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


  • A.G. Baltz
  • M. Munschauer
  • B. Schwanhaeusser
  • A. Vasile
  • Y. Murakawa
  • M. Schueler
  • N. Youngs
  • D. Penfold-Brown
  • K. Drew
  • M. Milek
  • E. Wyler
  • R. Bonneau
  • M. Selbach
  • C. Dieterich
  • M. Landthaler


  • Molecular Cell


  • Mol Cell 46 (5): 674-690


  • 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.