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Genome-Wide uH2A Localization Analysis Highlights Bmi1-Dependent Deposition of the Mark at Repressed Genes

Figure 5

Bmi1-dependent uH2A is enriched at repressed genes.

(A) Bmi1-dependent uH2A tag density surrounding the TSSs of genes was calculated and grouped into 10 bins (n≈1335 for each group) based on de novo gene expression levels in MEF cells. (B) Bmi1-dependent uH2A tag density was calculated for the region indicated in (A) for genes grouped based on de novo expression in MEF cells (n = 4007, n = 2674, n = 2668, n = 4005; highest expressed to lowest expressed). Error bars represent the s.e.m. of the highest expressed and lowest expressed gene groups. (C) WT MEF expression of genes with (+, n = 483) and without (−, n = 12,871) a peak of Bmi1-dependent uH2A was subjected to data distribution analysis by standard box plot. Red lines indicate median values. P value derived from Wilcoxon signed-rank test is indicated. (D) Gene promoters with (+) and without (−) peaks of uH2A were analyzed for the presence of H3K4/H3K27 methylation peaks. No K4/No K27, purple; both H3K4me3 and H3K27me3 (Bivalent), green; H3K27me3 only, blue; H3K4me3 only, red. (E) Box plot of expression data distribution for promoters with (+) and without (−) uH2A peaks in WT MEFs were further sub-divided by H3K4/H3K27 co-localization. No K4/No K27, purple; both H3K4me3 and H3K27me3 (Bivalent), green; H3K27me3 only, blue; H3K4me3 only, red. White lines indicate median values. P value derived from Wilcoxon signed-rank test is shown. (F) Genes containing a peak of Bmi1-dependent uH2A were divided into three groups based on increasing peak tag density (n = 157, 157, and 158, respectively) and the distribution of log2 expression change (Bmi1 null versus WT MEF cells) was presented by box plot. Red lines indicate median values. P value derived from Wilcoxon signed-rank test is shown.

Figure 5

doi: https://doi.org/10.1371/journal.pgen.1000506.g005