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Mol Cell. 2012 Jun 8;46(5):674-90. doi: 10.1016/j.molcel.2012.05.021.

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts.

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  • 1Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany.

Abstract

Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation, and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteomics and to display the protein occupancy on mRNA transcripts by next-generation sequencing. Application to a human embryonic kidney cell line identified close to 800 proteins. To our knowledge, nearly one-third were not previously annotated as RNA binding, and about 15% were not predictable by computational methods to interact with RNA. Protein occupancy profiling provides a transcriptome-wide catalog of potential cis-regulatory regions on mammalian mRNAs and showed that large stretches in 3' UTRs can be contacted by the mRNA-bound proteome, with numerous putative binding sites in regions harboring disease-associated nucleotide polymorphisms. Our observations indicate the presence of a large number of mRNA binders with diverse molecular functions participating in combinatorial posttranscriptional gene-expression networks.

Copyright © 2012 Elsevier Inc. All rights reserved.

PMID:
22681889
[PubMed - indexed for MEDLINE]
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