Letter abstract
Nature Biotechnology 27, 667 - 670 (2009)
Published online: 28 June 2009 | doi:10.1038/nbt.1550
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
Debashish Ray1,4, Hilal Kazan2,4, Esther T Chan3, Lourdes Peña Castillo1, Sidharth Chaudhry3, Shaheynoor Talukder1, Benjamin J Blencowe1,3, Quaid Morris1,2,3 & Timothy R Hughes1,3
Metazoan genomes encode hundreds of RNA-binding proteins (RBPs) but RNA-binding preferences for relatively few RBPs have been well defined1. Current techniques for determining RNA targets, including in vitro selection and RNA co-immunoprecipitation2, 3, 4, 5, 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.
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- These authors have contributed equally to this work.
Correspondence to: Timothy R Hughes1,3 e-mail: t.hughes@utoronto.ca
Correspondence to: Quaid Morris1,2,3 e-mail: quaid.morris@utoronto.ca
MORE ARTICLES LIKE THIS
These links to content published by NPG are automatically generated.
RESEARCH
Coordinated posttranscriptional mRNA population dynamics during T-cell activationMolecular Systems Biology Article (28 Jul 2009)
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAsMolecular Systems Biology Article (28 Apr 2009)
Structural basis for recognition of the tra mRNA precursor by the Sex-lethal proteinNature Article (15 Apr 1999)
