Our Research

Bacterial Genome Organization and Segregation

One of the main directions of my research in genome physics focuses on the organization and segregation of the bacterial genome. Bacterial genome segregation relies on the coordinated action of the ParA and ParB proteins together with the centromeric DNA sequence parS. The first step of this process is the formation of a ParB protein condensate around parS. My work on this topic aims to characterize the physical properties of this condensate, in particular its formation through a phase transition and its role in activating the ATPase activity of ParA. ATP hydrolysis by ParA generates the force dipole responsible for separating replicated DNA molecules. It currently involves the supervision of two PhD students (Linda Delimi, Laurin Hajjaj). My main collaborator is Jean-Yves Bouet (LMGM, CBI, Université Paul Sabatier, Toulouse).

A new project (2026), developed in collaboration with Stéphanie Bury-Moné (I2BC, Université Paris-Saclay), investigates the large-scale conformational reorganization of the Streptomyces chromosome during metabolic differentiation. By combining polymer physics and quantitative modeling with experimental microbiology, this project aims to understand how chromosome architecture is remodeled during the transition from exponential growth to the stationary phase and how these structural changes contribute to cellular differentiation and specialized metabolism.

Spatial Organization of the Eukaryotic Genome and Epigenetic Regulation

My second research theme focuses on the spatial organization of the eukaryotic genome and its role in epigenetic regulation. This work extends my expertise in bacterial chromosome organization to eukaryotic systems by combining polymer physics, protein-mediated interactions, and phase-separation phenomena.

My current research includes the project "Chronic Inflammation Shapes Non-Coding RNA-Mediated Transcriptional Condensates: Experimental and Modelling Approaches," conducted in collaboration with Rosemary Kiernan (IGH, Montpellier). This interdisciplinary project investigates how chronic inflammation remodels transcriptional condensates through non-coding RNAs, integrating quantitative modeling with experimental approaches.

Previous work has focused on chromatin organization in Drosophila. We demonstrated that pairwise interactions, rather than large Polycomb hubs, govern the spatial organization of Polycomb domains (Cell Reports, 2024). We also developed the first quantitative polymer model directly constrained by Hi-M super-resolution microscopy distance distributions, revealing two distinct regimes of chromatin organization (Physical Review E, 2024). This research is currently being extended to investigate how cell type-specific three-dimensional genome architecture shapes gene regulation in the fly brain, combining polymer modeling with imaging and genomics to understand how transcriptional states are associated with changes in promoter interactions with both cis-regulatory and non-canonical genomic elements (forthcoming, 2026).