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

Item Type:Article
Title:The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts
Creators Name:Baltz, A.G. and Munschauer, M. and Schwanhaeusser, B. and Vasile, A. and Murakawa, Y. and Schueler, M. and Youngs, N. and Penfold-Brown, D. and Drew, K. and Milek, M. and Wyler, E. and Bonneau, R. and Selbach, M. and Dieterich, C. and Landthaler, M.
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.
Keywords:Binding Sites, Cell Line, Mass Spectrometry, Messenger RNA, Proteomics, RNA-Binding Proteins, RNA Sequence Analysis
Source:Molecular Cell
ISSN:1097-2765
Publisher:Cell Press (U.S.A.)
Volume:46
Number:5
Page Range:674-690
Date:8 June 2012
Official Publication:https://doi.org/10.1016/j.molcel.2012.05.021
PubMed:View item in PubMed

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