Occupancy of PRC1 and PRC2 at Rest peaks in <i>Wt</i> and <i>Rest</i>−/− mES cells.

<p>(A) Average ChIP-seq read counts in <i>Wt</i> control and <i>Rest</i>−/− mES cells, normalized to IgG controls for Rnf2, Suz12 and Jarid2 within 3 Kb of the 3,378 peaks identified for Rest in the <i>Wt</i> control cells. Black arrow indicates the direction of the nearest TSS. (B) Heat-maps showing Rnf2, Suz12 and Jarid2 occupancy in a 2 Kb window centered around individual Rest peaks identified in <i>Wt</i> control mES cells. The ratiometric heat-maps depict the part of the profiles that were increased, unaffected, or decreased in <i>Rest−/−</i> mES cells as red, green and blue, respectively. Out of the 3,378 Rest peak positions identified in the <i>Wt</i> control mES cells, positions with very low levels or no PcG (Rnf2, Suz12 and Jarid2) ChIP-seq signal in either <i>Wt</i> control or <i>Rest−/−</i> mES cells were filtered out (for thresholds and genomic peak positions see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002494#pgen.1002494.s011" target="_blank">Table S3</a>). The regions were sorted according to the fold change in PcG (Rnf2, Suz12 and Jarid2) signal between the <i>Wt</i> control and <i>Rest−/−</i> mES cells, within the Rest peaks. P-values were calculated by comparing the number of Rest binding sites with 1.5 fold increase or decrease to those expected from a population with similar distribution as the matched control using chi²-tests (C) ChIP-seq profiles for the positions marked 1 to 6 in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002494#pgen-1002494-g004" target="_blank">Figure 4B</a> as examples. Data from <i>Wt</i> and <i>Rest−/−</i> mES cells are shown in black and grey, respectively (K27 = H3K27Me3). (D) Diagram showing the number of Rest peaks and matched control regions (no Rest peaks) scored positive for Rnf2, Suz12 or Jarid2 signal. The filtering process described in the legend for <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002494#pgen-1002494-g004" target="_blank">Figure 4B</a>. P-values compares binding sites scoring positive for PcG binding to those that scored positive by chance in the matched control regions using chi²-tests (E) Heat-maps of the matched control regions shown in 4D.