Fig. 7

Heterogeneity in histone modifications and gene expression in LADs. a Aggregation plots of H3K4me3, H3K27ac, and H3K4me1 levels around the TSS of DE genes in indicated LAD classes (top) in the T00–T24 time course (numbers of DE genes); mean ChIP-seq read counts normalized to library size at each time point. See Additional file 1, Fig. S7a for LAD edges. b Genome browser views of LADs, H3K4me3, H3K27ac, and H3K4me1 enrichment (range Log2(ChIP/input) ratios shown in brackets), and of RNA levels (read count scale in brackets) at the SMOC1 (gained LAD > LAD) and OTUD1 locus (gained LAD > i-LAD). Note that LADs at T24 extend beyond the area shown. c Expression levels of DE genes in indicated LAD classes averaged across the T00–T24 time course; bar, median; cross, mean; box, 25–75% percentile; whiskers, min-max. *P = 0.03, **P = 0.01, unpaired two-tailed t-tests with Welch’s correction