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

Jae Jin Kim, Seo Yun Lee, Fade Gong, Anna M. Battenhouse, Daniel R. Boutz, Aarti Bashyal, Samantha T. Refvik, Cheng Ming Chiang, Blerta Xhemalce, Tanya T. Paull, Jennifer S. Brodbelt, Edward M. Marcotte, Kyle M. Miller

Research output: Contribution to journalArticle

2 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1751-1774
Number of pages24
JournalGenes & development
Volume33
Issue number23-24
DOIs
StatePublished - Dec 1 2019

Keywords

  • DNA damage response
  • DNA repair
  • R-loops
  • bromodomain
  • chromatin
  • homologous recombination

ASJC Scopus subject areas

  • Genetics
  • Developmental Biology

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  • Cite this

    Kim, J. J., Lee, S. Y., Gong, F., Battenhouse, A. M., Boutz, D. R., Bashyal, A., Refvik, S. T., Chiang, C. M., Xhemalce, B., Paull, T. T., Brodbelt, J. S., Marcotte, E. M., & Miller, K. M. (2019). Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity. Genes & development, 33(23-24), 1751-1774. https://doi.org/10.1101/gad.331231.119