Genome binding/occupancy profiling by high throughput sequencing
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.