Natural Single-Nucleosome Epi-Polymorphisms in Yeast Muniyandi Nagarajan1., Jean-Baptiste Veyrieras1., Maud de Dieuleveult1, He´ le` ne Bottin1, Steffen Fehrmann 1 , Anne-Laure Abraham1, Se´ verine Croze2, Lars M. Steinmetz3, Xavier Gidrol4, Gae¨ l Yvert1* 1 Laboratoire de Biologie Mole´culaire de la Cellule, Ecole Normale Supe´rieure de Lyon, CNRS, Universite´ de Lyon, Lyon, France, 2 ProfileXpert, Bron, France, 3 Genome Biology, European Molecular Biology Laboratory, Heidelberg, Germany, 4 Laboratoire d’Exploration Fonctionnelle des Ge´nomes, Commissariat a` l’Energie Atomique, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Mole´culaire, Evry, France 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. Citation: Nagarajan M, Veyrieras J-B, de Dieuleveult M, Bottin H, Fehrmann S, et al. (2010) Natural Single-Nucleosome Epi-Polymorphisms in Yeast. PLoS Genet 6(4): e1000913. doi:10.1371/journal.pgen.1000913 Editor: Jianzhi Zhang, University of Michigan, United States of America Received August 14, 2009; Accepted March 18, 2010; Published April 22, 2010 Copyright: 2010 Nagarajan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Supported by a young investigator grant ATIP from Centre National de la Recherche Scientifique, France; grant ANR-07-BLAN-0070 from Agence Nationale de la Recherche, France; and the National Institutes of Health. J-BV was supported by an ASC postdoctoral fellowship from Institut National de la Recherche Agronomique, France. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: Gael.Yvert@ens-lyon.fr . These authors contributed equally to this work. Introduction Divergence of DNA sequences between individuals has been the basis of genetics for half a century. More recently, epimutations were identified where inter-individual differences resided in DNA methylation patterns rather than in the DNA sequence itself, with notable consequences on imprinting and phenotypes [1–4]. In addition to DNA methylation, nucleosome positioning and post- translational modifications of histone tails have received increasing interest as they can regulate gene activity and genome dynamics [5]. A wealth of stimulating research has been conducted on these modifications, leading to a more and more precise characteriza- tion of the machineries remodeling them (such as acetyl- or methyl-transferases), of the pathways regulating these machineries (such as environmental cues), of the factors recognizing these modifications (such as bromo- and chromo-domain containing proteins), and of the consequences of these interactions on cellular outcomes (such as cellular differentiation or disease) [6]. In addition, the genomic distributions of these histone marks have been described in various organisms and cell types [7–11], raising the hope to understand or predict outcomes of eukaryotic cells from the sequence of their epigenomes. Many laboratories are therefore intensively studying if and how information can be coded by epigenomes [12,13]. Whether epigenomic sequences vary in natural populations has only been poorly investigated. Recent studies showed a rather abundant natural epigenetic variation of methylated DNA in plants, which was shown to correlate to transcriptional differences and to be additively inherited [3,14]. In addition, cases of allele- specific histone modifications have been reported [15–17]. But a detailed comparison of histone-tail epigenomes has been lacking. Using two unrelated strains of the yeast Saccharomyces cerevisiae as a model system, we provide here a first estimate of this variability for one histone post-translational modification at a single- nucleosome resolution. The number of epi-polymorphisms was high, with notable enrichment in regions of conserved DNA sequences and numerous cases where a precise (isolated) nucleosome was targeted. This variability was not correlated to differential transcription but to the degree of transcriptional response to perturbations. Our observations provide a basis for population epigenomics and raise essential questions on the origin of this diversity and its contribution to inter-individual variability in the response to environmental changes. Results Genome-wide nucleosome positioning is largely conserved between two unrelated S. cerevisiae strains To provide a first estimate of nucleosome-level epigenomic diversity, we used two unrelated strains of the yeast S. cerevisiae (BY and RM) as a model system. These strains were previously used to investigate natural genetic variability within S. cerevisiae for various PLoS Genetics | www.plosgenetics.org 1 April 2010 | Volume 6 | Issue 4 | e1000913