Fig. 5

Quantitative analysis of the relationship between histone modifications and chromatin densities. Corresponds to data as shown in Figs. 1 and 3. A)&B) right panels show example intensity profiles along the indicated line in the left (merge) panels. X-axis of the plots gives the distance in µm, normalized intensities are along the y-axis. (A) H3K4me3 vs. histones, example from Fig. 1. (B) H3K27me3 vs. histones. (C) The scheme indicates the expected distribution of chromatin clusters in H3K4me3 vs. H3K27me3 enriched Y loop regions, and the distributions as observed by measuring the distances between histone intensity peaks. Quantifications are given in the box plots; left, for a tolerance factor for peak detection of 0.17, right, for a tolerance factor of 1.0 to avoid a bias caused by false positive or negative detections. Number of measured peak distances are 163, 266, 54 and 102. Total measured Y loop lengths are 22.5 μm (H3K4me3) and 37.76 μm (H3K27me3). D)&E) The cross correlation of fluorescence signal intensities along selected loops was computed for H3K27me3 vs. histones and H3K4me3 vs. histones respectively. (D) shows the overall displacement distributions in box plots. (E) Heat maps indicate the cross correlation values between the lagged signals of respective cluster intensities per nucleus. The x-axis shows the lag distances, the samples are stacked along y. (F) The scheme indicates the shift between histones and the respective histone marks, as well as their mutually exclusive organization (see Fig. 4). The question mark indicates our interpretation of the results that H3K27me3 enrichment at chromatin clusters is correlated with transcriptional pause, which would allow e.g. processing of the transcribed RNA or DNA repair to occur. H3K4me3 enrichment at the periphery of the clusters could indicate pause release into productive elongation