Appel SBCP_CEA-Gif

SPÉCIALITÉ DE MASTER 2
SYSTÈMES BIOLOGIQUES & CONCEPTS PHYSIQUES
Universités Paris Diderot, Paris Sud, Pierre et Marie Curie
« PROPOSITION DE STAGE ET/OU DE THESE »
Laboratoire : Institute of Integrative Biology of the Cell (I2BC) CNRS, CEA, Université Paris Sud, UMR 9198
Adresse : Avenue de la Terrasse - Bât. 26, 91198 GIF-SUR-YVETTE Cedex, FRANCE
Directeur du laboratoire :
Équipe de recherche (si pertinent) :
Responsable de l'équipe :
Responsable de stage : Kathrin MARHEINEKE / Arach Goldar
Adresse électronique : [email protected] / [email protected]
N° et intitulé de l’École Doctorale de rattachement :
Profil recherché : Physique, Biophysique, Physique-Chimi
Possibilité de poursuite en thèse : OUI
Si oui, financement envisagé : Ecole doctoral, Idex Paris-saclay, CEA
Titre du stage : Out of Equilibrium analysis of DNA replication regulation in Xenopus early embryos.
Résumé :
Comprehensive knowledge of genetic inheritance at different developmental stages relies on elucidating the
mechanisms that regulate the spatio-temporal DNA replication program and their possible conservation during
evolution. Replication regulations in the nucleus are the culmination of the action of diverse range of molecular
factors (origin initiator factors, chromatin remodellers, polymerases, helicases, topoisomerases, kinases,
chaperones, proteasomes, acetyltransferases, deacetylases and methyltransferases). Determining how these
molecules work in concert in the eukaryotic nucleus to regulate genome duplication remains a central challenge in
molecular biology. Multi-proteins complexes assemble and disassemble on replication origins within seconds,
nucleosome turnover ranges from minutes to hours, replication origin firing demonstrates complex spatio-temporal
patterns. New experimental advances have enabled the study of dynamic of replication regulation at the singlemolecule levels. Single-molecule techniques demonstrate a great variability in replication origin location and firing
time among cells in a population, owing in part to the stochastic nature of replication. Despite these tremendous
advances in understanding the behavior of individual factors, this technique falls short of capturing the sequence of
events that is required to activate or repress a replication origin. The gulf between actual mechanisms of DNA
replication regulation and experimental capability could be bridged by using quantitative models.
The common feature of existing theoretical methods that describe the kinetics of DNA replication is that they do not
take into account the details of the dynamics path of this process. Here, we will study explicitly the dynamics of
replication process in Xenopus early embryos. We will measure the dynamic of DNA replication using DNA
combing technique in an in vitro system of replicating Xenopus nuclei by inhibiting or/and over expressing the
principal kinase (Chk1) that is involved in the regulation of replication origin firing. By building a macroscopic
model of DNA replication without a priori considerations on the processes that induce the duplication of the
genome and by using thermodynamics arguments, we will show that the replication process evolves as an out-ofequilibrium phenomenon. We will carry out, the development of a general non-equilibrium framework that will use
concepts from equilibrium and non-equilibrium statistical mechanics. In this way we will show that the dynamics of
DNA replication could be mapped to a Langevin type equation, whose generic properties will allow us to define the
source of entropy production that drives these processes out of equilibrium. The other advantage to map these
processes to a dynamics stochastic equation is that we will have the opportunity to make an analogy with the
dynamics of an overdumped oscillator. This analogy would help us to define a potential in which the replication
process evolve. This potential will allows us to infer from our produced experimental data the local rate of DNA
replication, and therefore, to analyze the effect of inhibition/ over expression of Chk1 kinase on the spatio-temporal
pattern of DNA replication. We will backup our theoretical studies with numerical ones, where by using dynamical
MonteCarlo method we will simulate DNA replication.