The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

Alexander G. Baltz, Mathias Munschauer, Björn Schwanhäusser, Alexandra Vasile, Yasuhiro Murakawa, Markus Schueler, Noah Youngs, Duncan Penfold-Brown, Kevin Drew, Miha Milek, Emanuel Wyler, Richard Bonneau, Matthias Selbach, Christoph Dieterich, Markus Landthaler

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)674-690
Number of pages17
JournalMolecular Cell
Volume46
Issue number5
DOIs
StatePublished - Jun 8 2012

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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