Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity

Genes Dev. 2019 Dec 1;33(23-24):1751-1774. doi: 10.1101/gad.331231.119. Epub 2019 Nov 21.


Bromodomain proteins (BRD) are key chromatin regulators of genome function and stability as well as therapeutic targets in cancer. Here, we systematically delineate the contribution of human BRD proteins for genome stability and DNA double-strand break (DSB) repair using several cell-based assays and proteomic interaction network analysis. Applying these approaches, we identify 24 of the 42 BRD proteins as promoters of DNA repair and/or genome integrity. We identified a BRD-reader function of PCAF that bound TIP60-mediated histone acetylations at DSBs to recruit a DUB complex to deubiquitylate histone H2BK120, to allowing direct acetylation by PCAF, and repair of DSBs by homologous recombination. We also discovered the bromo-and-extra-terminal (BET) BRD proteins, BRD2 and BRD4, as negative regulators of transcription-associated RNA-DNA hybrids (R-loops) as inhibition of BRD2 or BRD4 increased R-loop formation, which generated DSBs. These breaks were reliant on topoisomerase II, and BRD2 directly bound and activated topoisomerase I, a known restrainer of R-loops. Thus, comprehensive interactome and functional profiling of BRD proteins revealed new homologous recombination and genome stability pathways, providing a framework to understand genome maintenance by BRD proteins and the effects of their pharmacological inhibition.

Keywords: DNA damage response; DNA repair; R-loops; bromodomain; chromatin; homologous recombination.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acetylation
  • Cell Line
  • DNA Breaks, Double-Stranded
  • DNA Topoisomerases, Type I / metabolism
  • DNA Topoisomerases, Type II / metabolism
  • Genomic Instability*
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • R-Loop Structures*
  • Recombinational DNA Repair / genetics*
  • Trans-Activators / metabolism
  • Transcription Factors / analysis
  • Transcription Factors / genetics*
  • Ubiquitination
  • p300-CBP Transcription Factors / genetics
  • p300-CBP Transcription Factors / metabolism


  • Trans-Activators
  • Transcription Factors
  • p300-CBP Transcription Factors
  • p300-CBP-associated factor
  • DNA Topoisomerases, Type I
  • DNA Topoisomerases, Type II