Fig. 2

Analysis of A/B-like chromatin compartment structure of the studied genomic region. a Heatmap of the differentiated HD3 cells demonstrating an increased interaction frequency between gene-rich zones I and III. A-like and B-like chromatin compartments are outlined using black rectangle and black stipple triangle, respectively. The first principal component value is shown below the heatmap. Structural zones I (5′-terminal gene-rich area), II (gene desert), and III (3′-terminal gene-rich area) were selected manually based on the density of CpG-islands and annotated genes. b The averaged interaction profiles of 18 genomic bins #74-91 from zone III (virtual “anchor”) with all bins from the remaining part of the studied region. Circles show average values of 5C counts between genomic bins #74-91 with each of the other bins in the studied region; standard deviation is shown. c 5C counts corresponding to interactions of the AgGD and flanking regions from the TAD T3 with the gene desert. Thick black lines represent median values. Two asterisks represent a significant difference with a P-value <0.01 calculated using a one-tailed Wilcoxon’s signed-rank test. Three asterisks represent a significant difference with a P-value <0.001. The same notations are in panels (d) and (e). d The distributions of 5C counts within the A-like chromatin compartment. e 5C counts between genomic bins #74-91 and the remaining part of zone III and the gene desert. f 5C counts between four groups of bins from zones I and III (differentiated HD3 cells); bins were divided into groups according to their transcription level. g 5C counts between four groups of bins from zones I and III; bins were divided into groups according to their degree of the transcription level increase in the HD3dif cells as compared to the HD3pr cells