Fig. 3

Characterization of rhythmically expressed gene-centered chromatin interactions and dynamics of chromatin loops. a Boxplot showing the expression levels of rhythmically and non-rhythmically expressed genes involved or not involved in RNAPII-mediated chromatin interactions at 08:00. ***p < 0.0001. b Boxplot showing the positive correlation between the degrees (connection frequency) and transcript abundance of anchor genes at 08:00. c Boxplot showing the positive relationship between the degrees and transcript abundance of rhythmically and non-rhythmically expressed anchor genes at 08:00. d As the degree increases, rhythmically expressed anchor genes showed higher transcript abundance than did non-rhythmically expressed anchor genes did at 08:00. The correlation coefficients between transcript abundance and degree among rhythmically, non-rhythmically, and non-expressed genes were 0.94, 0.42, and 0.51, respectively. Rhythmically vs. non-rhythmically, p = 9.669e−06 (binomial test). e Expression breadth (number of tissues in which a gene is expressed) of RNAPII-mediated anchor and basal genes with rhythmic or non-rhythmic characteristics. Random genes served as controls. f Distribution of rhythmically expressed gene-centric interactions at 08:00. The percentages of RG (rhythmically expressed gene)-RG, RG-NG (non-rhythmically expressed gene), and RG-NEG (non-expressed gene) interactions are listed. ***p < 0.0001. g Distribution of phase spans of RG-RG interaction gene pairs and randomly picked gene pairs from rhythmically expressed anchor genes and rhythmically expressed basal genes in the 08:00 datasets. Actual vs. random anchor, p = 6.469e−11; actual vs. random basal, p < 2.2e−16, random anchor vs. random basal, p = 1.057e−07 (Kolmogorov-Smirnov test). h Distribution of Pearson’s correlation coefficient for RNAPII-bound interacting gene pairs, gene pairs with a loop connecting rhythmically expressed genes, and gene pairs with a loop connecting non-rhythmically expressed genes in the 08:00 datasets. i Bar chart showing the percentages of overlap (common) and dynamic chromatin loops across the day. j Heatmap showing the time-specific chromatin loops, ordered by the number of paired-end tag (PET) counts. Pseudo-color reflects the normalized contact frequencies between the loop anchors for each stage-specific loop. RR, RG-RG; RN/NR, RG-NG or NG-RG; NN, and NG-NG. k Enriched KEGG pathways for genes located at the loop anchors of distinct clusters in j along with their adjusted p values. l Over-represented transcription factor-binding motifs for distal open chromatin regions located at the loop anchors of distinct clusters in j and their corresponding p values