Fig. 5
From: Cellular reprogramming is driven by widespread rewiring of promoter-enhancer interactions
C/EBPα binds to promoters and PIRs and modulates gene expression during Pre-B cell trans-differentiation. a Percentage of significant interactions that overlap with C/EBPα binding peaks. Both: Percentage of significant interactions bound by C/EBPα at both promoter and PIRs anchors; PIRs: Percentage of significant interactions bound by C/EBPα only at PIRs anchors; Promoters: Percentage of significant interactions bound by C/EBPα only at Promoter anchors. b Overlap of C/EBPα peaks with significant PIRs versus randomly shuffled distance-matched fragments (control) 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. c, d Box and whisker plots show DEGs expression between 0h and other time points based on differential C/EBPα binding at (c) promoters or (d) promoter interaction regions. Induced: Additional time specific C/EBPα binding at promoters or PIRs. Unchange: Stable C/EBPα binding at promoters or PIRs. No peak: no C/EBPα binding at promoters or promoter interaction regions. Promoter: 1h vs 0h, Induced (n = 52), Unchanged (n = 70), No peaks (n = 283). 12h vs 0h, Induced (n = 89), Unchanged (n = 172), No peak (n = 1168). 48h vs 0h, Induced (n = 94), Unchanged (n = 286), No peak (n = 2592). PIRs: 1h vs 0h, Induced (n = 76), Unchanged (n = 72), No peaks (n = 77). 12h vs 0h, Induced (n = 152), Unchanged (n = 262), No peak (n = 428). 48h vs 0h, Induced (n = 251), Unchanged (n = 427), No peak (n = 1067). The box plot represents 25 and 75 percentiles with the median. A two-sided Mann–Whitney U test is performed for the significance test. e Btg1 region that shows promoter interaction changes accompanied by H3K27ac (pink) and C/EBPα ChiP-seq peaks (red) at interacting regions, along with gene expression (green). The gray box shows gained PIRs of the Btg1 promoter with increased C/EBPα binding and gain of H3K27ac