Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.
Identifieur interne : 002769 ( Main/Exploration ); précédent : 002768; suivant : 002770Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.
Auteurs : Debashish Ray [Canada] ; Hilal Kazan ; Esther T. Chan ; Lourdes Pe A Castillo ; Sidharth Chaudhry ; Shaheynoor Talukder ; Benjamin J. Blencowe ; Quaid Morris ; Timothy R. HughesSource :
- Nature biotechnology [ 1546-1696 ] ; 2009.
Descripteurs français
- KwdFr :
- ARN (), ARN (génétique), ARN (métabolisme), Animaux, Bases de données d'acides nucléiques, Courbe ROC, Données de séquences moléculaires, Génome, Protéines de liaison à l'ARN (), Protéines de liaison à l'ARN (génétique), Protéines de liaison à l'ARN (métabolisme), Sites de fixation (génétique), Spécificité du substrat, Séquence nucléotidique, Séquençage par oligonucléotides en batterie ().
- MESH :
- génétique : ARN, Protéines de liaison à l'ARN, Sites de fixation.
- métabolisme : ARN, Protéines de liaison à l'ARN.
- ARN, Animaux, Bases de données d'acides nucléiques, Courbe ROC, Données de séquences moléculaires, Génome, Protéines de liaison à l'ARN, Spécificité du substrat, Séquence nucléotidique, Séquençage par oligonucléotides en batterie.
English descriptors
- KwdEn :
- Animals, Base Sequence, Binding Sites (genetics), Databases, Nucleic Acid, Genome, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis (methods), RNA (chemistry), RNA (genetics), RNA (metabolism), RNA-Binding Proteins (chemistry), RNA-Binding Proteins (genetics), RNA-Binding Proteins (metabolism), ROC Curve, Substrate Specificity.
- MESH :
- chemical , chemistry : RNA, RNA-Binding Proteins.
- genetics : Binding Sites, RNA, RNA-Binding Proteins.
- chemical , metabolism : RNA, RNA-Binding Proteins.
- methods : Oligonucleotide Array Sequence Analysis.
- Animals, Base Sequence, Databases, Nucleic Acid, Genome, Molecular Sequence Data, ROC Curve, Substrate Specificity.
Abstract
Metazoan genomes encode hundreds of RNA-binding proteins (RBPs) but RNA-binding preferences for relatively few RBPs have been well defined. Current techniques for determining RNA targets, including in vitro selection and RNA co-immunoprecipitation, require significant time and labor investment. Here we introduce RNAcompete, a method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. We tested RNAcompete by analyzing nine diverse RBPs (HuR, Vts1, FUSIP1, PTB, U1A, SF2/ASF, SLM2, RBM4 and YB1). RNAcompete identified expected and previously unknown RNA binding preferences. Using in vitro and in vivo binding data, we demonstrate that preferences for individual 7-mers identified by RNAcompete are a more accurate representation of binding activity than are conventional motif models. We anticipate that RNAcompete will be a valuable tool for the study of RNA-protein interactions.
DOI: 10.1038/nbt.1550
PubMed: 19561594
Affiliations:
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Le document en format XML
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Chan</name></author><author><name sortKey="Pe A Castillo, Lourdes" sort="Pe A Castillo, Lourdes" uniqKey="Pe A Castillo L" first="Lourdes" last="Pe A Castillo">Lourdes Pe A Castillo</name></author><author><name sortKey="Chaudhry, Sidharth" sort="Chaudhry, Sidharth" uniqKey="Chaudhry S" first="Sidharth" last="Chaudhry">Sidharth Chaudhry</name></author><author><name sortKey="Talukder, Shaheynoor" sort="Talukder, Shaheynoor" uniqKey="Talukder S" first="Shaheynoor" last="Talukder">Shaheynoor Talukder</name></author><author><name sortKey="Blencowe, Benjamin J" sort="Blencowe, Benjamin J" uniqKey="Blencowe B" first="Benjamin J" last="Blencowe">Benjamin J. Blencowe</name></author><author><name sortKey="Morris, Quaid" sort="Morris, Quaid" uniqKey="Morris Q" first="Quaid" last="Morris">Quaid Morris</name></author><author><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R" last="Hughes">Timothy R. Hughes</name></author></analytic><series><title level="j">Nature biotechnology</title><idno type="eISSN">1546-1696</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Binding Sites (genetics)</term><term>Databases, Nucleic Acid</term><term>Genome</term><term>Molecular Sequence Data</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>RNA (chemistry)</term><term>RNA (genetics)</term><term>RNA (metabolism)</term><term>RNA-Binding Proteins (chemistry)</term><term>RNA-Binding Proteins (genetics)</term><term>RNA-Binding Proteins (metabolism)</term><term>ROC Curve</term><term>Substrate Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ()</term><term>ARN (génétique)</term><term>ARN (métabolisme)</term><term>Animaux</term><term>Bases de données d'acides nucléiques</term><term>Courbe ROC</term><term>Données de séquences moléculaires</term><term>Génome</term><term>Protéines de liaison à l'ARN ()</term><term>Protéines de liaison à l'ARN (génétique)</term><term>Protéines de liaison à l'ARN (métabolisme)</term><term>Sites de fixation (génétique)</term><term>Spécificité du substrat</term><term>Séquence nucléotidique</term><term>Séquençage par oligonucléotides en batterie ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA</term><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Binding Sites</term><term>RNA</term><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN</term><term>Protéines de liaison à l'ARN</term><term>Sites de fixation</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA</term><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN</term><term>Protéines de liaison à l'ARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Databases, Nucleic Acid</term><term>Genome</term><term>Molecular Sequence Data</term><term>ROC Curve</term><term>Substrate Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN</term><term>Animaux</term><term>Bases de données d'acides nucléiques</term><term>Courbe ROC</term><term>Données de séquences moléculaires</term><term>Génome</term><term>Protéines de liaison à l'ARN</term><term>Spécificité du substrat</term><term>Séquence nucléotidique</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Metazoan genomes encode hundreds of RNA-binding proteins (RBPs) but RNA-binding preferences for relatively few RBPs have been well defined. 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We anticipate that RNAcompete will be a valuable tool for the study of RNA-protein interactions.</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><noCountry><name sortKey="Blencowe, Benjamin J" sort="Blencowe, Benjamin J" uniqKey="Blencowe B" first="Benjamin J" last="Blencowe">Benjamin J. Blencowe</name><name sortKey="Chan, Esther T" sort="Chan, Esther T" uniqKey="Chan E" first="Esther T" last="Chan">Esther T. Chan</name><name sortKey="Chaudhry, Sidharth" sort="Chaudhry, Sidharth" uniqKey="Chaudhry S" first="Sidharth" last="Chaudhry">Sidharth Chaudhry</name><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R" last="Hughes">Timothy R. Hughes</name><name sortKey="Kazan, Hilal" sort="Kazan, Hilal" uniqKey="Kazan H" first="Hilal" last="Kazan">Hilal Kazan</name><name sortKey="Morris, Quaid" sort="Morris, Quaid" uniqKey="Morris Q" first="Quaid" last="Morris">Quaid Morris</name><name sortKey="Pe A Castillo, Lourdes" sort="Pe A Castillo, Lourdes" uniqKey="Pe A Castillo L" first="Lourdes" last="Pe A Castillo">Lourdes Pe A Castillo</name><name sortKey="Talukder, Shaheynoor" sort="Talukder, Shaheynoor" uniqKey="Talukder S" first="Shaheynoor" last="Talukder">Shaheynoor Talukder</name></noCountry><country name="Canada"><region name="Ontario"><name sortKey="Ray, Debashish" sort="Ray, Debashish" uniqKey="Ray D" first="Debashish" last="Ray">Debashish Ray</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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