Fig. 2: Hnf4a knockout alters the genome-wide epigenetic landscape. | Nature Communications

Fig. 2: Hnf4a knockout alters the genome-wide epigenetic landscape.

From: HNF4A defines tissue-specific circadian rhythms by beaconing BMAL1::CLOCK chromatin binding and shaping the rhythmic chromatin landscape

Fig. 2

a, b Heatmap of H3K4me1 (a) or H3K27ac (b) ChIP-seq signals at ZT6 in control (left) or HKO (right) liver centered at all peaks in control liver. Peaks are ordered vertically by signal strength. c Motif analysis of HKO-deprived H3K4me1 sites. Known consensus motifs are shown with corresponding enrichment significance values. d H3K4me1 peaks in control and HKO livers were partitioned into three categories with DiffBind (the HKO-enriched group has only 23 peaks and could not be plotted), and then the corresponding HNF4A occupancy (at ZT16) at each H3K4me1 site was plotted. Each horizontal line represents a single H3K4me1 site. Peaks were ordered vertically by the strength of the H3K4me1 ChIP signal in control liver. e Motif analysis of all H3K4me1 marked sites in the control liver. Known consensus motifs are shown with corresponding enrichment significance values. f Metaplot showing the average intensity of BMAL1, H3K4me1, and H3K27ac ChIP-seq signals (all at ZT6) in control or HKO livers surrounding HKO-unchanged (upper panel) or HKO-reduced (lower panel) BMAL1 peak centers.

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