(RNA-seq) USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3

Ubiquitin-specific protease 7 (USP7) has been implicated in cancer progression and neurodevelopment. However, its molecular targets remain poorly characterized. We combined quantitative proteomics, transcriptomics, and epigenomics to define the core USP7 network. Our multi-omics analysis reveals USP7 as a control hub that links genome regulation, tumor suppression, and histone H2A ubiquitylation (H2AK119ub1) by noncanonical Polycomb-repressive complexes (ncPRC1s). USP7 strongly stabilizes ncPRC1.6 and, to a lesser extent, ncPRC1.1. Moreover, USP7 represses expression of AUTS2, which suppresses H2A ubiquitylation by ncPRC1.3/5. Collectively, these USP7 activities promote the genomic deposition of H2AK119ub1 by ncPRC1, especially at transcriptionally repressed loci. Notably, USP7-dependent changes in H2AK119ub1 levels are uncoupled from H3K27me3. Even complete loss of the PRC1 catalytic core and H2AK119ub1 has only a limited effect on H3K27me3. Besides defining the USP7 regulome, our results reveal that H2AK119ub1 dosage is largely disconnected from H3K27me3. RNA-seq analysis of wild-type or USP7-KO DLD1 cells. DOX treatment for 1, 3, or 9 days was carried out to rescue USP7 expression. contributor: Erasmus Genomics CTU

泛素特异性蛋白酶7（Ubiquitin-specific protease 7, USP7）已被证实参与癌症进展及神经发育过程，但其分子靶标仍未得到充分解析。本研究结合定量蛋白质组学、转录组学与表观基因组学技术，明确了USP7的核心调控网络。多组学分析显示，USP7作为调控枢纽，可通过非经典多梳抑制复合体（noncanonical Polycomb-repressive complexes, ncPRC1s）介导基因组调控、肿瘤抑制及组蛋白H2A泛素化（H2AK119ub1）过程。USP7可显著稳定ncPRC1.6，并在较弱程度上稳定ncPRC1.1。此外，USP7可抑制AUTS2的表达，而AUTS2本身会抑制ncPRC1.3/5介导的H2A泛素化。综上，USP7的上述活性可促进ncPRC1介导的H2AK119ub1在基因组中的沉积，尤其富集于转录沉默位点。值得注意的是，USP7依赖性的H2AK119ub1水平变化与H3K27me3修饰完全解偶联；即便完全缺失PRC1催化核心及H2AK119ub1，对H3K27me3的影响也仅较为有限。本研究不仅明确了USP7调控组，还揭示H2AK119ub1的剂量水平在很大程度上与H3K27me3无关。本研究针对野生型或USP7基因敲除的DLD1细胞开展了RNA测序（RNA-seq）分析，并通过强力霉素（DOX）处理1、3或9天以挽救USP7的表达。贡献者：伊拉斯谟基因组学CTU（Erasmus Genomics CTU）