Fig. 2
From: Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders
Genomic annotation of TOP2B binding sites in mouse liver. a Genome-wide distribution of TOP2B binding sites compared to the general distribution of mouse genomic regions. Promoter regions were defined as 3 kb upstream from transcription start site (TSS); downstream is defined as 3 kb from transcription end site (TES). b Aggregate TOP2B liver ChIP-seq read density (x-axis) across liver-expressed genes separated into high, medium, and low expression categories (y-axis). ChIP-seq read density is shown as reads per million mapped reads (RPM). c Genome browser view for ChIP-seq signal tracks for TOP2B and a variety of liver-enriched TFs, members of the cohesin complex and histone modifications (y-axis, RPM). d Fraction of peaks for various factors that overlap TOP2B peaks (red bars) (p values <10–16). e Hierarchical clustering of genome-wide binding intensities (reads per kilobase per million mapped reads (RPKM)) for TOP2B and a variety of factors. Color intensity represents pair-wise Pearson correlation coefficients. Red lines indicate the main clusters: actively transcribed regions (i.e. H3K36me3, H3K79me2), genome architectural regions (i.e. RAD21), enhancers (i.e. ONECUT1), and promoters (i.e. H3K4me3). f TOP2B localizes to rDNA loci in mouse liver. The top panel shows a schematic representation of a single mouse rDNA repeat relative to the transcription start site of the rDNA repeat (x-axis; based off of GenBank BK000964). Normalized ChIP-seq read counts of TOP2B, CTCF, RAD21, STAG1, STAG2, and H3K4me3 are shown on the y-axis. rDNA mappability track from Zentner GE et al. [78] is plotted as a heatmap below the genome tracks with black representing bases that are 100 % mappable. The TSS is labeled with an arrow. The 18S, 5.8S, and 28S coding regions are shown as large rectangles. The external transcribed spacer; (ETS), internal transcribed spacer (ITS), spacer promoter (SP), upstream control element (UCE), and core promoter element (CPE), are shown as narrow rectangles. The intergenic spacer (IGS) is shown as a thin line