Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing

Abstract

Posttranslational histone modifications play important roles in regulating chromatin-based nuclear processes. Histone H2AK119 ubiquitination (H2Aub) is a prevalent modification and has been primarily linked to gene silencing. However, the underlying mechanism remains largely obscure. Here we report the identification of RSF1 (remodeling and spacing factor 1), a subunit of the RSF complex, as a H2Aub binding protein, which mediates the gene-silencing function of this histone modification. RSF1 associates specifically with H2Aub, but not H2Bub nucleosomes, through a previously uncharacterized and obligatory region designated as ubiquitinated H2A binding domain. In human and mouse cells, genes regulated by RSF1 overlap significantly with those controlled by RNF2/Ring1B, the subunit of Polycomb repressive complex 1 (PRC1) which catalyzes the ubiquitination of H2AK119. About 82% of H2Aub-enriched genes, including the classic PRC1 target genes, are bound by RSF1 around their transcription start sites. Depletion of H2Aub levels by Ring1B knockout results in a significant reduction of RSF1 binding. In contrast, RSF1 knockout does not affect RNF2/Ring1B or H2Aub levels but leads to derepression of H2Aub target genes, accompanied by changes in H2Aub chromatin organization and release of linker histone H1. The action of RSF1 in H2Aub-mediated gene silencing is further demonstrated by chromatin-based in vitro transcription. Finally, RSF1 and Ring1 act cooperatively to regulate mesodermal cell specification and gastrulation during early embryonic development. Taken together, these data identify RSF1 as a H2Aub reader that contributes to H2Aub-mediated gene silencing by maintaining a stable nucleosome pattern at promoter regions.

Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression

“…Moving forward, an important challenge remains to examine in detail the molecular mechanisms by which H2AK119ub1 could contribute to gene repression. This may involve reader proteins that recognize H2AK119ub1 (Cooper et al., 2016, Kalb et al., 2014, Richly et al., 2010, Zhang et al., 2017), or H2AK119ub1 may directly counteract transcription, as suggested by recent observations using in vitro assays (Aihara et al., 2016).…”

PRC1 Catalytic Activity Is Central to Polycomb System Function

“…One possibility is that H2AK119ub1 directly disrupts RNA Pol II activity (Stock et al, 2007;Zhou et al, 2008), as suggested by in vitro transcription assays (Aihara et al, 2016;Nakagawa et al, 2008). Alternatively, H2AK119ub1 could recruit reader proteins that elicit gene repression (Ali et al, 2018;Cooper et al, 2016;Qin et al, 2015;Richly et al, 2010;Zhang et al, 2017) or interfere with deposition of histone modifications that facilitate transcription (Nakagawa et al, 2008;Yuan et al, 2013). Finally, it is possible that PRC1 drives gene repression via ubiquitylation of histone H2A variants (Surface et al, 2016) or other non-histone substrates (Ben-Saadon et al, 2006).…”

Ubiquitin Specific Peptidase 22 Regulates Histone H2B Mono-Ubiquitination and Exhibits Both Oncogenic and Tumor Suppressor Roles in Cancer

“…As indicated above, USP22 regulates the abundance of H2Aub1 and H2Bub1 to promote gene expression and is therefore considered a transcriptional activator. H2Aub1, which is catalyzed by the Polycomb Repressive Complex 1 (PRC1), is enriched within the promoter regions of polycomb target genes, promotes the recruitment of PRC2 repressive complex and promotes transcriptional repression [ 25 , 59 , 60 ]. Therefore, USP22 is proposed to promote transcription of polycomb targets by reversing H2A ubiquitination [ 9 ].…”