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Series GSE17284 Query DataSets for GSE17284
Status Public on Aug 31, 2009
Title Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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)
 
Contributor(s) Gu SG, Fire AZ
Citation(s) 19705140
Submission date Jul 23, 2009
Last update date May 15, 2019
Contact name Sam Guoping Gu
E-mail(s) ggu@dls.rutgers.edu
Organization name Rutgers University
Department Molecular Biology and Biochemistry
Lab Sam Gu
Street address Nelson Labs A125, 604 Allison Road
City Piscataway
State/province NJ
ZIP/Postal code 08854
Country USA
 
Platforms (1)
GPL9269 Illumina Genome Analyzer II (Caenorhabditis elegans)
Samples (5)
GSM432720 Total Nucleosome N2 seq
GSM432721 H3K4me2/3 N2 chipSeq
GSM432722 H3K9me3 N2 chipSeq
Relations
SRA SRP001332
BioProject PRJNA119151

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Supplementary file Size Download File type/resource
GSE17284_RAW.tar 480.9 Mb (http)(custom) TAR (of BED, TXT)
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Processed data provided as supplementary file
Raw data are available in SRA

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