RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.
Identifieur interne : 000C16 ( Main/Exploration ); précédent : 000C15; suivant : 000C17RNAcompete-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
Affiliations:
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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><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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