A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.
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.
Valouev
Anton
A
Departments of Pathology and Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.
Ichikawa
Jeffrey
J
Tonthat
Thaisan
T
Stuart
Jeremy
J
Ranade
Swati
S
Peckham
Heather
H
Zeng
Kathy
K
Malek
Joel A
JA
Costa
Gina
G
McKernan
Kevin
K
Sidow
Arend
A
Fire
Andrew
A
Johnson
Steven M
SM
D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics*; D002843:Chromatin / Q000235:genetics; D002874:Chromosome Mapping; D018509:DNA, Helminth / Q000032:analysis* / Q000235:genetics; D005819:Genetic Markers; D049751:Genome, Helminth; D009707:Nucleosomes / Q000235:genetics*
D002843:Chromatin; D018509:DNA, Helminth; D005819:Genetic Markers; D009707:Nucleosomes