Journal
NUCLEIC ACIDS RESEARCH
Volume 40, Issue 19, Pages 9897-9902Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gks746
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Funding
- Max Planck Society for the Advancement of Science
- European Union [HEALTH-F4-2008-201648]
- Charles H. Revson Foundation
- National Institutes of Health [1RC1CA145442]
- Starr Foundation
- Max Planck Society
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Systematic analysis of the RNA-protein interactome requires robust and scalable methods. We here show the combination of two completely orthogonal, generic techniques to identify RNA-protein interactions: PAR-CLIP reveals a collection of RNAs bound to a protein whereas SILAC-based RNA pull-downs identify a group of proteins bound to an RNA. We investigated binding sites for five different proteins (IGF2BP1-3, QKI and PUM2) exhibiting different binding patterns. We report near perfect agreement between the two approaches. Nevertheless, they are non-redundant, and ideally complement each other to map the RNA-protein interaction network.
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