4 results on '"Arnéodo, Alain"'
Search Results
2. Nucleosome Positioning by Genomic Excluding-Energy Barriers
- Author
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Milani, Pascale, Chevereau, Guillaume, Vaillant, Cédric, Audit, Benjamin, Haftek-Terreau, Zofia, Marilley, Monique, Bouvet, Philippe, Argoul, Françoise, Arneodo, Alain, and Widom, Jonathan
- Published
- 2009
- Full Text
- View/download PDF
3. Evidence for DNA Sequence Encoding of an Accessible Nucleosomal Array across Vertebrates
- Author
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Brunet, Frédéric, Audit, Benjamin, Drillon, Guénola, Argoul, Françoise, Volff, Jean-Nicolas, Arnéodo, Alain, Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Laboratoire Ondes et Matière d'Aquitaine (LOMA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Institut National du Cancer (PLBIO16-302), the Fondation pour la Recherche Medicale (DEI20151234404), ANR-15-CE12-0011,LIGHTCOMB,Méthodes de peignage moléculaire à haut débit pour une cartographie rapide de la réplication du génome humain(2015), ANR-11-LABX-0048,ECOFECT,Dynamiques eco-évolutives des maladies infectieuses(2011), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), ANR-15-CE12-0011,LightComb, Etude des systèmes biologiques, de leur dynamique, des interactions et inter-conversions au niveau moléculaire (DS0401) 2015, and ANR-11-IDEX-0007-02/11-LABX-0048,ECOFECT,Dynamiques eco-évolutives des maladies infectieuses(2011)
- Subjects
Base Sequence ,Biophysical Letter ,Evolution ,[PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] ,Nucleosome positioning ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,DNA ,Vertebrate genomes ,Chromatin ,Nucleosomes ,[SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics ,Vertebrates ,[PHYS.PHYS.PHYS-MED-PH]Physics [physics]/Physics [physics]/Medical Physics [physics.med-ph] ,Animals ,Humans - Abstract
International audience; 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.
- Published
- 2018
4. Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences.
- Author
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Audit, Benjamin, Vaillant, CÉdric, ArnÉodo, Alain, D'Aubenton-Carafa, Yves, and Thermes, Claude
- Subjects
NUCLEOTIDE sequence ,WAVELETS (Mathematics) ,NUCLEOTIDES ,DNA ,CHROMATIN ,NUCLEOPROTEINS ,GENOMES - Abstract
Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlations between nucleotides (letters) result in fact from long-range correlations (LRC) between sequence-dependent DNA structural elements (words) involved in the packaging of DNA in chromatin. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. This exploration through the optics of the so-called `wavelet transform microscope' reveals a characteristic scale of 100-200 bp that separates two regimes of different LRC. We focus here on the existence of LRC in the small-scale regime (≲ 200 bp). Analysis of genomes in the three kingdoms reveals that this regime is specifically associated to the presence of nucleosomes. Indeed, small scale LRC are observed in eukaryotic genomes and to a less extent in archaeal genomes, in contrast with their absence in eubacterial genomes. Similarly, this regime is observed in eukaryotic but not in bacterial viral DNA genomes. There is one exception for genomes of Poxviruses, the only animal DNA viruses that do not replicate in the cell nucleus and do not present small scale LRC. Furthermore, no small scale LRC are detected in the genomes of all examined RNA viruses, with one exception in the case of retroviruses. Altogether, these results strongly suggest that small-scale LRC are a signature of the nucleosomal structure. Finally, we discuss possible interpretations of these small-scale LRC in terms of the mechanisms that govern the positioning, the stability and the dynamics of the nucleosomes along the DNA chain. This paper is maily devoted to a pedagogical presentation of the theoretical concepts and physical methods which are well suited to perform a statistical analysis of genomic sequences. We review the results obtained with the so-called wavelet-based multifractal analysis when investigating the DNA sequences of various organisms in the three kingdoms. Some of these results have been announced in B. Audit et al. [1, 2]. [ABSTRACT FROM AUTHOR]
- Published
- 2004
- Full Text
- View/download PDF
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