Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning
- PDF / 6,760,658 Bytes
- 15 Pages / 595.276 x 790.866 pts Page_size
- 5 Downloads / 160 Views
RESEARCH ARTICLE
Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning Sam Guoping Gu & Andrew Fire
Received: 14 May 2009 / Revised: 2 August 2009 / Accepted: 3 August 2009 / Published online: 25 August 2009 # Springer-Verlag 2009
Abstract We have characterized two post-translational histone modifications in Caenorhabditis 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. Enrichment of H3K9 methylation 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 Communicated by E.A. Nigg Electronic supplementary material The online version of this article (doi:10.1007/s00412-009-0235-3) contains supplementary material, which is available to authorized users. S. G. Gu : A. Fire Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA A. Fire (*) Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA e-mail: [email protected]
methylation shows an intricate pattern within the chromosome arms with a particular anticorrelation to regions that display a strong ~10.5 bp periodicity of AA/TT dinucleotides that is known to associate with germline transcription. 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 3,903 C. elegans genes and allowing a precise analysis of nucleosome positioning in the context of transcriptional initiation.
Introduction Eukaryotic genomic DNA is packaged into arrays of nucleosomes (Kornberg 1974) in which 147 bp of DNA wraps 1.65 times around the histone octamer core (Davey et al. 2002; Luger et al. 1997). The tightly wrapped coreassociated DNA can be substantially less accessible than flanking “linker” DNA for a variety of binding interactions and enzymatic reactions. Nucleosome positioning and dynamics are thus important factors determining the rates of many chromatin-templated processes. Certain DNA sequences have been shown to contribute to constrained nucleosome positioning in v
Data Loading...
