Figure 4

Crosstalk of epigenome and interactome. (A) Principal component analysis (PCA) using mean epigenetic modification densities (EMDs) of control and prey regions for each viewpoint. EMDs included in the PCA were: H3K4me2, H3K4me3, H3K9me2, H3K27me1, H3K27me3, H3K36me2, H3K36me3, H3K9ac, and H3K18ac. Colored arrows represent the two highest contributing EMDs to the variance of the first component in positive and negative direction, respectively. Note that the first principal component explains almost all the variance (97%), and therefore, this was the only component plotted. Prey regions are represented by green dots, control regions by yellow dots. (B) Mean CG methylation densities of prey and control regions for individual viewpoints. The mean was calculated across 1000 times randomly sampled 50 prey and 50 control regions, respectively. Green bars represent preys and yellow bars represent controls. (C) Examples of the interactome-epigenome interplay for three different viewpoints and one of their corresponding prey regions. Top track: log summed 4C reads per window (100 fragments, starting every fragment). 4C reads of replicate A are plotted in the positive intercept, and 4C reads of replicate B are plotted in the negative intercept. Middle Track: EMD of the highest contributing factors of the PCA in positive and negative direction, respectively. In order to achieve comparable representation of H3K36me3 and H3K27me1 densities, the density of every window (25 fragments, starting every 5 fragments) was divided by the mean density of each histone modification. Arrowheads point at regions where the 4C interactome and local EMD peaks appeared to correlate. FWA: viewpoint on chromosome 4, 12 to 14 Mb; prey on chromosome 5, 23 to 25 Mb. PHE: viewpoint on chromosome 1, 23.5 to 25.5 Mb; prey on chromosome 1, 20 to 22 Mb. hk4s: viewpoint on chromosome 4, 0.8 to 2.8 Mb; prey on chromosome 2, 4 to 6 Mb.