Condensin II binding overlaps with transcription factors non-randomly, and expression analysis suggests a repressive function for condensin II. (A) Transcription factor sites from modENCODE are ranked by the fold enrichment of overlap with condensin binding sites. Fold enrichment is determined as the ratio of percentage overlap in observed versus average of random distributions of condensin sites 10,000 times across the genome. The results indicate that condensin binding is not random with respect to TF binding sites. (B) Venn diagrams show the overlap of condensin II binding sites with LIN-13 (modENCODE_3342, embryos) and LIN-35 (modENCODE_3925, late embryos) (top), with LIN-13 only (bottom left), and with LIN-35 only (bottom right). The proportion of overlap between condensin II and LIN-13 and LIN-35 is higher at sites that are occupied by both proteins. The given overlap represents the number of condensin II peaks overlapping with the respective LIN-13 and LIN-35 sites. (C) Average ChIP-seq enrichment from condensin II, LIN-13 and LIN-35 are plotted across the summit of each condensin II peak. Condensin II binding sites are divided into four groups. The top group consists of condensin II binding sites overlapping with LIN-13 and LIN-35, the second overlaps with LIN-13 only, the third with LIN-35 only and the last group does not overlap with either LIN-13 or LIN-35. The peaks are in decreasing ordered based on their ChIP enrichment. A large number of condensin II sites show high LIN-13, but not LIN-35, binding. Condensin II binding is stronger at sites bound by both LIN-13 and LIN-35. (D) Differential expression analysis (RNA-seq) in kle-2 null heterozygote versus homozygote larval stage 2/3 (L2/L3) larvae. The proportions of genes bound or unbound by KLE-2 with increase or decrease in transcript level in homozygous mutant are shown. Transcript levels of proportionally more genes increase in kle-2 mutant. TF, transcription factor.