Fig. 3

Integrative analysis of promoter-anchored chromatin interactions, transcriptome, and epigenetics during Pre-B cell trans-differentiation. a Similarity score between replicates and different time points of PCHi-C interaction matrix at 500-kb resolution was quantified using stratum-adjusted correlation coefficient (SCC) method. b Distribution of distances between promoter and promoter interacting regions (PIRs) at 0h, 1h, 12h, and 48h time points. Red dashed line indicates the median distance of significant interactions. c Number of interactions per gene classified based on different expression levels (TPM = 0 (n1), TPM = 0–1 (n2), TPM = 1–5 (n3), TPM > 5 (n4)) at 0 h (n1 = 9601, n2 = 4669, n3 = 4116, n4 = 2202), 1h (n1 = 9025, n2 = 4588, n3 = 3772, n4 = 3203), 12h (n1 = 9184, n2 = 4721, n3 = 3970, n4 = 2713), and 48h (n1 = 9266, n2 = 5837, n3 = 3828, n4 = 1657) time points. An unpaired two-sided t-test is performed for the significance test. d Overlap of H3K27ac, H3K4me1, H3K27me3, and p300 peaks with significant versus randomly shuffled PIRs for cells at different time points. The gray bar represents the number of overlaps across 100 sets of randomly shuffled distance-matched PIRs (control) with 95% confidence interval for the means plotted. The chi-squared test is performed for the significance test. e The box plot displays gene expression values (log2(TPM + 1)) of promoters categorized into four groups based on the number of promoter-interacting regions (PIRs) marked by H3K27ac at four different time points. The groups are defined as follows: Group 0: Promoters without any PIRs marked by H3K27ac. Group 1: Promoters with only one PIR marked by H3K27ac. Groups 1–5: Promoters with one to five PIRs marked by H3K27ac. Group > 5: Promoters with more than five PIRs marked by H3K27ac. An unpaired two-sided t-test is performed for the significance test. All the box plot represents 25 and 75 percentiles with the median