Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) patterns of the three condensins in Caenorhabditis elegans embryos. (A) Subunit composition of the three C. elegans condensin complexes. Condensin I and II share SMC-4 and MIX-1, and are distinguished by three non-SMC subunits. DPY-27, an SMC protein, is the only subunit different between condensin I and the dosage compensation condensin IDC. Non-SMC subunits of condensin I-IDC and condensin II are in orange and blue, respectively. (B) Median ChIP-seq enrichment in 1 kb contiguous windows across the genome were used to calculate pairwise Pearson correlation coefficients, clustered with hierarchical clustering, and plotted as a heat map. The subunits of each condensin type cluster closer together. (C) University of California Santa Cruz (UCSC) genome browser view of ChIP-seq enrichment scores of each condensin subunit across a 200 kb region on chromosome I (left) and X chromosome (right). Note that on the X chromosome condensin I-IDC subunit (orange) ChIP-enrichment scores are much greater; the scale is five times larger than that of condensin II subunits (blue). (D) The number of ChIP-seq binding peaks per condensin subunit per chromosome is shown. Condensin IDC mostly binds to the X chromosome, whereas condensin II is similarly distributed across all chromosomes. (E) Average ChIP-seq enrichment score from non-SMC subunits of condensin I-IDC and II are plotted across the summit of each condensin I-IDC or condensin II peak. The peaks are ordered by ChIP enrichment (highest ChIP value on top), to illustrate that condensin II binds to highest ChIP enrichment sites of condensin I-IDC. ChIP-seq, chromatin immunoprecipitation followed by high-throughput sequencing; SMC, structural maintenance of chromosomes.
Kranz et al. Genome Biology 2013 14:R112 doi:10.1186/gb-2013-14-10-r112