Fig. 4: The MNase accessibility of the H2A.Z nucleosome at the TSS correlates with the level of expression.
From: Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells
a H2A.Z MNase sensitivity data was sorted with a clustering window ±50 bp surrounding the TSS by k-means clustering (k = 3) to produce a heat map that reveals H2AZ MNase resistant and sensitive nucleosomes at the TSS in MCF-10A cells. Adjacent heat maps display H2A.Z and total nucleosome profiles dependent on the H2A.Z MNase sensitivity sort. Below each heatmap are average nucleosomal occupancy profiles. b Gene expression box plots for each TSS H2A.Z MNase sensitivity cluster. P-values determined by two-tailed Welch’s t-test assuming unequal variances. Box plots represent the data in quartiles with the median shown as a notch, with the middle 50% of the data contained in the box, and the minima and maxima shown with the upper and lower whiskers representing Q1 and Q4. RNA-seq was performed in three independent biological replicates. c Total MNase digestion fragment size distribution for each respective cluster in panel a, centred on the 1000 bp surrounding the TSS. DNA fragment size analysis was performed on immunoprecipitated H2A.Z nucleosomes, total MTSS-seq nucleosomes, and shH2A.Z nucleosomes for MCF10-A cells. Following H2A.Z knockdown, a distinct population of subnucleosomal-sized DNA fragments is observed in the red and green clusters 1 and 2, respectively. d Representative promoters, TIMP1 and S100A3 demonstrating the appearance of subnucleosomal-sized DNA fragments at the TSS following H2A.Z knockdown.
