NlmUniqueID><ISSNLinking>1046-2023</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D016601">RNA-Binding Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016601" MajorTopicYN="N">RNA-Binding Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">High-throughput sequencing</Keyword><Keyword MajorTopicYN="Y">In vitro selection</Keyword><Keyword MajorTopicYN="Y">Motif discovery</Keyword><Keyword MajorTopicYN="Y">Motif scanning</Keyword><Keyword MajorTopicYN="Y">RNA secondary structure</Keyword><Keyword MajorTopicYN="Y">RNA-binding protein</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>03</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>06</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>06</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>6</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>5</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>6</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28651966</ArticleId><ArticleId IdType="pii">S1046-2023(17)30031-2</ArticleId><ArticleId IdType="doi">10.1016/j.ymeth.2017.06.024</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country><region><li>Ontario</li></region><settlement><li>Toronto</li></settlement><orgName><li>Université de Toronto</li></orgName></list><tree><country name="Canada"><region name="Ontario"><name sortKey="Cook, Kate B" sort="Cook, Kate B" uniqKey="Cook K" first="Kate B" last="Cook">Kate B. Cook</name></region><name sortKey="Ha, Kevin C H" sort="Ha, Kevin C H" uniqKey="Ha K" first="Kevin C H" last="Ha">Kevin C H. Ha</name><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R" last="Hughes">Timothy R. Hughes</name><name sortKey="Laverty, Kaitlin U" sort="Laverty, Kaitlin U" uniqKey="Laverty K" first="Kaitlin U" last="Laverty">Kaitlin U. Laverty</name><name sortKey="Morris, Quaid D" sort="Morris, Quaid D" uniqKey="Morris Q" first="Quaid D" last="Morris">Quaid D. Morris</name><name sortKey="Ray, Debashish" sort="Ray, Debashish" uniqKey="Ray D" first="Debashish" last="Ray">Debashish Ray</name><name sortKey="Vembu, Shankar" sort="Vembu, Shankar" uniqKey="Vembu S" first="Shankar" last="Vembu">Shankar Vembu</name><name sortKey="Zheng, Hong" sort="Zheng, Hong" uniqKey="Zheng H" first="Hong" last="Zheng">Hong Zheng</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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