Physics Reports 498 (2011) 45–188
Contents lists available at ScienceDirect
Physics Reports
journal homepage: www.elsevier.com/locate/physrep
Multi-scale coding of genomic information: From DNA sequence to
genome structure and function
Alain Arneodo
a,b,∗
, Cédric Vaillant
a,b
, Benjamin Audit
a,b
, Françoise Argoul
a,b
,
Yves d’Aubenton-Carafa
c
, Claude Thermes
c
a
Université de Lyon, F-69000 Lyon, France
b
Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
c
Centre de Génétique Moléculaire, CNRS, Allée de la Terrasse, 91198 Gif-sur-Yvette, France
a r t i c l e i n f o
Article history:
Accepted 24 September 2010
Available online 8 October 2010
editor: H. Orland
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
a b s t r a c t
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.
© 2010 Elsevier B.V. All rights reserved.
Contents
1. Introduction............................................................................................................................................................................................. 48
1.1. Multi-scale coding of genomic information.............................................................................................................................. 48
1.2. Outline of the report................................................................................................................................................................... 50
2. Long-range correlations in eukaryotic DNA sequences: a footprint of nucleosome packaging ........................................................ 52
2.1. About the controversy concerning the existence of long-range correlations in DNA sequences ......................................... 52
2.2. Coding DNA sequences for statistical analysis.......................................................................................................................... 53
2.2.1. DNA walk representation............................................................................................................................................ 53
2.2.2. DNA bending profile .................................................................................................................................................... 54
∗
Corresponding author at: Laboratoire Joliot-Curie and Laboratoire de Physique, CNRS, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France.
E-mail addresses: alain.arneodo@ens-lyon.fr (A. Arneodo), cedric.vaillant@ens-lyon.fr (C. Vaillant), benjamin.audit@ens-lyon.fr (B. Audit),
francoise.argoul@ens-lyon.fr (F. Argoul), daubenton@cgm.cnrs-gif.fr (Y. d’Aubenton-Carafa), claude.thermes@cgm.cnrs-gif.fr (C. Thermes).
0370-1573/$ – see front matter © 2010 Elsevier B.V. All rights reserved.
doi:10.1016/j.physrep.2010.10.001