Skip to main content
Fig. 3 | Genome Biology

Fig. 3

From: The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Fig. 3

Promoter Capture-Hi-C and chromatin contact dynamics during a circadian cycle. a Summary of the experimental workflow of Promoter-CHi-C technology. Cells are fixed, chromatin is digested, filled-in, and biotin-labeled inside the nucleus. Pull down with streptavidin beads is then performed and Hi-C libraries prepared for sequencing. Using the Hi-C material as a template hybiridization is done using the designed RNA biotinilated probes to capture promoters. A second pull down is performed to recover the hybrid molecules, DNA purified and sequenced. b Left, Obs/Exp signal ratio at promoter interacting regions of liver chromatin features including enhancers producing eRNAs, H3K27ac, H3K4me1, H3K4me3, DNase I hypersensitive sites, superenhancers, H3K27me3, and CTCF (left) (all p values < 8.632642e−123, t test). Obs/Exp signal ratio of the same chromatin features but for interacting regions for all oscillating gene promoters and intronically oscillating gene promoters compared to a random set of non-oscillating gene promoters (all p values < 2.525639e−42 except H3K27me3). c Right, the same as in d but for the enrichment of circadian transcription factors including Bmal1, Clock, Cry1, Cry2, Npas2, Per1, and Per2 for all gene promoter interacting regions and left, oscillatory gene promoter interacting regions (all p values < pval< 3.870992e−205, t test). e Obs/Exp enrichment of enhancers producing eRNAs at dynamic contacts over stable contacts (p value < 2e−16, t-test). f Number of circadian gene promoters making the maximum number of contacts at ZT0, 6, 12, and 18 (p value < 0.001, chi-square test). g Transcription factor DNA binding motifs significantly enriched at dynamic, stable, or both circadian gene promoter chromatin contacts (E-value < 1.00e−002). g ChIP-qPCR against Nr5a2. The regions analyzed include the Arntl gene promoter, the Arntl dynamically interacting enhancer, a constant interacting element of the Pppr1r3c circadian gene, and a dynamic interacting element of the Gsk3a circadian gene. In all regions, the DNA binding motif of Nr5a2 was found. As a negative control, a region where the DNA binding motif for Nr5a2 is not present was amplified (*p value < 0.05, ** p value 0.01, *** p value < 0.001, one-way ANOVA, Tukey post hoc test, n = 6 from 2 biological replicates per timepoint)

Back to article page