The Role of Nucleosome Positioning in Genome Function and Evolution

Arnéodo, A.; Drillon, Guénola; Argoul, Françoise; Audit, Benjamin

doi:10.1016/b978-0-12-803480-4.00002-8

Cited by 2 publications

(5 citation statements)

References 140 publications

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“…In contrast, it could be advantageous in human to adopt the opposite default organization of "closed and repressed" chromatin at promoters and to open specifically the few genes needed in each cell. The comparison of sequence-predicted chromatin conformation at promoters of several species confirmed this hypothesis [29,90]. The nucleosomal organization at promoters follows a gradient, from "mostly NDR" to "mostly NAR", that corresponds to the complexity of the organisms (identified as the number of different tissues composing the organism) [29].…”

Section: Nucleosome Positioning and The Evolution Of Gene Regulationmentioning

confidence: 68%

“…Such experiment in C. elegans showed that fragile nucleosomes are associated with high AT content of the underlying DNA sequence, and low expression plus high transcriptional plasticity when they are localized at the promoter of genes [52]. In S. cerevisiae, it has been shown that genes can be classified according to their nucleosomal organization [55,80,90]. Some genes have a "cristal" nucleosomal organization, with n nucleosomes on the body of the genes and a precise, constant NRL.…”

Section: Nucleosome Positioning and The Evolution Of Gene Regulationmentioning

confidence: 99%

“…These two classes of nucleosomal organization are, like in maize, associated with different transcription plasticity. Indeed, growth genes are associated with "cristal" organization, where stress genes exhibit a "bistable" organization [55,80,90]. Finally, in human, about 70% of promoters are associated to CpG islands (GC rich regions with a CpG dinucleotide content higher than elsewhere on the genome) [91].…”

Section: Nucleosome Positioning and The Evolution Of Gene Regulationmentioning

confidence: 99%

“…Selection of nucleosomal positioning at genes has also been linked to the complexity of organisms (Figure 2) [29,90]. In yeast, the majority of promoter exhibit a NDR, both in vivo and in vitro, indicating that this nucleosomal conformation is encoded directly in the DNA sequence.…”

Section: Nucleosome Positioning and The Evolution Of Gene Regulationmentioning

confidence: 99%

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Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution

Barbier

Vaillant

Volff

et al. 2021

Genes

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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.

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Section: Nucleosome Positioning and The Evolution Of Gene Regulationmentioning

confidence: 68%

Section: Nucleosome Positioning and The Evolution Of Gene Regulationmentioning

confidence: 99%

Section: Nucleosome Positioning and The Evolution Of Gene Regulationmentioning

confidence: 99%

Section: Nucleosome Positioning and The Evolution Of Gene Regulationmentioning

confidence: 99%

See 2 more Smart Citations

Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution

Barbier

Vaillant

Volff

et al. 2021

Genes

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“…Aerobic yeast exhibit intrinsic NDRs at the promoter of genes associated to respiration, whereas anaerobic yeast exhibit intrinsic NDRs at the promoter of genes associated to fermentation (Field et al , 2009; Tsankov et al , 2010). The prevalence of intrinsic NDRs at the promoter of genes has also been linked to organism complexity (defined here by the estimation of the number of different cell types in an organism), with the more complex organism having « closed » promoters with nucleosome attracting sequences and simpler organisms having « open » promoters with sequence-encoded nucleosomal barriers (Tompitak et al , 2017b; Arneodo et al , 2018). These findings highlight the importance of intrinsic NDRs during evolution.…”

Section: Discussionmentioning

confidence: 99%

Decoding Nucleosome-Depleted Regions: Insights from Epigenetic Marks, Nucleosome Size, and Thermodynamic Modelling

Tartour,

Barbier,

Hungyo

et al. 2023

Preprint

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Elucidating the global and local rules that govern genome-wide nucleosome organisation and chromatin architecture remains a critical challenge. Thermodynamic modelling based on DNA elastic properties predicts the presence of sequence-encoded nucleosome-inhibiting energy barriers (NIEBs) along vertebrate genomes. They delineate in vivo nucleosome-depleted regions (NDRs) flanked by 2-3 well positioned nucleosomes. Here, we compared mouse NIEBs to NDRs observed at CTCF binding sites and active TSSs to reveal specific chromatin organizations. We uncover in MNase-seq chromatin profiles the presence of particles of subnucleosomal length specifically positioned at the border of NIEBs with an enrichment of H3.3 and its modification H3.3 S31Ph, whereas the positioning of nucleosomes bearing H3K27ac appears insensitive to NIEBs. Surprisingly, post-translational modifications affect the size distribution of nucleosomes as seen by MNase digestion and so likely their breathing capability. We implemented an extension of our thermodynamic model allowing for variable particle size and suggest that subnucleomes at NIEB borders would result from the recruitment of chromatin remodellers at NIEBs. Our findings provide new insights into the mechanisms by which the DNA sequence and epigenetic marks shape the nucleosome positioning and breathing.

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The Role of Nucleosome Positioning in Genome Function and Evolution

Cited by 2 publications

References 140 publications

Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution

Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution

Decoding Nucleosome-Depleted Regions: Insights from Epigenetic Marks, Nucleosome Size, and Thermodynamic Modelling

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