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 journalArticle

96 Scopus citations

Abstract

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
Volume64
Issue number2
DOIs
StatePublished - Oct 20 2016

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Fingerprint Dive into the research topics of 'High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells'. Together they form a unique fingerprint.

  • Cite this

    He, C., Sidoli, S., Warneford-Thomson, R., Tatomer, D. C., Wilusz, J. E., Garcia, B. A., & Bonasio, R. (2016). High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. Molecular Cell, 64(2), 416-430. https://doi.org/10.1016/j.molcel.2016.09.034