Fig. 5: Subnucleosomal-sized DNA fragments at the TSS is correlated with high levels of gene expression.

a Subnucleosomal DNA fragments (<125 bp) were extracted and sorted for the maximum occupancy on 100 bp surrounding the TSS for MCF-10A, MCF-10A+TGF-β, MCF-10CA1a and shH2A.ZMCF-10A cells to produce heatmaps. The heatmaps were divided into quartiles from high to low occupancy. Below each heatmap are average subnucleosomal DNA fragment occupancy and gene expression box plots for each quartile. 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. b Total subnucleosomal fragments from each experimental condition, MCF-10A+TGF-β, MCF-10CA1a cells and shH2A.ZMCF-10A, were each independently subtracted from total subnucleosomal fragments in MCF-10A and the resulting difference matrix was used to produce a differential heatmap. Red and cyan coloured SFs at the TSS indicate more abundant subnucleosomal DNA fragments in MCF-10A cells or more abundant subnucleosomal DNA fragments in the matched experimental condition, respectively. Below each heatmap are average subnucleosomal DNA fragment occupancy and gene expression box plots for each sextile. 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 Gene ontology analysis of 110 genes of interest using the GOrilla algorithm, p-values are determined by hypergeometric null model as described in Eden et al.⁶⁵.