Condensin sites are enriched at promoters and tRNAs, and binding positively correlates with transcription. (A) Enrichment or depletion of condensin binding sites at various genomic annotations are given. Random enrichment and p-values were calculated by a permutation test randomly distributing the condensin peaks 10,000 times. For both condensin I-IDC and II, there is a significant enrichment of binding sites at 1 kb promoters and near non-coding RNAs (P = 0.0002), depletion within gene bodies (transcription start site (TSS) to transcription end site (TES)) (P = 0.0002), and no significant enrichment or depletion at the 3′ of genes (P > 0.05). (B) Condensin ChIP signal is aligned at the TSSs of expressed genes (top 25% by RNA level, solid lines) and not expressed genes (bottom 25% by RNA level, dashed lines). The surrounding dots represent the 95% confidence level. As a control, immunoglobulin G (IgG) ChIP signal at the TSSs is plotted in grey. (C) Spearman rank correlation coefficient between median ChIP score at 500 bp promoters and RNA level at respective genes are given for the whole genome and the X chromosome. There is a slight positive correlation between condensin binding and transcription. (D) Median ChIP score within 500 bp upstream of the TSS is plotted against the RNA level of each gene. Condensin promoter-bound genes (defined by overlap with a condensin site within 1 kb of the TSS) are highlighted in orange (condensin I-IDC) and blue (condensin II). (E) GC content of 50 bp windows is plotted across condensin I-IDC and II binding summits. As a control, the GC content over 1500 random coordinates was determined and plotted in the same way as the actual condensin summits. Average GC content is high around the peak of condensin binding.
Kranz et al. Genome Biology 2013 14:R112 doi:10.1186/gb-2013-14-10-r112