title: Natural single-nucleosome epi-polymorphisms in yeast.
abstract: Epigenomes commonly refer to the sequence of presence/absence of specific epigenetic marks along eukaryotic chromatin. Complete histone-borne epigenomes have now been described at single-nucleosome resolution from various organisms, tissues, developmental stages, or diseases, yet their intra-species natural variation has never been investigated. We describe here that the epigenomic sequence of histone H3 acetylation at Lysine 14 (H3K14ac) differs greatly between two unrelated strains of the yeast Saccharomyces cerevisiae. Using single-nucleosome chromatin immunoprecipitation and mapping, we interrogated 58,694 nucleosomes and found that 5,442 of them differed in their level of H3K14 acetylation, at a false discovery rate (FDR) of 0.0001. These Single Nucleosome Epi-Polymorphisms (SNEPs) were enriched at regulatory sites and conserved non-coding DNA sequences. Surprisingly, higher acetylation in one strain did not imply higher expression of the relevant gene. However, SNEPs were enriched in genes of high transcriptional variability and one SNEP was associated with the strength of gene activation upon stimulation. Our observations suggest a high level of inter-individual epigenomic variation in natural populations, with essential questions on the origin of this diversity and its relevance to gene x environment interactions.
authors.affiliation: Laboratoire de Biologie Moléculaire de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France.
authors.forename: Muniyandi
authors.initials: M
authors.lastname: Nagarajan
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Veyrieras
authors.forename: Maud
authors.initials: M
authors.lastname: de Dieuleveult
authors.forename: Hélène
authors.initials: H
authors.lastname: Bottin
authors.forename: Steffen
authors.initials: S
authors.lastname: Fehrmann
authors.forename: Anne-Laure
authors.initials: AL
authors.lastname: Abraham
authors.forename: Séverine
authors.initials: S
authors.lastname: Croze
authors.forename: Lars M
authors.initials: LM
authors.lastname: Steinmetz
authors.forename: Xavier
authors.initials: X
authors.lastname: Gidrol
authors.forename: Gaël
authors.initials: G
authors.lastname: Yvert
mesh_terms: D000107:Acetylation; D017124:Conserved Sequence; D044127:Epigenesis, Genetic; D016681:Genome, Fungal; D009707:Nucleosomes / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism
chemical_list: D009707:Nucleosomes