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| Item Type: | Article |
|---|---|
| Title: | The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts |
| Creators: |
Baltz, A.G., Munschauer, M.  ORCID: https://orcid.org/0000-0001-6143-4548, Schwanhaeusser, B., Vasile, A. ORCID: https://orcid.org/0000-0001-5452-9960, Murakawa, Y., Schueler, M., Youngs, N., Penfold-Brown, D., Drew, K., Milek, M. ORCID: https://orcid.org/0000-0002-0803-8439, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Bonneau, R., Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Dieterich, C. ORCID: https://orcid.org/0000-0001-9468-6311 and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
|
| 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 |
| 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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