Fig. 2

Circadian TADs isolate circadian genes with shared time of transcription. a Observed Hi-C contact matrices showing the TADs landscape of the genomic region including the Arntl1 circadian gene locus at four timepoints during the circadian cycle. b Left, 50 kb resolution median observed/expected ZT0 and ZT12 Hi-C signal around 1000 randomly selected TADs from ZT0 plotted on ZT0 and ZT12 Hi-Cs. TADs were scaled to fit the five central bins. Right, the same metaplots but for 1000 randomly CTCF peaks found at ZT0. CTCF peaks are at the central bin of the metaplot. c Proportion of cTADs harboring 1, 2, 3, or 4 circadian genes. d Phase distribution of circadian genes sharing TADs. e Observed and expected proportion of TADs with 2 circadian genes sharing transcriptional peak phase (p value < 0.05, chi-square test). f Observed and expected number of circadian TADs overlapping and non-overlapping OCCs (Wilcoxon test, p < 0.0001). g Examples of cTAD Hi-C contact matrices from ZT0. Left, cTADs with one circadian gene allocating Mical2, Micalcl, Arntl1, and Copb1 circadian genes. Right, cTADs with more than one circadian gene allocating Tmem41b, Wee1, Swap70, and Sbf2 circadian genes. Close up to each circadian gene with genomic tracks showing RNA-seq signal at all timepoints and CTCF ChIP-seq peaks at ZT0 and ZT12