Première réunion annuelle du GDR ADN-Phys

Liste des abstracts

2. A quantitative and predictive computational model of homology search during DNA repair by homologous recombination

Nicolas Mendiboure (CNRS)

Homologous recombination (HR) is a conserved DNA repair mechanism that uses an intact DNA molecule as a template to mend double-strand breaks (DSBs) and single-stranded gaps, ensuring genomic stability. The accurate search and choice of an homologous donor is of prime importance for HR fidelity, as repairing using non-allelic repetitive sequences can lead to structural variations. Multiple...

10. Biophysics of condensin-mediated loop extrusion on chromatin

Nicolas Pellet (ENS LYON - Laboratoire de Biologie et Modélisation de la Cellule)

Inside the cellular nucleus, DNA is compacted into a highly dynamic polymer-like structure known as chromatin. This organization enables the storage of genetic information while still allowing regulated access for processes such as transcription, replication, and repair. The self-organization of chromatin into functional domains, facilitated by a combination of physical interactions and...

14. Capturing motifs of folding from single-cell chromatin tracing data using unsupervised topic modelling

Gautham Ganesh (University of Montpellier)

Over the past decade, imaging-based chromatin tracing has emerged as a reliable method to simultaneously visualise the spatial organisation of chromatin and transcription of specific genomic loci at single-cell resolution. However, extracting interpretable structural patterns from these datasets remains a major challenge. To address this, our lab recently developed 3DTopic, a topic modelling...

1. Chromatin architecture mapping by multiplex proximity tagging

Axel Delamarre

Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a proximity-tagging method to map molecules that associate in 3D space. Using this method - PCP (proximity copy paste) - we mapped the positioning and connectivity of individual nucleosomes in Saccharomyces cerevisiae. We show that chromatin is...

5. Chromatin dynamics during the seed-to-seedling transition

Aline Probst (GReD)

The transition from seed to seedling involves major changes in nuclear organization and gene expression. However, the extent to which this developmental transition requires chromatin reprogramming - particularly changes in the histone variant repertoire - remains largely unexplored.
To dissect the molecular mechanisms that drive these chromatin reprogramming events we are combining chromatin...

3. Chromosome mechanics and relaxation from ensembles of polymer conformations

Samuele Lipani (Insitut Curie)

DNA in the nucleus is not randomly packed: it folds into 3D structures that help regulate genes and must be reestablished each time the cell divides. This folding is controlled by molecular motors that consume energy. For example, cohesin and condensin can actively pull DNA to form loops (“loop extrusion”). Because these processes use energy, they push chromosomes away from equilibrium...

4. Expliquer les dépendances entre tracks génomiques grâce à l’IA

Prof. julien mozziconacci (string)

Les modèles d’apprentissage profond en génomique ont fortement progressé : à partir de la séquence d’ADN, ils prédisent des cartes d’activité chromatinienne (marques d’histones, accessibilité) et l’expression les gènes. Reste toutefois une question centrale : comment ces modèles articulent‐ils les différentes sorties, et que se passerait‑il si l’on modifiait localement un signal ?
Nous...

9. How Linker DNA Architecture and Nucleosome States Shape Chromatin Fiber Structure

Elham Ghobadpour (TIMC-Grenoble university/ ENS-lyon)

In this work, we investigate how linker DNA length and chromatin state shape the physical properties of chromatin fibers using physics-based polymer models. To this end, we have developed an open-source simulation framework that models DNA at 10.5 bp resolution and represents nucleosomes explicitly as 14–15 DNA segments wrapped around a histone core.

We compare chromatin fibers in open...

7. Interrogating the functional roles of H3K9me3 at pericentromeres

Judith Lopes (INSERM)

Centromeric regions of eukaryotic chromosomes contain large arrays of tandemly repeated DNA sequences, known as satellite DNA. In mouse NIH3T3 cells, pericentromeric satellite sequences from distinct chromosomes cluster into chromocenters. These structures consist of constitutive heterochromatin enriched in specific epigenetic modifications, including H3K9me3, and they recruit HP1...

13. Modeling the 3D organization of centromeres

Flavia Corsi

Centromeres are essential for accurate chromosome segregation, yet their 3D organization remains largely unknown. Holocentric chromosomes distribute centromeric activity along their entire length, while monocentric chromosomes, like those in humans and chickens, localize it to a single region. Despite this morphological difference, both systems rely on conserved biophysical mechanisms,...

12. Nucleosomes act as barriers to Condensin-driven mitotic genome folding

Dr Pascal BERNARD (LBMC, CNRS & ENS-Lyon)

Nucleosomes and DNA-loop extruding SMC protein-complexes such as condensin and cohesin shape the 3D genome in eukaryotes, but their mutual functional relationships remain largely unclear. Using the fission yeast Schizosaccharomyces pombe as model, we investigated the interplays between nucleosomes and condensin-mediated mitotic chromosome assembly. We found that purified condensin fails to...

8. Promoter-proximal elements restrict pleiotropic enhancer inputs to achieve tissue specificity

Yad Ghavi-Helm (CNRS)

Developmental enhancers are regulatory elements that establish precise spatio-temporal patterns of gene expression, yet how they selectively regulate one gene over its neighbors remains unclear. Current hypotheses suggest that such specificity arises from the 3D organization of the genome or from the sequence of the core promoter. Here, we provide evidence that the core promoter acts in...

6. RAD51 regulates eukaryotic chromatin motions in the absence of DNA damage

Pierre-Alexandre Vidi (Institut de Cancérologie de l'Ouest)

In yeasts and higher eukaryotes, chromatin motions may be tuned to genomic functions, with transcriptional activation and the DNA damage response both leading to profound changes in chromatin dynamics. The RAD51 recombinase is a key mediator of chromatin mobility following DNA damage. As functions of RAD51 beyond DNA repair are being discovered, we asked if RAD51 modulates chromatin dynamics...

11. Revealing 3D contacts with time resolution in vivo using a new enzymatic technique

Leo Tarbouriech (LBMC, ENS de Lyon)

In the nucleus of eukaryotic cells, the DNA is folded in a structure called chromatin. It has been shown that there is a strong connection between the three-dimensional organisation of the genome and the expression of genes. The domain of 3D genomics is now moving forward to find fundamental principles of genome organisation. Many methods exist in the domain to reveal the three-dimensional...

15. Spatial organization of chromatin accessibility states in human cancer tissues revealed by spatial multiomics network analysis (poster)

Joel Herrera Martinez (Centre de Recherches en Cancérologie de Toulouse, CRCT, Université de Toulouse, INSERM, CNRS,)

Chromatin accessibility is a key indicator of the cell's regulatory state in normal and cancerous tissues (1). However, whether it is shaped by the local cellular context remains unexplored. Recent spatial multiomics technologies that simultaneously profile chromatin accessibility and gene expression while preserving tissue architecture now make it possible to address this question directly...