Polycomb-like proteins link the PRC2 complex to CpG islands

Abstract

The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression1,2 and plays essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like proteins (PCLs), including PHF1, MTF2 and PHF19, are PRC2 associated factors that form sub-complexes with PRC2 core components3, and have been proposed to modulate PRC2’s enzymatic activity or its recruitment to specific genomic loci4–13. Mammalian PRC2 binding sites are enriched in CG content, which correlate with CpG islands that display a low level of DNA methylation14. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. In this study, we solved the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We found that the extended homologous (EH) regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a manner completely different from the canonical winged-helix motif-DNA recognition. We further showed that the PCL EH domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic cells. Our research provides the first direct evidence demonstrating that PCLs are critical for PRC2 recruitment to CpG islands, thereby further clarifying their roles in transcriptional regulation in vivo.

PRC1 catalytic activity is central to Polycomb system function

“…One possibility is that H2AK119ub1 could directly disrupt RNA Polymerase II activity (Stock et al, 2007;Zhou et al, 2008), as recently suggested by in vitro transcription assays, in which incorporation of H2AK119ub1 into recombinant chromatin templates blocked transcription (Aihara et al, 2016;Nakagawa et al, 2008). Alternatively, PRC1 catalytic activity and H2AK119ub1 could have an indirect effect on transcription, for example by creating a binding site for reader proteins which would then elicit repression (Ali et al, 2018;Cooper et al, 2016;Qin et al, 2015;Richly et al, 2010;Zhang et al, 2017). In addition, incorporation of a bulky ubiquitin moiety may interfere with deposition of other histone modifications that facilitate gene expression (Nakagawa et al, 2008;Yuan et al, 2013).…”

“…Biochemical studies have identified two subtypes of PRC2 complexes with distinct targeting modules (reviewed in Laugesen et al, 2019;Yu et al, 2019). The PRC2.1 complex contains PCL proteins, which have been shown to bind to non-methylated CpG-rich DNA and methylated histone tails (Ballare et al, 2012;Brien et al, 2012;Cai et al, 2013;Li et al, 2017;Musselman et al, 2012a;Perino et al, 2018), while the PRC2.2 complex contains the JARID2 subunit, which has been recently implicated in direct recognition of H2AK119ub1 (Cooper et al, 2016;Kalb et al, 2014). Based on the major reductions in SUZ12 binding and H3K27me3 levels in the tamoxifen-treated PRC1 CPM cells, we wanted to test whether occupancy of PRC2.1 and PRC2.2 was differentially affected by loss of PRC1 catalytic activity.…”

“…It has been widely proposed that Polycomb chromatin domains are formed via a PRC2-initiated mechanism, in which PRC2 is actively recruited to Polycomb target genes via DNA binding accessory subunits, transcription factors or non-coding RNAs (Brockdorff, 2013;Dietrich et al, 2012;Herranz et al, 2008;Li et al, 2010;Li et al, 2017;Perino et al, 2018) and deposits H3K27me3 that is recognised by chromodomain-containing CBX proteins within so-called canonical PRC1 (cPRC1) complexes (Cao et al, 2002;Min et al, 2003;Wang et al, 2004b). cPRC1 complexes can support local chromatin compaction and long-range interactions between Polycomb chromatin domains, which has been proposed to underpin Polycomb-mediated gene repression (Eskeland et al, 2010;Francis et al, 2004;Grau et al, 2011).…”

Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands

“…It is well established that DNA methylation plays an important role in restricting H3K27me3 to unmethylated CpG islands. This is evident from preferential localization of H3K27me3 to endogenous The EMBO Journal Isoform-specific DNMT3A function Massimiliano Manzo et al and ectopic unmethylated CpG-rich regions (Tanay et al, 2007;Mikkelsen et al, 2007;Mohn et al, 2008;Mendenhall et al, 2010;Jermann et al, 2014;Wachter et al, 2014), the identification of PRC complex members that preferentially bind unmethylated CpGs and GC-rich sequences (Farcas et al, 2012;Wu et al, 2013;Li et al, 2017), and numerous studies that reported spreading of H3K27me3 in the absence of DNA methylation (Lynch et al, 2011;Brinkman et al, 2012;Marks et al, 2012;Reddington et al, 2013;Jermann et al, 2014;King et al, 2016). We suggest that the balance between DNMT3A1 and TET activity is required to fine-tune the distribution of methylated and unmethylated CpGs and for restricting Polycomb domain boundaries to the promoters of developmentally regulated genes.…”

Cell signaling coordinates global Polycomb Repressive Complex 2 recruitment and gene expression in murine embryonic stem cells

“…Although the genome-wide binding sites of PRCs in mESCs have been well documented, the molecular mechanisms for recruiting PRCs to specific genomic loci in mammalian cells have not been fully elucidated (Laugesen, Hojfeldt, and Helin 2019). A variety of factors, such as JARID2 and MTF2, have been reported to mediate the PRC2 recruitment (Landeira et al 2010;Pasini et al 2010;Shen et al 2009;Casanova et al 2011;Li et al 2017;Oksuz et al 2018). On the other hand, histone lysine demethylase 2b (KDM2B) recruits a non-canonical PRC1.1 variant to the unmethylated CpG islands (CGIs) in mammalian cells through its CxxC-zinc finger (CxxC-ZF) domain (Wu, Johansen, and Helin 2013;He et al 2013;Farcas et al 2012).…”