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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pubmed:28651966Le document en format XML
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<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>
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<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>
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<PubMedPubDate PubStatus="entrez"><Year>2017</Year>
<Month>6</Month>
<Day>28</Day>
<Hour>6</Hour>
<Minute>0</Minute>
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<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>
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<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>
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