A high-resolution map of nucleosome positioning in the C. elegans genome
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
We have performed a high-resolution mapping of nucleosome positions in a mixed-stage mixed-cell population from a metozoan Caenorhabditis elegans. This was done by isolation of monocleosome DNA fragments from Micrococcal-nuclease treated chromatin followed by SOLiD sequencing of the resulting library. Obtained sequence reads were mapped to the C.elegans genome (WS170 release) resulting in read coordinates that correspond to genomic positions of 5' ends of retained of mononucleosome cores. We have also performed a control experiment in which we have treated naked worm DNA with limited amounts of Micrococcal nuclease, isolated resulting DNA and used it to construct a paired-end library for which we also performed SOLiD sequencing. Resulting raw data corresponded to sequence reads proximal to R3 or F3 sequencing primers representing mate-pairs from the DNA fragments in the control experiments. Resulting sequences for which both F3 and R3 proximal readout was present, were mapped to the C. elegans reference genome (WS170 release) using SOLiD mate-pair rescue pipeline and an insert size range of 300-900 bps
Using the massively parallel technique of Sequencing by Oligonucleotide Ligation and Detection (SOLiD) 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 dataset, 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.