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Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae

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dc.contributor.author Nikolaou, Christoforos
dc.contributor.author Althammer, Sonja Daniela
dc.contributor.author Beato, Miguel
dc.contributor.author Guigó Serra, Roderic
dc.date.accessioned 2016-01-12T13:46:50Z
dc.date.available 2016-01-12T13:46:50Z
dc.date.issued 2010
dc.identifier.citation Nikolaou C, Althammer S, Beato M, Guigó R. Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae. Epigenetics & chromatin. 2010; 3(1): 20. DOI 10.1186/1756-8935-3-20
dc.identifier.issn 1756-8935
dc.identifier.uri http://hdl.handle.net/10230/25557
dc.description.abstract BACKGROUND: Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed towards providing a better understanding of the process of nucleosome positioning, for which several models have been suggested. Nevertheless, questions regarding the sequence constraints of nucleosomal DNA and how they may have been shaped through evolution remain open. In this paper, we analyze in detail different experimental nucleosome datasets with the aim of providing a hypothesis for the emergence of nucleosome-forming sequences. RESULTS: We compared the complete sets of nucleosome positions for the budding yeast (Saccharomyces cerevisiae) as defined in the output of two independent experiments with the use of two different experimental techniques. We found that < 10% of the experimentally defined nucleosome positions were consistently positioned in both datasets. This subset of well-positioned nucleosomes, when compared with the bulk, was shown to have particular properties at both sequence and structural levels. Consistently positioned nucleosomes were also shown to occur preferentially in pairs of dinucleosomes, and to be surprisingly less conserved compared with their adjacent nucleosome-free linkers. CONCLUSION: Our findings may be combined into a hypothesis for the emergence of a weak nucleosome-positioning code. According to this hypothesis, consistent nucleosomes may be partly guided by nearby nucleosome-free regions through statistical positioning. Once established, a set of well-positioned consistent nucleosomes may impose secondary constraints that further shape the structure of the underlying DNA. We were able to capture these constraints through the application of a recently introduced structural property that is related to the symmetry of DNA curvature. Furthermore, we found that both consistently positioned nucleosomes and their adjacent nucleosome-free regions show an increased tendency towards conservation of this structural feature.
dc.description.sponsorship This work was funded by grants from the Spanish Ministry of Education and Science (Plan Nacional BIO2006-03380) and Consolider project CSD2006-0004 as well as the European Union International Project HEROIC (018883).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof Epigenetics. 2010; 5(3): 180-184
dc.rights © 2010 Landes Bioscience. This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
dc.rights.uri https://creativecommons.org/licenses/by-nc/3.0/
dc.subject.other ADN
dc.subject.other Saccharomyces cerevisiae
dc.title Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1756-8935-3-20
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP6/18883
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2006-03380
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/CSD2006-0004
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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