Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes

Abstract

Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed.

Fig. 1. Mammalian H2AK119ub (H2Aub) regulation by writers (ubiquitin E3 ligases), readers (ubiquitin-binding proteins) and erasers (deubiquitinases).

a Schematic representation of chromatin and the mammalian H2AK119 ubiquitination site by PRC1 E3 ligase. Note that the mammalian H2AK120 site is a minor site for PRC1-mediated ubiquitination. b Schematic representation of known modulators of H2Aub. Important functional domains are indicated. RING: Really Interesting New Gene, UBD: Ubiquitin-Binding Domain, UIM: Ubiquitin Interaction Motif, NZF: Nuclear protein localization 4 Zinc Finger, UAB: Ubiquitin-Associated Domain, RAWUL: Ring-finger and WD40 associated Ubiquitin-Like, PHD: Plant Homeodomain, UCH: Ubiquitin C-terminal Hydrolase, CTD: C-Terminal Domain, NLS: Nuclear Localization Signal, DEUBAD (DEU): DEUBiquitinase Activating Domain, ASXH: HARE-HTH of ASXLs.

Fig. 2. PcG complexes in Drosophila and PRC1 complexes in mammals.

a Schematic representation of the five PcG complexes in Drosophila: canonical (cPRC1) and variant (vPRC1:dRAF) PRC1 complexes, PRC2 complex, PR-DUB complex and PhoRC complex. PhoRC binds to gene regulatory regions via the interaction of its subunit Pho with specific DNA sequences, PRE (PcG Responsive Elements). Pho can also directly bind to components of cPRC1 complexes to mediate their recruitment even in the absence of H3K27me3. The arrows indicate protein interactions responsible for the recruitment of PcG complexes to the PRE. b Schematic representation of the canonical (cPRC1) and variant (vPRC1) PRC1 complexes in mammalians. RING1A or RING1B are obligate components of the PRC1 complexes. Their association with either PCGF2/PCGF4 or other PCGFs (PCGF1, PCGF3, PCGF5, PCGF6) lead to the formation of cPRC1 or variants vPRC1 complexes, respectively. CBXs/HPHs and RYBP/YAF2 associate in mutually exclusive manner with RING1A/RING1B for the formation of cPRC1 and vPRC1 complexes, respectively. H3K27me3 and CpG islands recruit cPRC1 and vPRC1/PCGF1 complexes respectively. Transcription factors (TF), USF and other chromatin factors (E2F6, MGA, MYC) might also be involved in the recruitment of PRC1 to chromatin. The arrows indicate protein-protein or protein DNA/RNA interactions responsible for the recruitment of PRC1 complexes to chromatin. Ubiquitination is shown as the yellow circle and H3K27me3 is shown by the three red circles (a, b). c In the center, crystal structure of a minimal human PRC1 complex (RING1B /BMI1-UbcH5c) interacting with the nucleosome core particle (NCP) (PDB: 4R8P). The left panels show the contact between RING1B and H2A/H2B acidic patch. The top right panel shows the DNA-UBCH5 interactions. BMI1 also makes polar contacts with Histone H3 and H4 as shown in the bottom right panel. Interaction of RING1B with BMI1 on one hand and histone H2A on the other hand is essential for establishing H2Aub on the latter.

Fig. 3. PR-DUB and BAP1 as major deubiquitinase complexes for H2Aub.

a Schematic representation of the Drosophila PR-DUB (Calypso/ASX) and mammalian BAP1 complexes (BAP1/ASXLs). The dotted arrows indicate potential interactions of ASX with chromatin. Calypso and ASX form an oligomer of 2:2 molecules. This specific arrangement is important for the recruitment to chromatin and H2Aub deubiquitination. Note that the mammalian PR-DUB complex (BAP1 complexes) is composed of many additional subunits including HCF-1, OGT, and FOXK1/2. Other BAP1-interacting partners, KDM1B, UBE2O, YY1 and HAT1 are shown. The arrows in circle indicate the mutually exclusive binding of ASXLs to BAP1. b Structural model of the Drosophila core PR-DUB complex (Calypso/DEUBAD (DEUBAD of Asx)) bound to ubiquitin. The model was obtained by superimposing the crystal structure of Calypso/DEUBAD (PDB: 6HGC) with the UCH-L5-RPN13-Ub crystal structure (PDB: 4UEL). Hydrogen bound interactions between calypso catalytic domain and ubiquitin are shown (left panels). DEUBAD also makes contact with the CTD domain of Calypso and ubiquitin (right top panel). The DEUBAD interaction with Calypso stabilizes Calypso’s crossover loop (shown in red, right bottom panel) which promotes Calypso’s catalytic activity towards ubiquitin. The triad catalytic sites: C131, H214, D228 are shown in red (right bottom panel).

Fig. 4. H2Aub readers in transcription regulation.

a The vPRC1 component RYBP uses its NZF-UBD to bind H2Aub. This binding is increased with nucleosome compaction with histone H1 to promote H2Aub spreading and a repressive state of chromatin. b Positive-feedback loop between PRC1 and PRC2 complexes is ensured by the binding of vPRC1 component, KDM2B to unmethylated CpGs island promoting H2Aub deposition. This results in a specific binding of nucleosomal H2Aub by the PRC2 component JARID2 through its UIM domain. JARID2 binding promotes the recruitment of the PRC2 complex and eventually the establishment of H3K27me3 by EZH2 and maintenance of gene repression. c RSF1 binds H2Aub through its UAB domain and promotes the recruitment of the RSF1 chromatin-remodeling complex. This ensures proper nucleosome arrangement at target gene promoters with maintenance of histone H1 positioning, ensuring gene transcription repression in collaboration with PRC1 complexes. d ZRF1 uses its UBD Ubiquitin-Binding Domain to bind H2Aub, thus blocking the access of PRC1 to the nucleosomes, and likely promoting recruitment of DUBs, allowing ubiquitin removal and transcription activation. Ubiquitin is shown as a yellow circle and H3K27me3 is shown by the three red circles.

Fig. 5. Regulation of gene transcription by H2Aub ubiquitination and deubiquitination.

a Recruitment of PRC1 complexes to compact chromatin regions in H2Aub-independent manner. These chromatin domains become inaccessible to the transcriptional machinery and are thus repressed. b H2A ubiquitination could contribute to gene repression by blocking the FACT histone chaperone. This would block nucleosome rearrangement resulting in maintenance of poised RNA PolII at promoters and inhibition of transcription elongation of specific target genes. Poised PolII is phosphorylated on serine 5. c BAP1 DUB complexes act at enhancers to recruit MLL3 and UTX to deposit H3K4me1 and demethylate H3K27me3, respectively. These events along with deubiquitination of H2Aub promote gene activation. Ubiquitination is shown in yellow circle, H3K27me3 is shown by the three red circles, H3K4me1/3 is shown by green circles and phosphorylation by bigger red circle.

Fig. 6. Involvement of H2Aub in DNA double strand break signaling and replication fork progression.

a Induction of DNA double strand breaks (DSBs) induces a rapid recruitment of PARP to DNA damage sites and subsequent protein poly(ADP-ribosyl)ation. Poly(ADP-ribose) serves as an anchor for the PRC1 complex, through its CBX4 subunit which leads to the recruitment of PRC1 to DNA damage site and ubiquitination of the histone variant H2AX. This ubiquitination event induces a more efficient recruitment of ATM and phosphorylation of H2AX (γH2AX), a hallmark of the DNA damage response. This in turn leads to the recruitment of RNF168 with catalyzes H2AXK13/K15 ubiquitination. Altogether, this cascade of posttranslational modifications leads to effective recruitment of the DNA repair machinery and inhibition of transcription. b Specific recruitment of the PRC1 complex to DNA DSB sites could be enhanced through interaction between BMI1 and the phosphorylated form of the transcription elongation factor MLLT1. Phosphorylation of PBAF also promotes the recruitment of the PRC1 complex to the site of DNA damage. c BAP1 is phosphorylated following DNA damage and is also recruited to DSB site to promote homologous recombination (HR). BAP1 appears to deubiquitinate H2Aub only near the DSB site, likely promoting DNA-end resection. Once the repair process is completed, the deubiquitinase USP16 or other DUBs could remove H2Aub mark more widely, allowing normal gene transcription. CD1 and CD2: the two parts of the catalytic domain. d During DNA synthesis, the chromatin-remodeling factor INO80 is protected from proteasomal degradation by BAP1. On the other hand, BAP1 deubiquitinates H2A and promotes coordinated DNA replication. HSA, Helicase-SANT associated domain. Ubiquitination is shown by the yellow circle, and phosphorylation by the red circle.

Fig. 7. Model for the potential role of H2Aub in cancer development.

PRC1 mediates H2Aub deposition and represses target genes that are negative regulators of cell cycle progression and cell death. PRC1 also promotes stem cell self-renewal. PRC1 overexpression results in increased cell ability to overcome cell cycle control, reduced apoptosis as well as increased capacity of stem cell self-renewal. BAP1 regulates cell proliferation and promotes cell death. Inactivation of BAP1 results in increased H2Aub deposition at target genes and modulation of cell cycle and resistance to cell death. PRC1 and BAP1 also regulate DNA repair, defect of which can promote carcinogenesis. BAP1 cancer-associated mutations disrupting BAP1 functional domains are shown by the red cross. Ubiquitination is shown by the yellow circle.