title: Broad chromosomal domains of histone modification patterns in C. elegans.
abstract: Chromatin immunoprecipitation identifies specific interactions between genomic DNA and proteins, advancing our understanding of gene-level and chromosome-level regulation. Based on chromatin immunoprecipitation experiments using validated antibodies, we define the genome-wide distributions of 19 histone modifications, one histone variant, and eight chromatin-associated proteins in Caenorhabditis elegans embryos and L3 larvae. Cluster analysis identified five groups of chromatin marks with shared features: Two groups correlate with gene repression, two with gene activation, and one with the X chromosome. The X chromosome displays numerous unique properties, including enrichment of monomethylated H4K20 and H3K27, which correlate with the different repressive mechanisms that operate in somatic tissues and germ cells, respectively. The data also revealed striking differences in chromatin composition between the autosomes and between chromosome arms and centers. Chromosomes I and III are globally enriched for marks of active genes, consistent with containing more highly expressed genes, compared to chromosomes II, IV, and especially V. Consistent with the absence of cytological heterochromatin and the holocentric nature of C. elegans chromosomes, markers of heterochromatin such as H3K9 methylation are not concentrated at a single region on each chromosome. Instead, H3K9 methylation is enriched on chromosome arms, coincident with zones of elevated meiotic recombination. Active genes in chromosome arms and centers have very similar histone mark distributions, suggesting that active domains in the arms are interspersed with heterochromatin-like structure. These data, which confirm and extend previous studies, allow for in-depth analysis of the organization and deployment of the C. elegans genome during development.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Andreas
authors.initials: A
authors.lastname: Rechtsteiner
authors.forename: Thea A
authors.initials: TA
authors.lastname: Egelhofer
authors.forename: Anne
authors.initials: A
authors.lastname: Vielle
authors.forename: Isabel
authors.initials: I
authors.lastname: Latorre
authors.forename: Ming-Sin
authors.initials: MS
authors.lastname: Cheung
authors.forename: Sevinc
authors.initials: S
authors.lastname: Ercan
authors.forename: Kohta
authors.initials: K
authors.lastname: Ikegami
authors.forename: Morten
authors.initials: M
authors.lastname: Jensen
authors.forename: Paulina
authors.initials: P
authors.lastname: Kolasinska-Zwierz
authors.forename: Heidi
authors.initials: H
authors.lastname: Rosenbaum
authors.forename: Hyunjin
authors.initials: H
authors.lastname: Shin
authors.forename: Scott
authors.initials: S
authors.lastname: Taing
authors.forename: Teruaki
authors.initials: T
authors.lastname: Takasaki
authors.forename: A Leonardo
authors.initials: AL
authors.lastname: Iniguez
authors.forename: Arshad
authors.initials: A
authors.lastname: Desai
authors.forename: Abby F
authors.initials: AF
authors.lastname: Dernburg
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kimura
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
authors.forename: Julie
authors.initials: J
authors.lastname: Ahringer
authors.forename: Susan
authors.initials: S
authors.lastname: Strome
authors.forename: X Shirley
authors.initials: XS
authors.lastname: Liu
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism*; D002875:Chromosomes / Q000378:metabolism*; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics; D050172:Genes, X-Linked / Q000235:genetics; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D008745:Methylation; D008780:Methyltransferases / Q000378:metabolism; D009685:Nuclear Envelope / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics
chemical_list: D006657:Histones; D008780:Methyltransferases; D012319:RNA Polymerase II