BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome [ChIP-seq]

Histone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A monoubiquitylation (H2AK119ub1), which is enriched at Polycomb-repressed gene promoters but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we found that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive genome-wide accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 preferentially counteracts Ser5 phosphorylation on the C-terminal domain of RNA polymerase II at gene regulatory elements and causes reductions in transcription and transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes, which leads to their derepression, providing a potential molecular rationale for why the BAP1 ortholog in Drosophila has been characterized as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification. Mouse embryonic stem cells in which BAP1 can be conditionally removed were profiled for genomic distribution of histone modifications associated with active transcription (H3K27ac, H3K4me3, and H3K4me1) or Polycomb-mediated gene repression (H2AK119ub1 and H3K27me3), Polycomb factors (RING1B and SUZ12) and RNA Polymerase II (total occupancy (Pol II NTD) and phosphorylated forms associated with transcription initiation or elongation (Pol II Ser5P or Ser2P respectively)), using spike-in calibrated ChIP-seq (cross-linked - for Polycomb factors and Pol II, and native - for histone modifications). Please note that, as each processed data is associated with multiple samples, they are linked as Series supplementary file and described in the corresponding sample description field.

组蛋白修饰系统在基因调控与多细胞生物发育中发挥核心作用。尽管在基因调控元件处富集的组蛋白修饰已被广泛研究，但广泛分布于全基因组的组蛋白修饰的功能仍未被充分阐明。以组蛋白H2A单泛素化（histone H2A monoubiquitylation, H2AK119ub1）为例，该修饰不仅富集于多梳蛋白抑制的基因启动子区域，还以较低水平覆盖整个基因组。本研究通过诱导型遗传扰动与定量基因组学技术，发现BAP1去泛素化酶在维持全基因组H2AK119ub1水平稳态中发挥关键作用。敲除BAP1会导致全基因组范围内H2AK119ub1的广泛积累，进而引发全基因组范围的基因表达下调。研究表明，升高的H2AK119ub1会优先拮抗RNA聚合酶II（RNA polymerase II）羧基末端结构域（C-terminal domain, CTD）在基因调控元件处的丝氨酸5磷酸化，从而抑制转录并降低与转录相关的组蛋白修饰水平。此外，无法维持全基因组H2AK119ub1的稳态水平会损害部分多梳蛋白靶基因的多梳蛋白复合物占据，最终导致这些基因的去抑制，这为果蝇中BAP1同源物被归类为多梳群基因提供了潜在的分子机制解释。综上，本研究揭示了通过调控广泛分布的组蛋白修饰水平，可以调节基因组的转录潜能。本研究对可条件性敲除BAP1的小鼠胚胎干细胞进行了组学分析，采用spike-in校准染色质免疫共沉淀测序（spike-in calibrated ChIP-seq）技术，分别检测了与活跃转录相关的组蛋白修饰（H3K27ac、H3K4me3及H3K4me1）、多梳蛋白介导的基因沉默相关修饰（H2AK119ub1及H3K27me3）、多梳蛋白复合物因子（RING1B与SUZ12）以及RNA聚合酶II的相关指标：包括总聚合酶结合水平（Pol II N端结构域抗体，Pol II NTD）、与转录起始或延伸相关的磷酸化形式（分别对应Pol II丝氨酸5磷酸化形式Pol II Ser5P与丝氨酸2磷酸化形式Pol II Ser2P）。其中，针对多梳蛋白复合物因子与RNA聚合酶II的检测采用交联法染色质免疫共沉淀测序，针对组蛋白修饰的检测采用天然法染色质免疫共沉淀测序。请注意，由于每份处理数据关联多个样本，相关样本已作为系列补充数据集文件上传，并在对应的样本描述字段中进行了详细说明。