Conserved substitution patterns around nucleosome footprints in eukaryotes and archaea derive from frequent nucleosome repositioning through evolution

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  • dc.contributor.author Warnecke, Tobias
  • dc.contributor.author Becker, Erin A.
  • dc.contributor.author Facciotti, Marc T.
  • dc.contributor.author Nislow, Corey
  • dc.contributor.author Lehner, Ben, 1978-
  • dc.date.accessioned 2025-02-03T07:42:52Z
  • dc.date.available 2025-02-03T07:42:52Z
  • dc.date.issued 2013
  • dc.description.abstract Nucleosomes, the basic repeat units of eukaryotic chromatin, have been suggested to influence the evolution of eukaryotic genomes, both by altering the propensity of DNA to mutate and by selection acting to maintain or exclude nucleosomes in particular locations. Contrary to the popular idea that nucleosomes are unique to eukaryotes, histone proteins have also been discovered in some archaeal genomes. Archaeal nucleosomes, however, are quite unlike their eukaryotic counterparts in many respects, including their assembly into tetramers (rather than octamers) from histone proteins that lack N- and C-terminal tails. Here, we show that despite these fundamental differences the association between nucleosome footprints and sequence evolution is strikingly conserved between humans and the model archaeon Haloferax volcanii. In light of this finding we examine whether selection or mutation can explain concordant substitution patterns in the two kingdoms. Unexpectedly, we find that neither the mutation nor the selection model are sufficient to explain the observed association between nucleosomes and sequence divergence. Instead, we demonstrate that nucleosome-associated substitution patterns are more consistent with a third model where sequence divergence results in frequent repositioning of nucleosomes during evolution. Indeed, we show that nucleosome repositioning is both necessary and largely sufficient to explain the association between current nucleosome positions and biased substitution patterns. This finding highlights the importance of considering the direction of causality between genetic and epigenetic change.en
  • dc.description.sponsorship TW is co-funded by Marie Curie Actions. Work by CN was funded by the CIHR (MOPS 86705). EAB and MTF were supported from NSF EF-094953. BL is funded by an ERC Starting Grant, ERASysBio+ ERANET, MICINN BFU2008-00365 and BFU2011- 26206, AGAUR, the EMBO Young Investigator Program, EU Framework 7 project 277899 4DCellFate, and by the EMBL-CRG Systems Biology Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Warnecke T, Becker EA, Facciotti MT, Nislow C, Lehner B. Conserved substitution patterns around nucleosome footprints in eukaryotes and archaea derive from frequent nucleosome repositioning through evolution. PLoS Comput Biol. 2013 Nov 21;9(11):e1003373. DOI: 10.1371/journal.pcbi.1003373
  • dc.identifier.doi http://dx.doi.org/10.1371/journal.pcbi.1003373
  • dc.identifier.issn 1553-734X
  • dc.identifier.uri http://hdl.handle.net/10230/69432
  • dc.language.iso eng
  • dc.publisher Public Library of Science (PLoS)
  • dc.relation.ispartof PLoS Computational Biology. 2013 Nov 21;9(11):e1003373
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/277899
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2008‐00365
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2011‐26206
  • dc.rights © 2013 Warnecke 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.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/3.0/
  • dc.subject.other Nucleòtidsca
  • dc.subject.other Histonesca
  • dc.subject.other Nucleosomesca
  • dc.title Conserved substitution patterns around nucleosome footprints in eukaryotes and archaea derive from frequent nucleosome repositioning through evolutionen
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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