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

77 Citations (Scopus)

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
Externally publishedYes

Fingerprint

Proteome
Embryonic Stem Cells
RNA
Chromatin
Protein Interaction Maps
Untranslated RNA
Proteins
RNA-Binding Proteins
Cell Nucleus
Proteomics
Mass Spectrometry
Peptides
Genes

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. / He, Chongsheng; Sidoli, Simone; Warneford-Thomson, Robert; Tatomer, Deirdre C.; Wilusz, Jeremy E.; Garcia, Benjamin A.; Bonasio, Roberto.

In: Molecular Cell, Vol. 64, No. 2, 20.10.2016, p. 416-430.

Research output: Contribution to journalArticle

He, C, Sidoli, S, Warneford-Thomson, R, Tatomer, DC, Wilusz, JE, Garcia, BA & Bonasio, R 2016, 'High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells', Molecular Cell, vol. 64, no. 2, pp. 416-430. https://doi.org/10.1016/j.molcel.2016.09.034
He, Chongsheng ; Sidoli, Simone ; Warneford-Thomson, Robert ; Tatomer, Deirdre C. ; Wilusz, Jeremy E. ; Garcia, Benjamin A. ; Bonasio, Roberto. / High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. In: Molecular Cell. 2016 ; Vol. 64, No. 2. pp. 416-430.
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