PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of chromatin compaction

Abstract

The Polycomb repressive complexes PRC1, PRC2, and PR-DUB repress target genes by modifying their chromatin. InDrosophila, PRC1 compacts chromatin and monoubiquitinates histone H2A at lysine 118 (H2Aub1), whereas PR-DUB is a major H2Aub1 deubiquitinase, but how H2Aub1 levels must be balanced for Polycomb repression remains unclear. We show that in early embryos, H2Aub1 is enriched at Polycomb target genes, where it facilitates H3K27me3 deposition by PRC2 to mark genes for repression. During subsequent stages of development, H2Aub1 becomes depleted from these genes and is no longer enriched when Polycomb maintains them repressed. Accordingly, Polycomb targets remain repressed in H2Aub1-deficient animals. In PR-DUB catalytic mutants, high levels of H2Aub1 accumulate at Polycomb target genes, and Polycomb repression breaks down. These high H2Aub1 levels do not diminish Polycomb protein complex binding or H3K27 trimethylation but increase DNA accessibility. We show that H2Aub1 interferes with nucleosome stacking and chromatin fiber folding in vitro. Consistent with this, Polycomb repression defects in PR-DUB mutants are exacerbated by reducing PRC1 chromatin compaction activity, but Polycomb repression is restored if PRC1 E3 ligase activity is removed. PR-DUB therefore acts as a rheostat that removes excessive H2Aub1 that, although deposited by PRC1, antagonizes PRC1-mediated chromatin compaction.

RINGs, DUBs and Abnormal Brain Growth—Histone H2A Ubiquitination in Brain Development and Disease

“…Given that ubiquitination is a highly abundant modification that operates, at least in part, through a limited pool of reader proteins, it is clear why the coordinated effort of PRC1 and PR-DUB to set the location and abundance of H2AK119ub1 is required to maintain robust and targeted gene repression ( Figure 3 ) [ 49 , 54 , 105 ]. Interestingly, recent work points towards a contrasting, dynamic interplay between PRC1 and PR-DUB during Drosophila development [ 194 ]. Whether this represents a functional divergence between mammals and flies is yet to be determined.…”

Goldilocks meets Polycomb

“…She next goes to sleep in the bed that is neither too hard nor too soft but just right. In this issue of Genes & Development, Bonnet et al (2022) show that the opposing activities of ncPRC1 and PR-DUB generate the just-right level of H2Aub1 for gene repression by the Polycomb system.…”

“…Moreover, although H2Aub1 accelerates the buildup of H3K27me3 domains at Hox and other developmental genes in early embryos, these domains are ultimately also established in animals lacking H2Aub1 (Fig. 1A; Pengelly et al 2015;Bonnet et al 2022). Likewise, in the mouse developing neocortex, H2Aub1 assists transient, reversible gene repression in neurogenic stem cells.…”

“…Puzzlingly, Polycomb repression also requires deubiquitylation of H2Aub1 by Polycomb repressive deubiquitinase (PR-DUB). In this issue of Genes & Development, Bonnet andcolleagues (pp. 1046-1061) resolve this paradox by showing that high levels of H2Aub1 in Drosophila lacking PR-DUB activity promotes open chromatin and gene expression in spite of normal H3K27me3 levels and PRC binding.…”

“…Next, Bonnet et al (2022) addressed the question of why the removal of H2Aub1 by PR-DUB promotes Polycomb repression. Surprisingly, in vitro biophysical analysis of nucleosome arrays revealed that H2Aub1 interferes with the association between the exposed surfaces of the histone octamers of the n and n+2 nucleosomes.…”