Genome-wide analysis of condensin binding in Caenorhabditis elegans

Anna Lena Kranz, Chen Yu Jiao, Lara H. Winterkorn, Sarah E. Albritton, Maxwell Kramer, Sevinç Ercan

Research output: Contribution to journalArticle

Abstract

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, IDC, 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 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.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 IDC and condensin II.

Original languageEnglish (US)
Article numberR112
JournalGenome Biology
Volume14
Issue number10
DOIs
StatePublished - Nov 14 2013

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Caenorhabditis elegans
genome
Genome
interphase
chromosome
transcription (genetics)
loaders
chromosomes
metazoan
X chromosome
protein subunits
developmental stage
meiosis
mitosis
condensation
embryo
binding sites
Interphase
promoter regions
analysis

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Kranz, A. L., Jiao, C. Y., Winterkorn, L. H., Albritton, S. E., Kramer, M., & Ercan, S. (2013). Genome-wide analysis of condensin binding in Caenorhabditis elegans. Genome Biology, 14(10), [R112]. https://doi.org/10.1186/gb-2013-14-10-r112

Genome-wide analysis of condensin binding in Caenorhabditis elegans. / Kranz, Anna Lena; Jiao, Chen Yu; Winterkorn, Lara H.; Albritton, Sarah E.; Kramer, Maxwell; Ercan, Sevinç.

In: Genome Biology, Vol. 14, No. 10, R112, 14.11.2013.

Research output: Contribution to journalArticle

Kranz, AL, Jiao, CY, Winterkorn, LH, Albritton, SE, Kramer, M & Ercan, S 2013, 'Genome-wide analysis of condensin binding in Caenorhabditis elegans', Genome Biology, vol. 14, no. 10, R112. https://doi.org/10.1186/gb-2013-14-10-r112
Kranz AL, Jiao CY, Winterkorn LH, Albritton SE, Kramer M, Ercan S. Genome-wide analysis of condensin binding in Caenorhabditis elegans. Genome Biology. 2013 Nov 14;14(10). R112. https://doi.org/10.1186/gb-2013-14-10-r112
Kranz, Anna Lena ; Jiao, Chen Yu ; Winterkorn, Lara H. ; Albritton, Sarah E. ; Kramer, Maxwell ; Ercan, Sevinç. / Genome-wide analysis of condensin binding in Caenorhabditis elegans. In: Genome Biology. 2013 ; Vol. 14, No. 10.
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