Evidence of selection for an accessible nucleosomal array in human

BMC Genomics

Research Article

Benjamin Audit¹  Guénola Drillon¹  Alain Arneodo²  Françoise Argoul² 

[1] Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France;Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France;LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, F-33405, Talence, France;

关键词: Nucleosome depleted regions;    Sequence evolution;    Nucleosome ordering;    Mutation rates;    GC content;    Human genome;   

DOI  :  10.1186/s12864-016-2880-2

 received in 2015-12-14, accepted in 2016-07-04,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundRecently, 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.ResultsWe 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.ConclusionThe 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.

【 授权许可】

CC BY   
© The Author(s) 2016

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