Fig. 4

Higher resolution chromatin interaction analyses indicated that Pol II loss alters actively transcribed local, small loop domains. a Left: Scatter plot of the log fold change of contact frequency compared to the normalized mean contact frequency of the chromatin loops before and after Pol II degradation. Contact frequency was measured by Hi-C (top), H3K27ac HiChIP (middle), and Ocean-C (bottom). Right: Box plot of the contact frequency of the loops in the untreated and degron cells. Significance was calculated by Student’s t test (***< 0.001, **< 0.01). b Mean contact frequency ranked by the length of the chromatin loops under untreated and degron conditions using the same data sets as used in a. Data were smoothed by loess regression. c Chromatin loop length (left) and changes in mean contact frequency inside the loop domains (right) at high levels of transcription (top) and low levels of transcription (bottom), based on the same data sets as used in a. Significance was calculated using a Kolmogorov-Smirnov test (***< 0.001). d Global analyses of the Pol II PLAC-Seq-identified chromatin loops at gene regulatory elements (enhancers, promoters, gene bodies, and terminators (TTS)) in wild-type mESCs [56]. The category is listed in the left panel, and the loop counts for each category are listed in the right panel. Contact enrichment (obs/exp) for promoter-promoter (average PET number 11.16, hypergeometric p value 3.563683e−04) and promoter-enhancer loops (average PET number 15.28, and hypergeometric p value 6.477318e−06) were quantified. e The top panel shows Pol II-mediated chromatin loops (red lines). ChIP-Seq profiles for Pol II and H3K27ac are shown for the Bclaf1 locus (middle). A schematic of the Pol II-mediated 3D chromatin structure at the Bclaf1 locus is shown in the right panel. The histogram of the loop counts ranked by the length of the loops is shown at the bottom