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Epigenetic marks, like histone H3 acetylation at Lysine 14 (H3K14ac), show significant natural variation between yeast strains. These Single Nucleosome Epi-Polymorphisms (SNEPs) highlight inter-individual epigenomic diversity and its potential role in gene regulation.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Epigenetics

Background:

  • Epigenomes, representing epigenetic mark patterns on chromatin, are well-studied across species and conditions.
  • However, the natural variation within a single species' epigenome has remained largely unexplored.

Purpose of the Study:

  • To investigate the intra-species natural variation of histone-borne epigenomes.
  • Specifically, to analyze the variation in histone H3 acetylation at Lysine 14 (H3K14ac) between two Saccharomyces cerevisiae strains.

Main Methods:

  • Utilized single-nucleosome chromatin immunoprecipitation and mapping techniques.
  • Interrogated 58,694 nucleosomes to identify differences in H3K14 acetylation levels.

Main Results:

  • Identified 5,442 nucleosomes with significant differences in H3K14 acetylation (Single Nucleosome Epi-Polymorphisms, SNEPs) between the two yeast strains (FDR < 0.0001).
  • SNEPs were found to be enriched at regulatory sites and conserved non-coding DNA sequences.
  • While higher acetylation didn't always correlate with increased gene expression, SNEPs were associated with genes exhibiting high transcriptional variability and influenced gene activation strength.

Conclusions:

  • Demonstrated substantial natural epigenomic variation within a species at single-nucleosome resolution.
  • Suggests that Single Nucleosome Epi-Polymorphisms (SNEPs) are a significant source of epigenomic diversity.
  • Raises questions about the origins of this variation and its implications for gene-environment interactions and phenotypic diversity.