High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells

Chongsheng He, Simone Sidoli, Robert Warneford-Thomson, Deirdre C. Tatomer, Jeremy E. Wilusz, Benjamin A. Garcia, Roberto Bonasio

Research output: Contribution to journalArticlepeer-review

162 Scopus citations


Interactions between noncoding RNAs and chromatin proteins play important roles in gene regulation, but the molecular details of most of these interactions are unknown. Using protein-RNA photocrosslinking and mass spectrometry on embryonic stem cell nuclei, we identified and mapped, at peptide resolution, the RNA-binding regions in ∼800 known and previously unknown RNA-binding proteins, many of which are transcriptional regulators and chromatin modifiers. In addition to known RNA-binding motifs, we detected several protein domains previously unknown to function in RNA recognition, as well as non-annotated and/or disordered regions, suggesting that many functional protein-RNA contacts remain unexplored. We identified RNA-binding regions in several chromatin regulators, including TET2, and validated their ability to bind RNA. Thus, proteomic identification of RNA-binding regions (RBR-ID) is a powerful tool to map protein-RNA interactions and will allow rational design of mutants to dissect their function at a mechanistic level.

Original languageEnglish (US)
Pages (from-to)416-430
Number of pages15
JournalMolecular Cell
Issue number2
StatePublished - Oct 20 2016
Externally publishedYes

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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