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. 2014 May;24(5):809–820. doi: 10.1101/gr.163642.113

Figure 1.

Figure 1.

Polycomb N-ChIP recovers nucleosomes and factor binding sites. N-ChIP was performed on MNase-digested chromatin from S2R+ cells with antisera to the H3K27me3 histone modification or to the Polycomb protein. (A) Polycomb binds nucleosomes within H3K27me3 domains; 555 domains were defined by contiguous H3K27me3 enrichment (see Methods), and the midpoints of each fragment recovered in N-ChIP experiments are plotted around aligned borders of those domains. Coincident midpoints are pseudo-colored. Plotting fragments from H3K27me3 (left) and from Polycomb (right) N-ChIP show the relative enrichment of nucleosome-sized fragments within domains in each experiment. (B) Chromatin features of focal Polycomb binding sites. Heat maps of 1945 aligned focal Polycomb binding sites, displaying read counts normalized within nucleosome (>120 bp) or factor (<76 bp) fragment size classes; 910 sites fall within H3K27me3 domains, and 1035 sites fall outside of domains. Each group is sorted by nucleosome occupancy at the binding site based on MNase-seq fragments >120 bp in length. Heat maps from left to right display the distributions of H3K27me3-marked nucleosomes (H3K27me3 N-ChIP fragments >120 bp), of nucleosomes (MNase-seq fragments >120 bp), of Polycomb-bound small fragments (Polycomb N-ChIP fragments <76 bp), and of Polycomb-bound nucleosomes (Polycomb N-ChIP fragments >120 bp). Intervals that include a gene TSS are annotated on the right. (C) Polycomb binds small DNA fragments at focal sites; 1945 focal Polycomb binding sites were called from Polycomb N-ChIP data, and midpoints of each fragment overlapping these sites are plotted. Polycomb N-ChIP strongly enriches DNA fragments ranging from 30 to 75 bp in length, and more moderately fragments up to 150 bp in length. (D) MEME discovery of motifs enriched at focal Polycomb binding sites. The four most frequent motifs are shown, with the percentages of focal sites with a significant (P < 5 × 10−4) match to each motif on the right; 77.7% of focal Polycomb binding sites contain at least one of these four motifs.