A fundamental aspect of cellular function is the accurate duplication of the genome and the preparation of resulting DNA copies for efficient cell division. How these complex tasks are accomplished in the context of the highly hierarchical 3D organization of chromatin remains elusive. In this thesis, we quantitatively address how the active, out-of-equilibrium process of DNA replication influences 3D chromatin folding, using a computational approach based on polymer modeling.
After a general introduction on the interplay between replication and genome organization (Chapter 1), we introduce in Chapter 2 a novel polymer model that explicitly accounts for the progression of the replication machinery (replication forks) and the resulting formation of sister chromatids (SCs). Applying the model to idealized toy systems, we systematically analyze the spatial effects of replication bubbles within a polymer — maternal chain. In particular, we investigate the putative consequences of interactions between the two sister forks emanating from one origin of replication. We demonstrate how the presence or absence of such interactions differentially impacts the pre-existing polymer structure, both at the local and global scale. We predict that this may lead to specific signatures that may be visible on Hi-C maps. I further uncover the emergence of catenations and intertwined structures between SCs, regulated by the number of fired origins.
In Chapter 3, we adapt our model to simulate chromosome IV of Saccharomyces cerevisiae, incorporating realistic replication timing to predict patterns around early origins on Hi-C-like contact maps. Using both existing and new unpublished experimental data, we validate our predictions, identifying a previously unreported replication-dependent and cohesin-independent signal, the so-called “fountain” pattern. While we observe a qualitative agreement with the predicted fountain pattern for the interacting sister-forks scenario, we also highlight a likely coexistence of a mixed population of interacting and non-interacting forks in vivo.
During yeast S-phase, cohesin is gradually loaded onto chromatin to mediate two distinct processes: tethering of the two sister chromatids (cohesion) and loop-extrusion activity that compacts the genome. In Chapter 4, we explore these phenomena by incorporating static loops and cohesive forces to investigate the structure of SCs after DNA replication and before mitotic division (G2/M-phase). Additionally, we explore two cohesion scenarios: symmetrical, where cohesive forces are applied strictly between homologous loci, and asymmetrical, where they are applied between non-homologous loci. While both models reproduce the experimentally observed global loose alignment of SCs, only the asymmetrical model is able to account for the contact patterns between the two SCs observed around cohesin-associated regions.
In Chapter 5, we expand the model to simulate the entire haploid genome of Saccharomyces cerevisiae, explicitly incorporating its large-scale Rabl organization. Specifically, we conduct preliminary analyses on the organization of replication forks at the nuclear level and investigate the G2/M phase chromosome organization under the newly introduced constraints of Rabl organization. In particular, we provide the first direct observation in silico on how replication propagates in time from one pole to the other of the nucleus and verify that the optimal parameters used to model cohesion at the single chromosome level well adapt to the full genome.
Finally, Chapter 6 contains an overall conclusion of my work and gives some perspectives.
Gratuit
Disciplines