MersV1, PubMed, Curation, bibRecord, 002008

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.

Identifieur interne : 002008 ( PubMed/Curation ); précédent : 002007; suivant : 002009

Rapid 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. Hughes

Source :

Nature biotechnology [ 1546-1696 ] ; 2009.

RBID : pubmed:19561594

Descripteurs français

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

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Le document en format XML

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<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. 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.</div>
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<Reference><Citation>Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11207-11</Citation>
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<Reference><Citation>Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14085-90</Citation>
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   |wiki=    Sante
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   |clé=     pubmed:19561594
   |texte=   Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.
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Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.

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