Fig. 5
From: A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at active genes
Loss of PWWP2A/B leads to an increase in H3K9ac and H3K27ac and Pol II elongation defect at PWWP2A occupancy genes. a Calibrated Meta-gene profile for H3K9ac (average of two biological replicates) at PWWP2A high occupancy genes in WT mESCs and two double knockout cells over the TSS ±5 kb region. b Boxplot showing the average calibrated H3K9ac ChIP-seq signal from two replicates at PWWP2A high and low occupancy genes over the region TSS ±5 kb. * indicates significance by Wilcoxon test. c, d same as (a, b) for H3K27ac calibrated ChIP-seq. e The meta-gene profile for RNA Pol II NTD ChIP-seq (average of two biological replicates) across the normalized genic regions and 5 kb flanking regions of PWWP2A high occupancy genes for WT (black) and two PWWP2A/B double knockout cells C7 (blue) and A1 (red). The y-axis represents the average signal. The inset figures show the signal around the TSS ±1 kb region. f The cumulative frequency plot showing the pausing index (based on RNA Pol II ChIP-seq) distribution for PWWP2A high occupancy genes in WT mESCs (black), and PWWP2A/B double knockout cells C7 (blue) and A1 (red). The p-value was calculated based on the one-sided Wilcoxon test. g Boxplot of the difference in the Pausing Index of PWWP2A/B knockout cells C7 (blue) and A1 (red) compared to WT at PWWP2A high occupancy and low occupancy genes. The asterisk indicates significance by Wilcoxon test. h The meta-gene profile for calibrated RNA Pol II Ser5P ChIP-seq (average of two biological replicates) across the normalized genic regions and 1 kb flanking regions of PWWP2A high occupancy genes for WT (black) and two PWWP2A/B double knockout cells C7 (blue) and A1 (red). The y-axis represents the average signal. The inset figure shows the signal over the TSS ±1 kb region. i The meta-gene profile for calibrated RNA Pol II Ser2P ChIP-seq (average of three biological replicates) across the normalized genic regions and 2 kb flanking regions of PWWP2A high occupancy genes for WT (black) and two PWWP2A/B double knockout cells C7 (blue) and A1 (red). For all the boxplots, the lower and upper edge of the box represents the first and third quartile, respectively. The horizontal line inside the box indicates the median. Whiskers identify the farthest data points within 1.5× the interquartile range (IQR)
