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Barbier J, Vaillant C, Volff JN, Brunet FG, Audit B. Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution. Genes (Basel) 2021; 12:genes12060851. [PMID: 34205881 PMCID: PMC8228248 DOI: 10.3390/genes12060851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
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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Affiliation(s)
- Jérémy Barbier
- 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; (J.B.); (F.G.B.)
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Cédric Vaillant
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
| | - Jean-Nicolas Volff
- 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; (J.B.); (F.G.B.)
- Correspondence: (J.-N.V.); (B.A.)
| | - Frédéric G. Brunet
- 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; (J.B.); (F.G.B.)
| | - Benjamin Audit
- Laboratoire de Physique, Univ Lyon, ENS de Lyon, CNRS, F-69342 Lyon, France;
- Correspondence: (J.-N.V.); (B.A.)
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Brunet FG, Audit B, Drillon G, Argoul F, Volff JN, Arneodo A. Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates. Biophys J 2018; 114:2308-2316. [PMID: 29580552 PMCID: PMC6028776 DOI: 10.1016/j.bpj.2018.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/07/2018] [Accepted: 02/20/2018] [Indexed: 12/15/2022] Open
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.
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Affiliation(s)
- Frédéric G Brunet
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, Lyon, France
| | - Benjamin Audit
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France
| | - Guénola Drillon
- Univ Lyon, ENS de Lyon, Univ Claude Bernard Lyon 1, CNRS Laboratoire de Physique, Lyon, France
| | - Françoise Argoul
- 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
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Univ Claude Bernard Lyon 1, Lyon, France
| | - Alain Arneodo
- 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.
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Boulos RE, Tremblay N, Arneodo A, Borgnat P, Audit B. Multi-scale structural community organisation of the human genome. BMC Bioinformatics 2017; 18:209. [PMID: 28399820 PMCID: PMC5387268 DOI: 10.1186/s12859-017-1616-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/28/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation. RESULTS We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines. We observed that there exist structural domains of all sizes up to chromosome length and demonstrated that the set of structural communities forms a hierarchy of chromosome segments. Hence, at all scales, chromosome folding predominantly involves interactions between neighbouring sites rather than the formation of links between distant loci. CONCLUSIONS Multi-scale structural decomposition of human chromosomes provides an original framework to question structural organisation and its relationship to functional regulation across the scales. By construction the proposed methodology is independent of the precise assembly of the reference genome and is thus directly applicable to genomes whose assembly is not fully determined.
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Affiliation(s)
- Rasha E Boulos
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.,Present address: Montpellier Cancer Institute (ICM), Montpellier Cancer Research Institute (IRCM) Inserm U1194, University of Montpellier, Montpellier, France
| | - Nicolas Tremblay
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.,Present address: CNRS, GIPSA-lab, Grenoble, France
| | - Alain Arneodo
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.,Present address: LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, 33405, France
| | - Pierre Borgnat
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France
| | - Benjamin Audit
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.
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Drillon G, Audit B, Argoul F, Arneodo A. Evidence of selection for an accessible nucleosomal array in human. BMC Genomics 2016; 17:526. [PMID: 27472913 PMCID: PMC4966569 DOI: 10.1186/s12864-016-2880-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/04/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Recently, 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. RESULTS We 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. CONCLUSION The 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.
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Affiliation(s)
- Guénola Drillon
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
| | - Benjamin Audit
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
| | - Françoise Argoul
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
- LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, F-33405 France
| | - Alain Arneodo
- Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, F-69342 France
- LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, F-33405 France
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Smith OK, Kim R, Fu H, Martin MM, Lin CM, Utani K, Zhang Y, Marks AB, Lalande M, Chamberlain S, Libbrecht MW, Bouhassira EE, Ryan MC, Noble WS, Aladjem MI. Distinct epigenetic features of differentiation-regulated replication origins. Epigenetics Chromatin 2016; 9:18. [PMID: 27168766 PMCID: PMC4862150 DOI: 10.1186/s13072-016-0067-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 04/25/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Eukaryotic genome duplication starts at discrete sequences (replication origins) that coordinate cell cycle progression, ensure genomic stability and modulate gene expression. Origins share some sequence features, but their activity also responds to changes in transcription and cellular differentiation status. RESULTS To identify chromatin states and histone modifications that locally mark replication origins, we profiled origin distributions in eight human cell lines representing embryonic and differentiated cell types. Consistent with a role of chromatin structure in determining origin activity, we found that cancer and non-cancer cells of similar lineages exhibited highly similar replication origin distributions. Surprisingly, our study revealed that DNase hypersensitivity, which often correlates with early replication at large-scale chromatin domains, did not emerge as a strong local determinant of origin activity. Instead, we found that two distinct sets of chromatin modifications exhibited strong local associations with two discrete groups of replication origins. The first origin group consisted of about 40,000 regions that actively initiated replication in all cell types and preferentially colocalized with unmethylated CpGs and with the euchromatin markers, H3K4me3 and H3K9Ac. The second group included origins that were consistently active in cells of a single type or lineage and preferentially colocalized with the heterochromatin marker, H3K9me3. Shared origins replicated throughout the S-phase of the cell cycle, whereas cell-type-specific origins preferentially replicated during late S-phase. CONCLUSIONS These observations are in line with the hypothesis that differentiation-associated changes in chromatin and gene expression affect the activation of specific replication origins.
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Affiliation(s)
- Owen K. Smith
- />DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - RyanGuk Kim
- />In Silico Solutions, Falls Church, VA 22033 USA
| | - Haiqing Fu
- />DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Melvenia M. Martin
- />DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Chii Mei Lin
- />DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Koichi Utani
- />DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Ya Zhang
- />DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Anna B. Marks
- />DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Marc Lalande
- />Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06032 USA
| | - Stormy Chamberlain
- />Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06032 USA
| | - Maxwell W. Libbrecht
- />Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 USA
| | - Eric E. Bouhassira
- />Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | | | - William S. Noble
- />Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 USA
- />Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA
| | - Mirit I. Aladjem
- />DNA Replication Group, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
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de Bruin L, Tompitak M, Eslami-Mossallam B, Schiessel H. Why Do Nucleosomes Unwrap Asymmetrically? J Phys Chem B 2016; 120:5855-63. [PMID: 26991771 DOI: 10.1021/acs.jpcb.6b00391] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleosomes, DNA spools with a protein core, engage about three-quarters of eukaryotic DNA and play a critical role in chromosomal processes, ranging from gene regulation, recombination, and replication to chromosome condensation. For more than a decade, micromanipulation experiments where nucleosomes are put under tension, as well as the theoretical interpretations of these experiments, have deepened our understanding of the stability and dynamics of nucleosomes. Here we give a theoretical explanation for a surprising new experimental finding: nucleosomes wrapped onto the 601 positioning sequence (the sequence used in most laboratories) respond highly asymmetrically to external forces by always unwrapping from the same end. Using a computational nucleosome model, we show that this asymmetry can be explained by differences in the DNA mechanics of two very short stretches on the wrapped DNA portion. Our finding suggests that the physical properties of nucleosomes, here the response to forces, can be tuned locally by the choice of the underlying base-pair sequence. This leads to a new view of nucleosomes: a physically highly varied set of DNA-protein complexes whose properties can be tuned on evolutionary time scales to their specific function in the genomic context.
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Affiliation(s)
- Lennart de Bruin
- Institute Lorentz for Theoretical Physics, Leiden University , Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Marco Tompitak
- Institute Lorentz for Theoretical Physics, Leiden University , Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - Behrouz Eslami-Mossallam
- Institute Lorentz for Theoretical Physics, Leiden University , Niels Bohrweg 2, 2333 CA Leiden, The Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Helmut Schiessel
- Institute Lorentz for Theoretical Physics, Leiden University , Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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Everaers R, Schiessel H. The physics of chromatin. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:060301. [PMID: 25563698 DOI: 10.1088/0953-8984/27/6/060301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Ralf Everaers
- Laboratoire de Physique de l'École Normale Supérieure, Université de Lyon, France. Instituut Lorentz, Leiden University, PO Box 9506, 2300 RA Leiden, The Netherlands
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