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.

中文翻译：

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系统的溴结构域蛋白筛选可识别参与基因组完整性的同源重组和 R 环抑制途径。

溴结构域蛋白 (BRD) 是基因组功能和稳定性的关键染色质调节剂，也是癌症的治疗靶点。在这里，我们使用几种基于细胞的测定和蛋白质组相互作用网络分析系统地描述了人类 BRD 蛋白对基因组稳定性和 DNA 双链断裂 (DSB) 修复的贡献。应用这些方法，我们将 42 种 BRD 蛋白中的 24 种鉴定为 DNA 修复和/或基因组完整性的启动子。我们确定了 PCAF 的 BRD 阅读器功能，该功能在 DSB 处结合 TIP60 介导的组蛋白乙酰化以募集 DUB 复合物以去泛素化组蛋白 H2BK120，以允许 PCAF 直接乙酰化，并通过同源重组修复 DSB。我们还发现了溴代和额外末端 (BET) BRD 蛋白 BRD2 和 BRD4，作为转录相关 RNA-DNA 杂交体 (R-loops) 的负调节因子，抑制 BRD2 或 BRD4 会增加 R-loop 的形成，从而产生 DSB。这些断裂依赖于拓扑异构酶 II，而 BRD2 直接结合并激活拓扑异构酶 I，这是一种已知的 R 环抑制剂。因此，BRD 蛋白的综合相互作用组和功能分析揭示了新的同源重组和基因组稳定性途径，为了解 BRD 蛋白的基因组维持及其药理学抑制作用提供了一个框架。