Multi-scale coding of genomic information: From DNA sequence to genome structure and function

Alain Arnéodo; Cédric Vaillant; Benjamin Audit; Françoise Argoul; Yves d'Aubenton-Carafa; Claude Thermes

doi:10.1016/j.physrep.2010.10.001

Multi-scale coding of genomic information: From DNA sequence to genome structure and function

Alain Arnéodo ^{1, 2, *} Cédric Vaillant ^{1, 2} Benjamin Audit ^{1, 2} Françoise Argoul ^{1, 2} Yves d'Aubenton-Carafa Claude Thermes

* Corresponding author

1 Phys-ENS - Laboratoire de Physique de l'ENS Lyon

2 Laboratoire Joliot Curie

Abstract : Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. Since the different orders of packaging in the hierarchical organization of DNA condition the accessibility of DNA sequence elements to trans-acting factors that control the transcription and replication processes, there is actually a wealth of structural and dynamical information to learn in the primary DNA sequence. In this review, we show that when using concepts, methodologies, numerical and experimental techniques coming from statistical mechanics and nonlinear physics combined with wavelet-based multi-scale signal processing, we are able to decipher the multi-scale sequence encoding of chromatin condensation–decondensation mechanisms that play a fundamental role in regulating many molecular processes involved in nuclear functions.

Keywords : DNA sequence Chromatin Nucleosome Genome organization Epigenetics Transcription Replication Compositional strand asymmetry Statistical physics Hetero-polymer Generalized worm-like-chain model Scale-invariance Multi-fractal Multi-scale analysis Wavelet transform Long-range correlations Atomic force microscopy

Document type :

Journal articles

Domain :

Life Sciences [q-bio] / Biochemistry, Molecular Biology / Genomics [q-bio.GN]

Liste complète des métadonnées

https://hal-ens-lyon.archives-ouvertes.fr/ensl-00572973
Contributor : Benjamin Audit <>
Submitted on : Wednesday, March 2, 2011 - 4:24:00 PM
Last modification on : Thursday, April 19, 2018 - 2:54:03 PM

Multi-scale coding of genomic information: From DNA sequence to genome structure and function

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Multi-scale coding of genomic information: From DNA sequence to genome structure and function

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