GSE17284
Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning
We have characterized two post-translational histone modifications in C. elegans on a genomic scale.  Micrococcal nuclease digestion and immunoprecipitation were used to obtain distinct populations of single nucleosome cores, which were analyzed using massively parallel DNA sequencing  to obtain positional and coverage maps.  Two methylated histone H3 populations were chosen for comparison:  H3K4 histone methylation (associated with active chromosomal regions) and H3K9 histone methylation (associated with inactivity).  From analysis of the sequence data, we found nucleosome cores with these modifications to be enriched in two distinct partitions of the genome; H3K4 methylation was particularly prevalent in promoter regions of widely-expressed genes while H3K9 methylation was enriched on specific chromosomal arms.  For each of the six chromosomes, the highest level of H3K9 methylation corresponds to the pairing center responsible for chromosome alignment during meiosis.  H3K9 enrichment at pairing centers appears to be an early mark in meiotic chromosome sorting, occurring in the absence of components required for proper pairing of homologous chromosomes.  H3K9 methylation shows an intricate pattern within the chromosome arms, with a particular anti-correlation to regions that display a strong ~10 bp periodicity of AA/TT dinucleotides that is known to associate with germline trancription. By contrast to the global features observed with H3K9 methylation, H3K4 methylation profiles were most striking in their local characteristics around promoters, providing a unique promoter-central landmark for 3903 C. elegans genes and allowing a precise analysis of nucleosome positioning in the context of transcriptional initiation. Keywords: epigenetics Overall design: Examination of total nucleosome and nucleosomes with 2 different histone modifications in  C. elegans.  5 samples are analyzed:  1. total mononucleosome core DNA from C. elegans wild type strain N2, 2. anti-H3K4me2/3 precipitated mononucleosome core DNA from C. elegans wild type strain N2, 3.  anti-H3K9me3 precipitated mononucleosome core DNA from C. elegans wild type strain N2, 4.  total mononucleosome core DNA from C. elegans mutant  strain zim-2(tm-574), 5. anti-H3K9me3 precipitated mononucleosome core DNA from C. elegans mutant  strain zim-2(tm-574)