RT Journal
A1 Liu, Tao
A1 Rechtsteiner, Andreas
A1 Egelhofer, Thea A.
A1 Vielle, Anne
A1 Latorre, Isabel
A1 Cheung, Ming-Sin
A1 Ercan, Sevinc
A1 Ikegami, Kohta
A1 Jensen, Morten
A1 Kolasinska-Zwierz, Paulina
A1 Rosenbaum, Heidi
A1 Shin, Hyunjin
A1 Taing, Scott
A1 Takasaki, Teruaki
A1 Iniguez, A. Leonardo
A1 Desai, Arshad
A1 Dernburg, Abby F.
A1 Kimura, Hiroshi
A1 Lieb, Jason D.
A1 Ahringer, Julie
A1 Strome, Susan
A1 Liu, X. Shirley
T1 Broad chromosomal domains of histone modification patterns in C. elegans
JF Genome Research 
JO Genome Research 
YR 2011 
FD February 01 
VO 21 
IS 2 
SP 227 
OP 236 
DO 10.1101/gr.115519.110 
UL http://genome.cshlp.org/content/21/2/227.abstract 
AB 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.