An interspecies analysis reveals a key role for unmethylated CpG dinucleotides in vertebrate Polycomb complex recruitment

Abstract

The role of DNA sequence in determining chromatin state is incompletely understood. We have previously demonstrated that large chromosomal segments from human cells recapitulate their native chromatin state in mouse cells, but the relative contribution of local sequences versus their genomic context remains unknown. In this study, we compare orthologous chromosomal regions for which the human locus establishes prominent sites of Polycomb complex recruitment in pluripotent stem cells, whereas the corresponding mouse locus does not. Using recombinationmediated cassette exchange at the mouse locus, we establish the primacy of local sequences in the encoding of chromatin state. We show that the signal for chromatin bivalency is redundantly encoded across a bivalent domain and that this reflects competition between Polycomb complex recruitment and transcriptional activation. Furthermore, our results suggest that a high density of unmethylated CpG dinucleotides is sufficient for vertebrate Polycomb recruitment. This model is supported by analysis of DNA methyltransferase-deficient embryonic stem cells.

Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation

“…Additionally, we demonstrate that DNA methylation inhibits H3K27me3 deposition at CpG-rich sequences and that this inhibition can be reversed upon chemical removal of DNA methylation. These observations readily explain the occupancy of H3K27me3 and DNA methylation observed throughout the genome (23,24,33,34). They extend previous studies that already suggested a role for CpG dinucleotides in PRC2 recruitment (22,23) but are also more comprehensive and provide novel mechanistic details.…”

“…Thus, loss of Polycomb recruitment coincides with increased susceptibility to DNA methylation. This finding is compatible with the observation of increased H3K27 methylation upon global loss of DNA methylation (23,24,33,34), which we also observe in our genome-wide datasets (Fig. S7A).…”

“…S4G), indicating that CpG dinucleotides are required for H3K27me3 recruitment. Such a model has previously been proposed based on the strong presence of H3K27me3 at CGIs (20,21) and the observation that two CpG-rich elements from the Escherichia coli genome become H3K27-methylated when placed into stem cells as part of larger transgenes (22,23). The identification of small endogenous sequences that can autonomously recruit H3K27me3 enabled us to rigorously test this model.…”

“…Several transcription factor (TF) binding motifs are enriched within fly PREs and might contribute to Polycomb recruitment (18,19). In mammals, PRC2 and the H3K27me3 mark localize mainly to transcriptionally inactive regions rich in CpG dinucleotides, referred to as CpG-islands (CGIs) (20)(21)(22)(23). CGIs are unique to vertebrate genomes that show global DNA methylation (24).…”

The Molecular Basis of -Thalassemia

“…histone deacetylases (HDACs) and another repressive Polycomb complex (called PRC1) (Lynch et al 2012). Experimental data suggest that together, these complexes (PRC1, PRC2, and HDACs) maintain the silence of the a genes in multipotent cells and differentiated nonerythroid cells Lynch et al 2012) but that they are cleared from the a-globin promoter before the activation steps described (see Fig.…”