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Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

Figure 4

CG-density and DNA motif occurrences predict genomewide PcG complex localization.

(A) Proportion of CpG islands with a given chromatin state in mouse ES cells. More than 97% of Ezh2 sites in mouse ES cells correspond to CpG islands or other highly CG-rich sequences. A systematic screen reveals sets of DNA motifs over-represented in (B) Ezh2-positive CpG islands or (C) Ezh2-negative CpG islands (enrichment in parentheses). (D) Expression levels of implicated TFs in mouse ES cells. Motifs enriched in Ezh2-positive CpG islands correspond to repressors or to TFs that are not expressed. Motifs enriched in Ezh2-negative CpG islands correspond to highly expressed activators. (E) Ezh2 ChIP-Seq signals for CpG islands predicted as PRC2-positive or PRC2-negative based on motif occurrences. (F) H3K27me3 ChIP-Seq signals for human ES cells for CpG islands predicted to be PRC2-positive or PRC2-negative based on occurrences of the motifs originally identified in mouse.

Figure 4

doi: https://doi.org/10.1371/journal.pgen.1000242.g004