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Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning

Chromosoma volume 119, pages 73–87 (2010)Cite this article

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 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.

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Acknowledgements

We thank Ayelet Lamm, Ziming Weng, and Phil Lacroute for running the high-throughput DNA sequencing; Arend Sidow, Anne Villeneuve, Jessica Bessler, Susan Strome, Steve Johnson, Edward Grow, Anton Valouev, Lia Gracey, Ayelet Lamm, Scott Boyd, Cecilia Mello, Julia Pak, Jonathan Gent, Poornima Parameswaran, Chaya Krishna, Michael Stadler, Jay Maniar, Rosa Alcazar, and Julie Ni for the help, suggestions, and support; and the National Institutes of Health (grant R01-GM37706).

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  1. Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA

    Sam Guoping Gu & Andrew Fire

  2. Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA

    Andrew Fire

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  1. Sam Guoping Gu
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Correspondence to Andrew Fire.

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Communicated by E.A. Nigg

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Supplementary Fig. 1
figure 8

Global profiles of H3K9me3 enrichment within the C. elegans genome. Relative enrichment of H3K9me3 (N2) and H3K9me3 (zim-2) is plotted as a function of position in the C. elegans genome. Relative enrichment is calculated for each 1-Mb region as the ratio of coverage levels for H3K9me3 over total nucleosome (normalized by total number of perfect unique alignments for each library)

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Supplementary Fig. 2
figure 9

Genome-wide histograms of start-to-start, start-to-end, and end-to-start coincidences for pairs of sequenced ends, plotted as of separation in base pairs. This analysis is the same as the one in Fig. 5b except that uncollapsed sequencing reads are used

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Supplementary Table 2

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Gu, S.G., Fire, A. Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning. Chromosoma 119, 73–87 (2010). https://doi.org/10.1007/s00412-009-0235-3

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Keywords

  • Histone Methylation
  • Nucleosome Position
  • H3K9 Methylation
  • Pairing Center
  • Chromosome Versus