BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome

Abstract

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 that are found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A mono-ubiquitylation (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 discover that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 represses gene expression by counteracting transcription initiation from gene regulatory elements, causing reductions in transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes leading to their derepression, therefore explaining the original genetic characterisation of BAP1 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, without the need for elaborate gene-specific targeting mechanisms.

BAP1 enhances Polycomb repression by counteracting widespread H2AK119ub1 deposition and chromatin condensation

“…This depletion of Polycomb complexes from their target sites allows aberrant activation of transcription, while simultaneously causing repressive chromatin compaction elsewhere. This model is further supported by key observations reported in a recent study from the Klose group (Fursova et al, 2021). This indirect regulation of transcription and chromatin conformation may help explain the tumor-suppressive functions of BAP1.…”

Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo

“…To investigate the mechanism by which loss of maternal SMCHD1 caused upregulation of anterior Hox genes, we assessed whether the histone marks H2AK119ub and H3K27me3 were perturbed in Smchd1 matΔ mESCs. These histone marks are laid down by polycomb repressive complex 1 (PRC1) and 2 (PRC2) respectively and induce a heterochromatic gene-silencing state at the Hox clusters in mESCs 41, 42 . Moreover, both marks are laid down on the maternal chromatin at Hox clusters and elsewhere in the genome 34, 35, 36 .…”

“…If this were the case, H3K27me3 and H2AK119ub would be unperturbed over Hox clusters in Smchd1 matΔ mESCs. We carried out CUT&RUN for H3K27me3 and H2AK119ub in biological triplicate samples of Smchd1 wt and Smchd1 matΔ mESCs, and compared our data to publicly available ChIP-seq datasets for these histone marks in mESCs (Supplementary Dataset 4, 41, 42 ). We observed enrichment of H3K27me3 and H2AK119ub at the expected regions for mESCs, including the four Hox clusters (Fig.…”

“…j . As in b. but for H2AKA119ub, peaks called from 42 . Pearson coefficient again indicates very high correlation between the genotypes.…”

“…Bam files were imported into SeqMonk v1.47.1, v1.47.2 or v1.48.0 57 . H3K27me3 and H2AK119ub MACS peaks were called from publicly available ChIP-sequencing datasets (settings for 300 bp, p < 1 × 10-5) ( 41 GEO accession number GSE73952, 42 GEO accession number GSE161996) between the histone mark ChIP and input libraries. The three biological replicates each for Smchd1 wt and Smchd1 matΔ were merged, and peaks were called against the MACS peaks from the publicly available data using the feature probe generator function in SeqMonk (±2.5kb).…”