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

Anton Valouev, Jeffrey Ichikawa, Thaisan Tonthat, Jeremy Stuart, Swati Ranade, Heather Peckham, Kathy Zeng, Joel Malek, Gina Costa, Kevin McKernan, Arend Sidow, Andrew Fire, Steven M. Johnson

Research output: Contribution to journalArticle

410 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1051-1063
Number of pages13
JournalGenome Research
Volume18
Issue number7
DOIs
Publication statusPublished - Jul 2008
Externally publishedYes

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Nucleosomes
Chromatin
Caenorhabditis elegans
Genome
Oligonucleotides
Nucleic Acid Conformation
High-Throughput Nucleotide Sequencing
Genetic Models
Ligation
Population

ASJC Scopus subject areas

  • Genetics

Cite this

Valouev, A., Ichikawa, J., Tonthat, T., Stuart, J., Ranade, S., Peckham, H., ... Johnson, S. M. (2008). A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Research, 18(7), 1051-1063. https://doi.org/10.1101/gr.076463.108

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. / Valouev, Anton; Ichikawa, Jeffrey; Tonthat, Thaisan; Stuart, Jeremy; Ranade, Swati; Peckham, Heather; Zeng, Kathy; Malek, Joel; Costa, Gina; McKernan, Kevin; Sidow, Arend; Fire, Andrew; Johnson, Steven M.

In: Genome Research, Vol. 18, No. 7, 07.2008, p. 1051-1063.

Research output: Contribution to journalArticle

Valouev, A, Ichikawa, J, Tonthat, T, Stuart, J, Ranade, S, Peckham, H, Zeng, K, Malek, J, Costa, G, McKernan, K, Sidow, A, Fire, A & Johnson, SM 2008, 'A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning', Genome Research, vol. 18, no. 7, pp. 1051-1063. https://doi.org/10.1101/gr.076463.108
Valouev, Anton ; Ichikawa, Jeffrey ; Tonthat, Thaisan ; Stuart, Jeremy ; Ranade, Swati ; Peckham, Heather ; Zeng, Kathy ; Malek, Joel ; Costa, Gina ; McKernan, Kevin ; Sidow, Arend ; Fire, Andrew ; Johnson, Steven M. / A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. In: Genome Research. 2008 ; Vol. 18, No. 7. pp. 1051-1063.
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