GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet 6:e1001244

Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
PLoS Genetics (Impact Factor: 8.17). 12/2010; 6(12):e1001244. DOI: 10.1371/journal.pgen.1001244
Source: PubMed

ABSTRACT Polycomb proteins are epigenetic regulators that localize to developmental loci in the early embryo where they mediate lineage-specific gene repression. In Drosophila, these repressors are recruited to sequence elements by DNA binding proteins associated with Polycomb repressive complex 2 (PRC2). However, the sequences that recruit PRC2 in mammalian cells have remained obscure. To address this, we integrated a series of engineered bacterial artificial chromosomes into embryonic stem (ES) cells and examined their chromatin. We found that a 44 kb region corresponding to the Zfpm2 locus initiates de novo recruitment of PRC2. We then pinpointed a CpG island within this locus as both necessary and sufficient for PRC2 recruitment. Based on this causal demonstration and prior genomic analyses, we hypothesized that large GC-rich elements depleted of activating transcription factor motifs mediate PRC2 recruitment in mammals. We validated this model in two ways. First, we showed that a constitutively active CpG island is able to recruit PRC2 after excision of a cluster of activating motifs. Second, we showed that two 1 kb sequence intervals from the Escherichia coli genome with GC-contents comparable to a mammalian CpG island are both capable of recruiting PRC2 when integrated into the ES cell genome. Our findings demonstrate a causal role for GC-rich sequences in PRC2 recruitment and implicate a specific subset of CpG islands depleted of activating motifs as instrumental for the initial localization of this key regulator in mammalian genomes.

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Available from: Manching Ku, Aug 17, 2015
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    • "However, a number of lines of evidence – most notably (i) the acquisition of H3K27me3 by bacterial non-methylated GC-rich sequences integrated into mouse genomes [156], (ii) the acquisition of H3K27me3 by CpG islands that have activating sequences removed [156], and (iii) the anticorrelation of H3K27me3 with DNA methylation [74] [146] – point to the requirement for CpG islands in establishing H3K27me3/polycomb repressed domains in mammals. In the absence of an obvious DNAbinding candidate for this role, indirect effects have been suggested, including the ability of H3K36me2 (which is removed from CpG islands through interactions with the ZF-CxxC-domain containing proteins Kdm2a/b, among other mechanisms) to inhibit PRC2 activity [157] [158]. "
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    • "PHO, in particular, binds numerous putative promoter and enhancer elements outside a PRE context (Schuettengruber et al., 2009), and it was shown to interact with the INO80 chromatin remodeling complex in addition to PcG complexes (Klymenko et al., 2006). Of note, the mammalian homolog of PHO, YY1, is able to rescue a pho zygotic mutant, but does not seem to play a major role in PcG recruitment in mammals (Atchison et al., 2003; Mendenhall et al., 2010). DSP1 was also shown to bind to many non-PRE loci in Drosophila embryos, which are marked strongly by GAGA motifs (Schuettengruber et al., 2009). "
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    • "Additionally , several studies have demonstrated a link between unmethylated CpG residues and PcG recruitment/binding. Specifically , PcG occupancy correlates closely with CpG density in CGIs at target gene promoters (Lynch et al., 2012; Mendenhall et al., 2010). Moreover, depletion of DNA methylation has been correlated with changes in patterns of PRC2 localization (Brinkman et al., 2012; Reddington et al., 2013). "
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