Broad chromosomal domains of histone modification patterns in C. elegans

Tao Liu, Andreas Rechtsteiner, Thea A. Egelhofer, Anne Vielle, Isabel Latorre, Ming Sin Cheung, Sevinc Ercan, Kohta Ikegami, Morten Jensen, Paulina Kolasinska-Zwierz, Heidi Rosenbaum, Hyunjin Shin, Scott Taing, Teruaki Takasaki, A. Leonardo Iniguez, Arshad Desai, Abby F. Dernburg, Hiroshi Kimura, Jason D. Lieb, Julie Ahringer & 2 others Susan Strome, X. Shirley Liu

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)227-236
Number of pages10
JournalGenome Research
Volume21
Issue number2
DOIs
StatePublished - Feb 2011

Fingerprint

Histone Code
Chromosomes
Heterochromatin
Chromatin
Chromatin Immunoprecipitation
Genes
Caenorhabditis elegans
X Chromosome
Methylation
Caenorhabditis elegans Proteins
Genome
Genetic Markers
Germ Cells
Histones
Transcriptional Activation
Genetic Recombination
Larva
Cluster Analysis
Embryonic Structures
Antibodies

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Liu, T., Rechtsteiner, A., Egelhofer, T. A., Vielle, A., Latorre, I., Cheung, M. S., ... Liu, X. S. (2011). Broad chromosomal domains of histone modification patterns in C. elegans. Genome Research, 21(2), 227-236. https://doi.org/10.1101/gr.115519.110

Broad chromosomal domains of histone modification patterns in C. elegans. / Liu, Tao; Rechtsteiner, Andreas; Egelhofer, Thea A.; Vielle, Anne; Latorre, Isabel; Cheung, Ming Sin; Ercan, Sevinc; Ikegami, Kohta; Jensen, Morten; Kolasinska-Zwierz, Paulina; Rosenbaum, Heidi; Shin, Hyunjin; Taing, Scott; Takasaki, Teruaki; Iniguez, A. Leonardo; Desai, Arshad; Dernburg, Abby F.; Kimura, Hiroshi; Lieb, Jason D.; Ahringer, Julie; Strome, Susan; Liu, X. Shirley.

In: Genome Research, Vol. 21, No. 2, 02.2011, p. 227-236.

Research output: Contribution to journalArticle

Liu, T, Rechtsteiner, A, Egelhofer, TA, Vielle, A, Latorre, I, Cheung, MS, Ercan, S, Ikegami, K, Jensen, M, Kolasinska-Zwierz, P, Rosenbaum, H, Shin, H, Taing, S, Takasaki, T, Iniguez, AL, Desai, A, Dernburg, AF, Kimura, H, Lieb, JD, Ahringer, J, Strome, S & Liu, XS 2011, 'Broad chromosomal domains of histone modification patterns in C. elegans', Genome Research, vol. 21, no. 2, pp. 227-236. https://doi.org/10.1101/gr.115519.110
Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung MS et al. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Research. 2011 Feb;21(2):227-236. https://doi.org/10.1101/gr.115519.110
Liu, Tao ; Rechtsteiner, Andreas ; Egelhofer, Thea A. ; Vielle, Anne ; Latorre, Isabel ; Cheung, Ming Sin ; Ercan, Sevinc ; Ikegami, Kohta ; Jensen, Morten ; Kolasinska-Zwierz, Paulina ; Rosenbaum, Heidi ; Shin, Hyunjin ; Taing, Scott ; Takasaki, Teruaki ; Iniguez, A. Leonardo ; Desai, Arshad ; Dernburg, Abby F. ; Kimura, Hiroshi ; Lieb, Jason D. ; Ahringer, Julie ; Strome, Susan ; Liu, X. Shirley. / Broad chromosomal domains of histone modification patterns in C. elegans. In: Genome Research. 2011 ; Vol. 21, No. 2. pp. 227-236.
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