Figure 4

Changes in nucleosome positioning affect higher-order structure. ( A) High-confidence contacts (P <0.05; determined using 3C-seq 0 or 30 min post-stimulation) made by the transcription start site (TSS; arrowhead) of TNFα-responsive SAMD4A with parts of the long arm of chromosome 14 (ideogram) are depicted as a domainogram (y-axis - contacts visualized in 2- to 200-kbp sliding windows). Most contacts are unique for each time point (Venn diagram). The magnified region (red rectangle) compares 3C-seq contacts (y-axis - reads per million) to changes in nucleosome occupancy (determined as in Figure 2). The table (bottom right) gives the fraction of 3C contacts embedded in nucleosome-depleted windows at 0 or 30 min, or shared at both times; a significant increase is seen for 30-min and shared contacts (*P <0.05; Fisher’s exact test). (B) Details as in panel (A), for the non-responsive EDN1 TSS (arrowhead) on the long arm of chromosome 6 (ideogram). Almost 40% of high-confidence contacts persist from 0 to 30 min (Venn diagram), and are significantly associated with nucleosome-depleted 5-kbp windows (*P <0.05; Fisher’s exact test). 3C-seq, chromosome conformation capture coupled to deep sequencing; TNFα, tumour necrosis factor alpha.