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Status |
Public on Jun 07, 2009 |
Title |
RNAcompete: a method for rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins |
Organism |
synthetic construct |
Experiment type |
Other
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Summary |
Metazoan genomes encode hundreds of RNA binding proteins (RBPs) but relatively few have well-defined RNA-binding preferences. Current techniques for determining RNA targets, including those involving in vitro selection and RNA co-immunoprecipitation, require significant time and labour investment. Here we introduce RNAcompete, a new method for the systematic analysis of RNA-binding specificities that employs a single binding reaction to determine the relative preferences of RBPs for short RNAs that containing 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 both 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 conventional motif models. We anticipate that RNAcompete will be a valuable tool for the large-scale study of RNA-protein interactions.
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Overall design |
The bound RNA from each RNA binding protein pulldown assay is analyzed on a custom Agilent microarray using a pool RNA control as a reference.
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Web link |
http://hugheslab.ccbr.utoronto.ca/supplementary-data/RNAcompete/
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Contributor(s) |
Ray D, Kazan H, Chan ET, Pena-Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris QD, Hughes TR |
Citation(s) |
19561594 |
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Submission date |
Apr 21, 2009 |
Last update date |
Mar 21, 2012 |
Contact name |
Esther T Chan |
Organization name |
Celgene Corporation
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Street address |
1500 Owens Street, Suite 500
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City |
San Francisco |
State/province |
California |
ZIP/Postal code |
94158 |
Country |
USA |
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Platforms (1) |
GPL8464 |
Agilent custom 244K oligo RNA Binding Protein microarray v2 |
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Samples (10)
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Relations |
BioProject |
PRJNA116807 |
Supplementary file |
Size |
Download |
File type/resource |
GSE15769_RAW.tar |
68.0 Mb |
(http)(custom) |
TAR (of TXT) |
Processed data included within Sample table |
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