Steven M. Johnson et al. (2007) International Worm Meeting "Toward a high-resolution nucleosome position map of the Caenorhabditis elegans genome."

Frederick J. Tan, Arend Sidow, Thaisan Tonthat, Heather L. McCullough, Anton Valouev, Kathy Zeng, Heather Peckham, Gina Costa, Andrew Fire, Daniel P. Riordan, Steven M. Johnson, Joel Malek, Jeremy Stuart, Kevin McKernan, Jeffrey Ichikawa, Swati Ranade

[International Worm Meeting, 2007]

We are working toward a detailed structural and dynamic picture of C. elegans chromatin. Nucleosome positions within the chromatin landscape are known to serve as a major determinant of DNA accessibility to transcription factors and other interacting components. To delineate nucleosomal patterns in C. elegans, we are carrying out a genome-wide analysis in which DNA fragments corresponding to nucleosome cores are liberated using Micrococcal nuclease. Sequence analysis of an initial set of putative nucleosome cores obtained in this manner from a mixed-stage population of C. elegans reveals a combined picture of flexibility and constraint in nucleosome positioning. As had previously been observed in studies of individual loci in diverse biological systems, we observe areas in the genome where nucleosomes can adopt a wide variety of positions in a given region, areas with little or no nucleosome coverage, and areas where nucleosomes reproducibly adopt a specific positional pattern. In addition to illuminating numerous aspects of chromatin structure for C. elegans, this analysis provides a reference from which to begin an investigation of relationships between the nucleosomal pattern, chromosomal architecture, and lineage-based gene activity on a genome-wide scale. We are currently extending this analysis using ultra-high-throughput sequencing techniques analyzing the genomic positions of millions of nucleosome cores toward the end of producing a high-resolution nucleosome position map of the C. elegans genome.