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Fig. 4 | Genome Biology

Fig. 4

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

Fig. 4

Transcriptional phase coherence between circadian genes and transcribed enhancers and the core-clock circadian genes display highly dynamic chromatin contacts. a Circadian gene promoter observed and expected contacts with enhancers producing eRNA rhythmically during the day (p value < 0.0001, t test). b Circadian genes oscillating at the intronic level observed and expected contacts with enhancers producing eRNAs rhythmically during the day (p value < 0.0001, t test). c Observed and expected contacts of circadian gene promoters detected through GRO-seq with enhancers producing eRNAs rhythmically during the day (p value < 0.0001, t test). d Phase distribution of eRNAs produced from enhancers contacting all diurnal and nocturnal circadian promoters (left), circadian genes oscillating at the intronic level (centre) and circadian genes detected by GRO-seq (right) (all p values < 0.001, Wilcoxon ranked sum test). e Partial virtual 4C landscape of the Rnf125 gene promoter at the four timepoints during the day. Acrophase is written next to the gene name. Significant contacts with enhancers producing oscillatory eRNA are shown. The majority of the eRNAs present a peak in transcription at ZT0 as Rnf125 does. Genomic tracks show significant contacts as arcs and chromatin features including liver H3K4me3, H3K4me1, H3K27ac, DNaseI, eRNAs, and TADs. f Number of total significant interactions for core clock circadian gene promoters and a random control set of non-core-clock circadian gene promoters (p value < 0.0001, Mann-Whitney test). g Proportion of dynamic contacts for core clock genes and a random control set of non-core-clock circadian gene promoters (p value < 0.0001, Mann-Whitney test). h, i Virtual 4C for Arntl and Nr1d1 core clock circadian gene promoters at all timepoints during the day. Features displayed are the same as described in e

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