Figure 2. Examples of coupled, large-scale chromatin changes mediated by Hairy.
Chromatin immunoprecipitation-high throughput sequencing (ChIP-seq) tracks for H4Ac, H3K27Ac, H3K4me1 and H3K4me3 are shown at repressed genes before (−) and after Hairy (+) induction, with gene models below. (A–D) Coupled reduction of active histone marks was observed in a wide-spread fashion on ftz, h, 18w and odd genes (scale at top left). (E–H) Relatively smaller blocks of chromatin changes were detected on HLHm7, gogo, pros and tup genes. Significantly changed regions (shaded boxes) were identified by the diffReps program. Hairy binding (top track) from MacArthur et al. (2009).
Figure 2—figure supplement 1. ChIP-seq reproducibility of biological replicates and variation between wild-type (wt) and transgenic embryos (H).
(A) Specific reduction of H4Ac signal at ftz locus (red box) in three biological replicates after induction of Hairy (H). (B) H4Ac peaks were not altered globally in genome by Hairy expression. Heatmaps show 5 kb window centered on called H4Ac peaks, ranked by peak height. (C) Measured global chromatin features were similar in wt and H samples, indicating that Hairy does not affect the majority of chromatin features throughout the genome. Scatter plots indicate the correlation (r = Pearson's correlation coefficient) between wt and H embryos for H4Ac, H3K27Ac, H3K4me1, H3K4me3, H3K36me3 and H3K9me3 marks. Each dot represents a peak. ChIP-seq read counts on the axis are transformed to log2 base.