A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

  1. Anton Valouev1,
  2. Jeffrey Ichikawa2,
  3. Thaisan Tonthat1,
  4. Jeremy Stuart2,
  5. Swati Ranade2,
  6. Heather Peckham2,
  7. Kathy Zeng1,
  8. Joel A. Malek2,
  9. Gina Costa2,
  10. Kevin McKernan2,
  11. Arend Sidow1,
  12. Andrew Fire1,3, and
  13. Steven M. Johnson1
  1. 1 Departments of Pathology and Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
  2. 2 Applied Biosystems, Beverly, Massachusetts 01915, USA

Abstract

Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome.

Footnotes

  • 3 Corresponding author.

    3 E-mail afire{at}stanford.edu; fax (650) 724-9070.

  • [Supplemental material is available online at www.genome.org. SOLiD raw sequencing data from this study have been submitted to the Short Read Archive at NCBI under accession no. SRA001023.]

  • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.076463.108.

    • Received January 22, 2008.
    • Accepted May 12, 2008.

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