Genome-wide analysis of condensin binding in Caenorhabditis elegans

Background: Condensins are multi-subunit protein complexes that are essential for chromosome condensation during mitosis and meiosis, and play key roles in transcription regulation during interphase. Metazoans contain two condensins, I and II, which perform different functions and localize to different chromosomal regions. Caenorhabditis elegans contains a third condensin, I-DC, that is targeted to and represses transcription of the X chromosome for dosage compensation. Results: To understand condensin binding and function, we performed ChIP-seq analysis of C. elegans condensins in mixed developmental stage embryos, which contain predominantly interphase nuclei. Condensins bind to a subset of active promoters, tRNA genes and putative enhancers. Expression analysis in kle-2-mutant larvae suggests that the primary effect of condensin II on transcription is repression. A DNA sequence motif, GCGC, is enriched at condensin II binding sites. A sequence extension of this core motif, AGGG, creates the condensin I-DC motif. In addition to differences in recruitment that result in X-enrichment of condensin I-DC and condensin II binding to all chromosomes, we provide evidence for a shared recruitment mechanism, as condensin I-DC recruiter SDC-2 also recruits condensin II to the condensin I-DC recruitment sites on the X. In addition, we found that condensin sites overlap extensively with the cohesin loader SCC-2, and that SDC-2 also recruits SCC-2 to the condensin I-DC recruitment sites. Conclusions: Our results provide the first genome-wide view of metazoan condensin II binding in interphase, define putative recruitment motifs, and illustrate shared loading mechanisms for condensin I-DC and condensin II.