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

Abstract

During mammalian neurodevelopment, signaling pathways converge upon transcription factors (TFs) to establish appropriate gene expression programmes leading to the production of distinct neural and glial cell types. This process is partially regulated by the dynamic modulation of chromatin states by epigenetic systems, including the polycomb group (PcG) family of co-repressors. PcG proteins form multi-subunit assemblies that sub-divide into distinct, yet functionally related families. Polycomb repressive complexes 1 and 2 (PRC1 and 2) modify the chemical properties of chromatin by covalently modifying histone tails via H2A ubiquitination (H2AK119ub1) and H3 methylation, respectively. In contrast to the PRCs, the Polycomb repressive deubiquitinase (PR-DUB) complex removes H2AK119ub1 from chromatin through the action of the C-terminal hydrolase BAP1. Genetic screening has identified several PcG mutations that are causally associated with a range of congenital neuropathologies associated with both localised and/or systemic growth abnormalities. As PRC1 and PR-DUB hold opposing functions to control H2AK119ub1 levels across the genome, it is plausible that such neurodevelopmental disorders arise through a common mechanism. In this review, we will focus on advancements regarding the composition and opposing molecular functions of mammalian PRC1 and PR-DUB, and explore how their dysfunction contributes to the emergence of neurodevelopmental disorders.

Keywords: H2AK119ub1; chromatin; chromosomal architecture; epigenetics; histone modifications; neurodevelopment; neurodevelopmental disorders; polycomb.

Figure 2

Schematic representation of Polycomb group (PcG) protein recruitment and chromatin binding. The PRC family is targeted to chromatin by a hierarchical process. Initial localisation occurs through sequence specific and/or direct recruitment mechanisms that in turn lead to the deposition of chromatin modifications that act to recruit or activate downstream PRCs. Transcriptionally silent, non-methylated CpG islands (CGIs), provide a direct recruitment platform for both PRC2.1 and PRC1.1 via affinity of their Polycomb-like (PCL; PCL1-3) and Lysine Demethylase 2B (KDM2B) subunits respectively [10,19,63,64,65,66]. In addition, other ncPRCs employ both sequence specific and RNA-mediated mechanisms to target specific sites in the genome (the varying subunits responsible for chromatin targeting of individual ncPRC1s, including KDM2B, are denoted as X for simplicity) [67,68,69,70,71,72]. This leads to the deposition of H3K27me3 by EZH1/2 (PRC2.1) and H2AK119ub1 by RING1A/B (ncPRC1). The resulting H2A ubiquitination leads to the recruitment and allosteric activation of PRC2.2, through association with JARID2 and AEBP2, which enhances H3K27me3 deposition [12,73,74,75]. Finally, cPRC1 is recruited to chromatin by CBX7-mediated recognition of PRC2-deposited H3K27me3, where it nucleates physical interactions between other cPRC1 target sites in the genome [22,29,31,37,38,42]. However, due to its very low E3 ubiquitin ligase activity, cPRC1 contributes little to the deposition of H2AK119ub1 (denoted by a faint dashed arrow), which is primarily carried out by ncPRC1s [54,55].

Figure 1

PRC1 complexes contain a highly conserved catalytic core consisting of one of two interchangeable E3 ubiquitin ligases (RING1A or RING1B), which form mutually exclusive heterodimers with one of six Polycomb group RING-finger domain proteins (PCGF1-6). Additional subunits allow the classification of PRC1 into cPRC1 and ncPRC1 forms. cPRC1 complexes assemble around a dimer of RING1A/B and either PCGF2 or PCGF4. Additional subunits including CBX2, CBX4, CBX6, CBX7 or CBX8 and PHC1, PHC2 or PHC3 proteins. CBX proteins have an affinity for histone H3 lysine methylation (e.g. H3K27me3) and are important for PRC1 targeting to chromatin alongside roles in chromatin compaction. In addition, the presence of PHC proteins enable cPRC1 to modulate higher order chromatin structure. In contrast, ncPRC1 complexes comprise dimers of RING1A/B and PCGF1, 3, 5 or 6 associated with either RING and YY1 Binding Protein (RYBP) or its homolog YY1 Associated Factor 2 (YAF2) in place of CBX. The inclusion of RYBP or YAF2 in ncPRC1 greatly enhances RING1A/B catalytic activity, such that ncPRC1s contribute to the majority of H2AK119ub1 in vivo. PR-DUB complexes contain a catalytic core of BAP1, which forms mutually exclusive complexes with one of three additional sex combs-like paralogues (ASXL1-3). PR-DUB complexes function in the cleavage of ubiquitin conjugates from both chromatin and soluble protein targets, including H2AK119ub1. Additional subunit interactions modulate PR-DUB targeting and function, including the transcription factors FOXK1/2, chromatin modifiers OGT and KDM1B, transcriptional cofactor HCF-1 and members of methyl-CpG-binding family MBD5 and 6.

Figure 3

Schematic representation of Polycomb group (PcG) complex activity and related histone ubiquitination levels. Top: Active (PRC1-low, H2AK119ub1-low) and repressed (PRC1-high, H2AK119ub1-high) gene promoter regions are represented in the context of balanced PRC1-ub deposition and PR-DUB deubiquitination function. PRC1 is highly localised to target gene promoter regions, ultimately resulting in enriched levels of H2AK119ub1 and the repression of key PcG target genes. PR-DUB regulates H2A ubiquitination, which may function to maintain balanced H2A ubiquitination levels across the genome, counteracting PRC1-mediated H2A ubiquitination and leading to transcription. Bottom: Mutations in several components that modulate H2A ubiquitination have been associated with several syndromes and brain pathologies. For example, germline mutations of ASXL1-3 subunits in PR-DUB have been identified in patients with rare congenital disorders. Notably, patients with Bainbridge-Ropers syndrome have been shown to exhibit higher levels of H2A ubiquitination and differential gene expression, suggesting disruption of PR-DUB function. Two promoter regions (first: PRC1-low, H2AK119ub1-high; second PRC1-high, H2AK119ub1-high) genes are represented in the context of perturbed PR-DUB function. Reduced PR-DUB deubiquitination function results in a global increase of H2AK119ub1 at target genes.