Institut de Génétique Moléculaire de Montpellier (IGMM) - UMR5535


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Home page > Bioinformatics and Modelling > Dynamics and Higher-Order Chromatin Organization in Physiological and Tumoral Contexts

Dynamics and Higher-Order Chromatin Organization in Physiological and Tumoral Contexts

BAUDEMENT Marie-Odile - PhD student - University of Montpellier
FORNE Thierry – DR2 - CNRS
LESNE Annick - DR2 - CNRS
VICTOR Jean-Marc— DR2 - CNRS

Our current project, which is supported by the INCa (National Institute of Cancer), aims at understanding how the tridimensional architecture of the genome is involved in the epigenetic regulation of gene expression in mammals. We are interested not only in specific biochemical factors (DNA/histone epigenetic marks, binding factors and transcriptional co-factors), but also in physical determinants involved in genomic processes (essentially transcription). In that aim, we are developing a multi-scale approach that combines the electrostatic and elastic properties of the different genome organization levels (from DNA and topological domains to whole chromosomes). This interdisciplinary project has been reinforced by two theoretical physic scientists, Annick Lesne and Jean-Marc Victor, who recently joined the group, allowing, on a daily basis, to bring the experimental biology at the interface with physical models and bioinformatics.

Our group has developed a unique method (3C-qPCR) allowing to measure with a high resolution (around 1 kilobase) contact frequencies between pairs of genomic sites. To exploit such data and to interpret their variations from one given physiological condition to another, we are developing models issued from polymer physics that allow describe chromatin dynamics at different scales as well as numerical simulations of this dynamics.

We are also developing a novel Next-Generation Sequencing approach that allows to perform the genomic profiling of chromatin regions associated with some specific nuclear compartments (lamina, Histone Locus-bodies…). The analysis and scientific exploitation of this totally original data involve the implementation of new statistical methods (under the R langage) as well as the creation of specific bioinformatics pipelines and methods for 3D reconstitutions of the nuclear architecture.

Publications related to the subject

Lesne A., Foray N., Cathala G., Forné T., Victor J.-M.. Chromatin fiber allostery and the epigenetic code (2015) Journal of physics: Condensed Matter, Special Issue, 27, 064114.

Lesne, A., Riposo J., Roger P., Cournac A., Mozziconacci J.. 3D genome reconstruction from chromosomal contacts (2014) Nature Methods 11, 1141-1143.

Caré B. R., Carrivain P., Forné T., Victor J.-M. and Lesne A.. Finite-size conformational transitions: a unifying concept underlying chromosome dynamics (2014) Commun. Theor. Phys. 62, 607-616.

Carrivain P., Barbi M., Victor J.-M.. In silico single molecule manipulation of DNA with rigid body dynamics (2014) PLoS Comp. Biol. 10, e1003456.

Institut de Génétique Moléculaire de Montpellier
CNRS-UMR 5535 - 1919, Route de Mende - 34293 Montpellier  Cedex 5
(+33) 04 34 35 96 01