Figure 4. CATCH-seq of enhancer downstream of SIAH2 reveals plasticity of genomic architecture.

y axis labels below IGV histograms represent number of sequencing reads after background subtraction. (a) The captured region is the downstream enhancer of SIAH2 (T47D human breast cancer cells). Interaction peaks can be seen at the intronic enhancer and SIAH2 promoter in both the presence and absence of oestradiol. (b) The CATCH-seq signal density within 2 kb of TSSs on chromosome 3 peaks at around +200 bp in both the presence (blue) and absence (grey) of oestradiol. There was no discernable peak in the randomized data set (red). (c) To-scale Venn diagram demonstrating the number of genes' promoters identified as interacting with the downstream enhancer of SIAH2. The majority of genes are unchanged with the addition of oestradiol (264); however, oestradiol treatment does induce the loss of interaction (107) and the gain of interaction (140) of a large subset of genes. (d) Examples of raw CATCH-seq histograms demonstrating the striking overlap between ERα-binding sites, enhancer marks and CATCH-seq peaks near the promoters of genes. Many of the peaks (which indicate physical interaction with the downstream enhancer of SIAH2) are reduced/not found in the absence of oestradiol, or enhanced upon the addition of oestradiol. (e, left) SIAH2 enhancer CATCH-seq interaction peaks significantly overlap with enhancer marks (green) and ER-binding sites (blue) compared with statistically random control (red); the frequency of these overlaps increases with peak height. (e, right) As expected, increasing peak height thresholds reduce the number of CATCH-seq peaks identified at gene promoters; however. at all thresholds, oestradiol treatment facilitates more DNA–DNA interactions than vehicle control. (f) IPA analysis of two statistically significant processes identified under vehicle- (grey; cell motility) and oestradiol-treated (blue; RNA expression) conditions. There is little overlap (orange) between the two processes.