Genome-wide analysis of condensin binding in Caenorhabditis elegans

Genome Biol. 2013;14(10):R112. doi: 10.1186/gb-2013-14-10-r112.

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, 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 IDC 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / genetics*
  • Adenosine Triphosphatases / metabolism*
  • Animals
  • Base Sequence
  • Binding Sites
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans / metabolism*
  • Chromatin Immunoprecipitation
  • Chromosomes / genetics
  • Chromosomes / metabolism
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism*
  • Genome-Wide Association Study*
  • High-Throughput Nucleotide Sequencing
  • Male
  • Multiprotein Complexes / genetics*
  • Multiprotein Complexes / metabolism*
  • Mutation
  • Nucleotide Motifs
  • Position-Specific Scoring Matrices
  • Promoter Regions, Genetic
  • Protein Binding
  • Reproducibility of Results
  • Transcription Factors / metabolism
  • Transcription, Genetic

Substances

  • DNA-Binding Proteins
  • Multiprotein Complexes
  • Transcription Factors
  • condensin complexes
  • Adenosine Triphosphatases