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Biophys J. 2018 May 22;114(10):2308-2316. doi: 10.1016/j.bpj.2018.02.025. Epub 2018 Mar 24.

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

Author information

1
Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, Lyon, France.
2
Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France.
3
Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France; LOMA, Université de Bordeaux, CNRS UMR 5798, Talence, France.
4
Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France; LOMA, Université de Bordeaux, CNRS UMR 5798, Talence, France. Electronic address: alain.arneodo@u-bordeaux.fr.

Abstract

Nucleosome-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.

PMID:
29580552
PMCID:
PMC6028776
[Available on 2019-05-22]
DOI:
10.1016/j.bpj.2018.02.025
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