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Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates

hal.structure.identifierInstitut de Génomique Fonctionnelle de Lyon [IGFL]
dc.contributor.authorBRUNET, Frédéric
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorAUDIT, Benjamin
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorDRILLON, Guénola
hal.structure.identifierLaboratoire Ondes et Matière d'Aquitaine [LOMA]
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorARGOUL, Françoise
hal.structure.identifierInstitut de Génomique Fonctionnelle de Lyon [IGFL]
dc.contributor.authorVOLFF, Jean-Nicolas
hal.structure.identifierLaboratoire Ondes et Matière d'Aquitaine [LOMA]
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorARNÉODO, Alain
dc.date.issued2018-05-22
dc.identifier.issn0006-3495
dc.description.abstractEnNucleosome-depleted regions around which nucleosomes order following the ''statistical'' positioning scenario were recently shown to be encoded in the DNA sequence in human. This intrinsic nucleosomal ordering strongly correlates with oscillations in the local GC content as well as with the interspecies and intraspecies mutation profiles, revealing the existence of both positive and negative selection. In this letter, we show that these predicted nucleosome inhibitory energy barriers (NIEBs) with compacted neighboring nucleosomes are indeed ubiquitous to all vertebrates tested. These 1 kb-sized chromatin patterns are widely distributed along vertebrate chromosomes, overall covering more than a third of the genome. We have previously observed in human deviations from neutral evolution at these genome-wide distributed regions, which we interpreted as a possible indication of the selection of an open, accessible, and dynamic nucleosomal array to constitutively facilitate the epigenetic regulation of nuclear functions in a cell-type-specific manner. As a first, very appealing observation supporting this hypothesis, we report evidence of a strong association between NIEB borders and the poly(A) tails of Alu sequences in human. These results suggest that NIEBs provide adequate chromatin patterns favorable to the integration of Alu retrotransposons and, more generally to various transposable elements in the genomes of primates and other vertebrates.
dc.description.sponsorshipMéthodes de peignage moléculaire à haut débit pour une cartographie rapide de la réplication du génome humain
dc.description.sponsorshipDynamiques eco-évolutives des maladies infectieuses
dc.language.isoen
dc.publisherBiophysical Society
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/
dc.subject.enEvolution
dc.subject.enVertebrate genomes
dc.subject.enChromatin
dc.subject.enNucleosome positioning
dc.title.enEvidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates
dc.typeArticle de revue
dc.identifier.doi10.1016/j.bpj.2018.02.025
dc.subject.halPhysique [physics]/Physique [physics]/Biophysique [physics.bio-ph]
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique humaine
dc.subject.halSciences du Vivant [q-bio]/Cancer
dc.subject.halPhysique [physics]/Physique [physics]/Physique Médicale [physics.med-ph]
bordeaux.journalBiophysical Journal
bordeaux.page2308-2316
bordeaux.volume114
bordeaux.issue10
bordeaux.peerReviewedoui
hal.identifierhal-01766614
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01766614v1
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