A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.
By Anton Valouev, J. Ichikawa, T. TonThat, Jeremy R Stuart, S. Ranade, H. Peckham, K. Zeng, J. Malek, G. Costa, K. McKernan and 3 more. Genome Research, 2008
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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.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/4f332a98b143b9988de03690fae1f71f6b57eff3
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In Molecular Biology
Citations in the corpus
- G+C content dominates intrinsic nucleosome occupancy (2009, methodology): “We predicted nucleosome occupancy in yeast and C. elegans genomes using the model scored on 150-base windows surrounding each data point in both in vitro and in vivo nucleosome maps [8, 34 ] at 1 bp intervals.”
- CNV-seq, a new method to detect copy number variation using high-throughput sequencing (2009, background): “The nextgeneration sequencing, such as 454 [8], Solexa [9] and SOLiD [10] have already showed advantages over microarrays in several aspects.”
- Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis (2012, methodology): “…and sequencing by ligation technology as implemented by Applied Biosystems, Inc. (Life Technologies Inc.), produces 100 million reads of 50 bp (Valouev et al., 2008) and sequencing by synthesis as implemented by Illumina Hi-Seq (Illumina Inc.) produces 320 to 640 million reads of 150 bp…”