Fig. 1
Significantly higher presence of highly stable DNA secondary structures at the TSS (± 250 nt) and co-localized with Pol II. a Gene location of highly stable secondary sites is plotted. Genomic regions were defined as described in “Methods”. The numbers of peaks were normalized by the total number of sites and the total size of genomic regions. b Null model analysis of the intersection of highly stable secondary structure sites with Pol II ChIP-seq peaks demonstrates enrichment patterns in five cell lines (p < 10− 4, permutation analysis). Fold enrichment is defined as the ratio of the actual number of intersecting regions over the mean of the number of intersections of 10,000 instances of randomly shuffled secondary structure sites. Solid line at fold enrichment = 1 corresponds to no change