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Evidence of selection for an accessible nucleosomal array in human

hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorDRILLON, Guénola
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]
hal.structure.identifierLaboratoire Ondes et Matière d'Aquitaine [LOMA]
dc.contributor.authorARGOUL, Françoise
hal.structure.identifierLaboratoire Ondes et Matière d'Aquitaine [LOMA]
hal.structure.identifierLaboratoire de Physique de l'ENS Lyon [Phys-ENS]
dc.contributor.authorARNEODO, Alain
dc.date.created2015-12-14
dc.date.issued2016-07-29
dc.identifier.issn1471-2164
dc.description.abstractEnBackground: Recently, a physical model of nucleosome formation based on sequence-dependent bending properties of the DNA double-helix has been used to reveal some enrichment of nucleosome-inhibiting energy barriers (NIEBs) nearby ubiquitous human " master " replication origins. Here we use this model to predict the existence of about 1.6 millions NIEBs over the 22 human autosomes. Results: We show that these high energy barriers of mean size 153 bp correspond to nucleosome-depleted regions (NDRs) in vitro, as expected, but also in vivo. On either side of these NIEBs, we observe, in vivo and in vitro, a similar compacted nucleosome ordering, suggesting an absence of chromatin remodeling. This nucleosomal ordering strongly correlates with oscillations of the GC content as well as with the interspecies and intraspecies mutation profiles along these regions. Comparison of these divergence rates reveals the existence of both positive and negative selections linked to nucleosome positioning around these intrinsic NDRs. Overall, these NIEBs and neighboring nucleosomes cover 37.5 % of the human genome where nucleosome occupancy is stably encoded in the DNA sequence. These 1 kb-sized regions of intrinsic nucleosome positioning are equally found in GC-rich and GC-poor isochores, in early and late replicating regions, in intergenic and genic regions but not at gene promoters. Conclusion: The source of selection pressure on the NIEBs has yet to be resolved in future work. One possible scenario is that these widely distributed chromatin patterns have been selected in human to impair the condensation of the nucleosomal array into the 30 nm chromatin fiber, so as to facilitate the epigenetic regulation of nuclear functions in a cell-type-specific manner.
dc.language.isoen
dc.publisherBioMed Central
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enNucleosome depleted regions
dc.subject.enSequence evolution
dc.subject.enNucleosome ordering
dc.subject.enMutation rates
dc.subject.enGC content
dc.subject.enHuman genome
dc.title.enEvidence of selection for an accessible nucleosomal array in human
dc.typeArticle de revue
dc.identifier.doi10.1186/s12864-016-2880-2
dc.subject.halPhysique [physics]/Physique [physics]/Biophysique [physics.bio-ph]
bordeaux.journalBMC Genomics
bordeaux.page526 (1-20)
bordeaux.volume17
bordeaux.issue1
bordeaux.peerReviewedoui
hal.identifierhal-01391690
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01391690v1
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