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Review

Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution

1
Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, F-69364 Lyon, France
2
Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France
*
Authors to whom correspondence should be addressed.
Academic Editor: Manuel A. Garrido-Ramos
Genes 2021, 12(6), 851; https://doi.org/10.3390/genes12060851
Received: 1 May 2021 / Revised: 27 May 2021 / Accepted: 27 May 2021 / Published: 1 June 2021
(This article belongs to the Special Issue Nucleotide Sequences and Genome Organization)
The nucleosome is a major modulator of DNA accessibility to other cellular factors. Nucleosome positioning has a critical importance in regulating cell processes such as transcription, replication, recombination or DNA repair. The DNA sequence has an influence on the position of nucleosomes on genomes, although other factors are also implicated, such as ATP-dependent remodelers or competition of the nucleosome with DNA binding proteins. Different sequence motifs can promote or inhibit the nucleosome formation, thus influencing the accessibility to the DNA. Sequence-encoded nucleosome positioning having functional consequences on cell processes can then be selected or counter-selected during evolution. We review the interplay between sequence evolution and nucleosome positioning evolution. We first focus on the different ways to encode nucleosome positions in the DNA sequence, and to which extent these mechanisms are responsible of genome-wide nucleosome positioning in vivo. Then, we discuss the findings about selection of sequences for their nucleosomal properties. Finally, we illustrate how the nucleosome can directly influence sequence evolution through its interactions with DNA damage and repair mechanisms. This review aims to provide an overview of the mutual influence of sequence evolution and nucleosome positioning evolution, possibly leading to complex evolutionary dynamics. View Full-Text
Keywords: DNA sequence-encoded nucleosome ordering; nucleosome depleted regions; DNA sequence mutation; chromatin evolution DNA sequence-encoded nucleosome ordering; nucleosome depleted regions; DNA sequence mutation; chromatin evolution
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MDPI and ACS Style

Barbier, J.; Vaillant, C.; Volff, J.-N.; Brunet, F.G.; Audit, B. Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution. Genes 2021, 12, 851. https://doi.org/10.3390/genes12060851

AMA Style

Barbier J, Vaillant C, Volff J-N, Brunet FG, Audit B. Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution. Genes. 2021; 12(6):851. https://doi.org/10.3390/genes12060851

Chicago/Turabian Style

Barbier, Jérémy, Cédric Vaillant, Jean-Nicolas Volff, Frédéric G. Brunet, and Benjamin Audit. 2021. "Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution" Genes 12, no. 6: 851. https://doi.org/10.3390/genes12060851

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