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

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 interspeci...

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Autores principales: Brunet, Frédéric G., Audit, Benjamin, Drillon, Guénola, Argoul, Françoise, Volff, Jean-Nicolas, Arneodo, Alain
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Biophysical Society 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028776/
https://www.ncbi.nlm.nih.gov/pubmed/29580552
http://dx.doi.org/10.1016/j.bpj.2018.02.025
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author Brunet, Frédéric G.
Audit, Benjamin
Drillon, Guénola
Argoul, Françoise
Volff, Jean-Nicolas
Arneodo, Alain
author_facet Brunet, Frédéric G.
Audit, Benjamin
Drillon, Guénola
Argoul, Françoise
Volff, Jean-Nicolas
Arneodo, Alain
author_sort Brunet, Frédéric G.
collection PubMed
description 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.
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spelling pubmed-60287762019-05-22 Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates Brunet, Frédéric G. Audit, Benjamin Drillon, Guénola Argoul, Françoise Volff, Jean-Nicolas Arneodo, Alain Biophys J Biophysical Letter 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. The Biophysical Society 2018-05-22 2018-03-24 /pmc/articles/PMC6028776/ /pubmed/29580552 http://dx.doi.org/10.1016/j.bpj.2018.02.025 Text en © 2018 Biophysical Society. http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Biophysical Letter
Brunet, Frédéric G.
Audit, Benjamin
Drillon, Guénola
Argoul, Françoise
Volff, Jean-Nicolas
Arneodo, Alain
Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates
title Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates
title_full Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates
title_fullStr Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates
title_full_unstemmed Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates
title_short Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates
title_sort evidence for dna sequence encoding of an accessible nucleosomal array across vertebrates
topic Biophysical Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028776/
https://www.ncbi.nlm.nih.gov/pubmed/29580552
http://dx.doi.org/10.1016/j.bpj.2018.02.025
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