Genome-wide analysis of condensin binding in Caenorhabditis elegans

Abstract

BackgroundCondensins 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, IDC, that is targeted to and represses transcription of the X chromosome for dosage compensation.ResultsTo 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 IDC motif. In addition to differences in recruitment that result in X-enrichment of condensin IDC and condensin II binding to all chromosomes, we provide evidence for a shared recruitment mechanism, as condensin IDC recruiter SDC-2 also recruits condensin II to the condensin IDC 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 IDC recruitment sites.ConclusionsOur 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 IDC and condensin II.

Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans

“…Our measurements also imply a DCC-independent mechanism that increases compaction of the X chromosome relative to autosomes in males. This may be due to a non-sex-specific loading of non-DCC condensins, which have a clear preference for loading at ncRNA genes (Kranz et al 2013), particularly abundant on the X chromosome. Alternatively, nuclear pore anchoring might also lead to increased compaction of the X chromosome (see below).…”

Disruption of a Conserved CAP-D3 Threonine Alters Condensin Loading on Mitotic Chromosomes Leading to Chromosome Hypercondensation

“…Condensin I binds after prophase, so one would presume this is a downstream effect of condensin II overloading. Indeed, genome-wide mapping stud- ies of condensin I and II find that they occupy different locations, but also significantly overlap (notably at promoter sequences) (32,49,50), although is not yet clear if condensin I and II interact directly at the same locus, or bind separately at different stages of mitosis. Whether the observed overcondensation of mitotic chromosomes is due to increased activity of condensin II or reduced activity of condensin I, or a combination of both, remains to be determined.…”

Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis

“…7D). In eukaryotes, sites of condensin enrichment have been identified in a few model organisms by ChIP (D'Ambrosio et al 2008;Kim et al 2013;Kranz et al 2013;Nakazawa et al 2015) and appear to be scattered throughout the chromosomes. If these represent loading sites that function similarly to ParB/parS, then alignment of flanking DNA could provide a mechanism to promote compaction and resolution of chromosomes into discrete bodies during the early stages of mitosis.…”