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Exploring the Link between Nucleosome Occupancy and DNA Methylation.

Cecilia Lövkvist1, Kim Sneppen1, Jan O Haerter1

  • 1Center for Models of Life, Niels Bohr Institue, University of Copenhagen, Copenhagen, Denmark.

Frontiers in Genetics
|January 31, 2018
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Nucleosome occupancy and CpG methylation patterns are linked near gene promoters but not elsewhere in the genome. Gene expression, not CpG organization, primarily influences nucleosome positioning in humans.

Keywords:
CpG sitesDNA methylationepigeneticsgene expressionnucleosome occupancy

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Nucleosomes and CpG sites exhibit distinct spatial patterns near gene promoters.
  • Previous research suggests correlations between nucleosome occupancy, CpG density, and CpG methylation, with debated causality.

Purpose of the Study:

  • To investigate the causal relationship between nucleosome occupancy, CpG density, and CpG methylation in human genomes.
  • To determine if these relationships are specific to promoter regions or extend to other genomic areas.

Main Methods:

  • Analysis of nucleosome occupancy, CpG density, and CpG methylation data in human genomic regions.
  • Comparison of promoter regions with non-promoter regions of similar CpG densities.

Main Results:

  • Observed correlations between nucleosome occupancy and CpG density/methylation are confined to promoter regions.
  • In non-promoter regions, nucleosome occupancy is independent of CpG positioning and methylation levels.
  • CpG density and methylation show a consistent anti-correlation in both promoter and non-promoter regions.
  • Gene expression level more strongly influences promoter nucleosome occupancy than CpG density or methylation.

Conclusions:

  • The correlation between nucleosome occupancy and CpG organization is specific to promoter regions.
  • Nucleosome occupancy in the human genome appears primarily driven by gene expression, not CpG methylation or density.
  • Findings challenge direct causal links between nucleosome occupancy and CpG organization, suggesting gene expression as the dominant factor.