Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity
- Jae Jin Kim1,2,9,
- Seo Yun Lee1,2,9,
- Fade Gong1,2,8,
- Anna M. Battenhouse1,2,3,
- Daniel R. Boutz1,2,3,
- Aarti Bashyal4,
- Samantha T. Refvik1,2,5,
- Cheng-Ming Chiang6,
- Blerta Xhemalce1,2,7,
- Tanya T. Paull1,2,5,7,
- Jennifer S. Brodbelt4,7,
- Edward M. Marcotte1,2,3 and
- Kyle M. Miller1,2,7
- 1Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA;
- 2Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA;
- 3Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712, USA;
- 4Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, USA;
- 5The Howard Hughes Medical Institute;
- 6Simmons Comprehensive Cancer Center, Department of Biochemistry, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA;
- 7Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, Texas 78712, USA
- Corresponding author: kyle.miller{at}austin.utexas.edu
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↵9 These authors contributed equally to this work.
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.
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Footnotes
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Supplemental material is available for this article.
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Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.331231.119.
- Received July 28, 2019.
- Accepted October 28, 2019.
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