PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination

Abstract

Polycomb group proteins are important for maintaining gene expression patterns and cell identity in metazoans. The mammalian Polycomb repressive deubiquitinase (PR-DUB) complexes catalyze removal of monoubiquitination on lysine 119 of histone H2A (H2AK119ub1) through a multiprotein core comprised of BAP1, HCFC1, FOXK1/2, and OGT in combination with either of ASXL1, 2, or 3. Mutations in PR-DUB components are frequent in cancer. However, mechanistic understanding of PR-DUB function in gene regulation is limited. Here, we show that BAP1 is dependent on the ASXL proteins and FOXK1/2 in facilitating gene activation across the genome. Although PR-DUB was previously shown to cooperate with PRC2, we observed minimal overlap and functional interaction between BAP1 and PRC2 in embryonic stem cells. Collectively, these results demonstrate that PR-DUB, by counteracting accumulation of H2AK119ub1, maintains chromatin in an optimal configuration ensuring expression of genes important for general functions such as cell metabolism and homeostasis.

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

“…The most extensively characterised and evolutionary conserved of these DUBs is BAP1, which interacts with ASXL proteins to form the Polycomb Repressive Deubiquitinase complex (PR-DUB) (Scheuermann et al 2010; Wu et al 2015; Sahtoe et al 2016; Kloet et al 2016; Hauri et al 2016; Campagne et al 2019). Previous attempts to understand how BAP1 regulates gene expression and whether this relies on its H2AK119ub1 deubiquitylase activity have primarily focused on examining how the PR-DUB complex is targeted to gene promoters and distal regulatory elements, and how this regulates binding and/or activity of chromatin-modifying transcriptional co-activators (Li et al 2017b; Wang et al 2018; Campagne et al 2019; Kuznetsov et al 2019; Kolovos et al 2020; Szczepanski et al 2020). While this has revealed that BAP1 can remove H2AK119ub1 at specific loci, its primary site of action in the genome and the mechanisms by which it controls gene expression have appeared to be context-dependent and in some cases difficult to reconcile with the known roles of H2AK119ub1 in gene regulation.…”

Deubiquitylases in developmental ubiquitin signaling and congenital diseases

“…This regulatory concept is frequently applied by histone-directed DUBs. For example, USP44 (through the N-CoR complex [ 106 ]), USP51, USP27X, and USP22 (through ATXN7L3 and ENY2 [ 107 ]), and BAP1 (through FOXK1/2 and ASXL1/2/3 [ 37 , 108 , 109 ]) are recruited to specific regions on chromatin, where they counteract monoubiquitylation of H2A and H2B to regulate gene expression changes required for various aspects of stem cell maintenance and differentiation (see below). In addition, DUB recruitment to substrates via adapter proteins can also be utilized to stabilize transcription factors.…”

“…3A ). In this context, the mechanistic details of histone deubiquitylation and recruitment to chromatin have been well-characterized for only a subset of these DUBs (e.g., USP22 [ 107 , 129 , 159 ] and BAP1 [ 37 , 108 , 109 , 111 – 114 ]). DUBs that have been reported to control developmental processes through deubiquitylating H2B include USP44, which represses genes involved in lineage commitment during mESC maintenance [ 79 ], and USP22, which specifically inhibits expression of the pluripotency factor SOX2 during hESC differentiation [ 81 ].…”

“…DUBs that have been reported to control developmental processes through deubiquitylating H2B include USP44, which represses genes involved in lineage commitment during mESC maintenance [ 79 ], and USP22, which specifically inhibits expression of the pluripotency factor SOX2 during hESC differentiation [ 81 ]. Examples of DUBs that are thought to elicit their functions through H2A deubiquitylation include BAP1, USP21, and USP16 [ 35 , 37 , 108 , 111 , 143 , 160 ]. BAP1 and USP21 activity are required for stem cell self-renewal by ensuring the expression of genes that are involved in basic cellular functions and that are under the control of the pluripotency factor NANOG, respectively [ 108 , 143 ].…”

“…Examples of DUBs that are thought to elicit their functions through H2A deubiquitylation include BAP1, USP21, and USP16 [ 35 , 37 , 108 , 111 , 143 , 160 ]. BAP1 and USP21 activity are required for stem cell self-renewal by ensuring the expression of genes that are involved in basic cellular functions and that are under the control of the pluripotency factor NANOG, respectively [ 108 , 143 ]. In contrast, the Down Syndrome-associated USP16 is not essential for stem cell maintenance, but its activity was proposed to alleviate H2A ubiquitylation-imposed repression of lineage-specific genes during differentiation [ 35 , 154 , 160 ].…”