Cinquième réunion annuelle du GDR Architecture et Dynamique du Noyau et des Génomes (ADN&G)

Liste des abstracts

8. Biophysical models of the genome structural organization

Marco Di Stefano (IGH)

The eukaryotic genome in interphase is organized in distinct layers. Chromosomes occupy different positions in the nucleus (chromosome territories) with limited overlaps and segregate into active (A) and inactive (B) compartments spanning several mega-bases (Mb) of DNA. At the sub-Mb level, chromatin is organized into self-interacting regions (topologically associating domains or TADs) and...

5. Chromatin State-Dependent Polymer Model: Bridging Nucleosome Positioning and Large-Scale Chromatin Organization

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

Chromatin organization plays a crucial role in regulating genome accessibility and nuclear processes. My research focuses on nucleosome positioning and chromatin accessibility, extending polymer physics models to incorporate state-dependent chromatin properties. The structural and dynamic behavior of chromatin—such as bending rigidity, compaction, and accessibility—is modulated by biochemical...

7. Cohesin complex oligomerization maintains end-tethering at dna double-strand breaks.

karine dubrana (IRCM-CEA)

DNA double-strand breaks (DSBs) must be repaired to ensure genome stability. Crucially, DSB-ends must be kept together for timely repair. In Saccharomyces cerevisiae, two pathways mediate DSB end-tethering. One employs the Mre11–Rad50–Xrs2 (MRX) complex to physically bridge DSB-ends. Another requires the conversion of DSB-ends into single-strand DNA (ssDNA) by Exo1, but the bridging proteins...

20. Cohesion vs loop extrusion: modeling the dual role of cohesins in budding yeast

Dr Daniel Jost (Laboratoire de Biologie et Modélisation de la Cellule, ENS Lyon)

In budding yeast, cohesins are central to maintain sister
chromatids cohesion and to shape the mitotic chromosomes. Here I'll
present our effort to model the interplay between cohesin-mediated
cohesion and loop extrusion and investigate how it shapes the
organization of mitotic chromosomes in yeast. By comparing model
predictions and Hi-C experimental data, we observe the signature...

2. Does the nuclear envelope’s structure and lipid composition impact genome stability?

Janélie Bâcle (CRBM, cnrs, Université de Montpellier)

The genome is compartmentalized from the rest of the cell by the nuclear envelope (NE), which consists of two concentric lipid bilayers separated by an inter-membrane space (IMS). The inner and the outer nuclear membranes (INM, ONM) face the nucleoplasm and the cytoplasm, respectively, and are maintained at a constant distance by bridging proteins demarcating the IMS. In humans, this bridging...

14. Elucidating chromosome dynamics in vivo by trajectory analyses and Brownian dynamics simulations

Manoel MANGHI (Université de Toulouse - Laboratoire de Physique Théorique)

To decipher the mechanisms linking chromatin dynamics and the control of transcription, we combine high-throughput in vivo imaging of the whole nucleus and Brownian dynamics simulations. We compare the chromatin mean squared displacement obtained using our high resolution diffusing mapping on human mammary tumor cells, to the one measured on numerical simulations of chromatin with RNA...

4. Epigenetic mechanisms and treatment approaches for Mantle Cell Lymphoma

Yelena Grishina (CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, 94800 Villejuif, France)

Mantle cell lymphoma (MCL) is an aggressive B-cell malignancy with a poor prognosis. Over 90% of MCL cases are associated with a t(11;14) recurrent chromosomal translocation which drives the overexpression of cyclin D1 (CCND1), a critical regulator of the cell cycle. However, animal models show that CCND1 overexpression alone is insufficient to induce malignancy, suggesting that additional...

11. Extracellular matrix stiffness modulates the nuclear lamina organisations and set nuclear conditions for PRC2 repression.

Dr Cyril Esnault (Institut de Génétique Moléculaire de Montpellier (IGMM))

Although the cells of a multicellular organism share the same genetic material, their functions, structures, and behaviours can vary significantly. Many of these differences arise from distinct gene expression programs. Environmental cues are integrated and mediate epigenetic changes that regulate cell activity, differentiation and development. Cells sense their microenvironment not only...

3. Genome-Wide Modeling of 3D Chromosome Organization in Yeast S-Phase

Dario D'Asaro (ENS-lyon)

From the basic structure of two diverging sister forks to their organization at the nuclear scale, the mechanistic details of how DNA replication influences 3D chromatin organization remain highly debated. To quantitatively address some of these questions, we simulate the entire Saccharomyces cerevisiae genome, integrating its 3D Rabl architecture with realistic 1D replication timing...

13. Inferring chromatine structure from m-FISH data: A unified picture from human and mouse cells

Loucif Remini (L2C)

We analyze multiplexed fluorescence in situ hybridization (m-FISH) data for human and mouse cell lines. The m-FISH technique uses fluorescently-labeled single-stranded probes which hybridize to specific chromosomal regions, thereby allowing the measurement of the spatial positions of up to tagged sites for several thousands of interphase chromosomes. Our analysis focuses on a wide range of...

21. Is physical proximity required for enhancer action?

marcelo nollmann (CNRS)

22. Poster : Applying Latent Dirichlet Allocation(LDA) to decompose single-cell chromatin conformations

Jean-Bernard Fiche (Centre de Biologie Structurale)

Chromatin structure varies dramatically between cells, but the specific
motifs that underlie this organization remain poorly understood. Using
imaging-based chromatin tracing techniques, we visualized 3D chromatin
organization in mouse pancreatic tissue. We show that individual
chromatin traces can be decomposed into loop and domain chromatin
folding motifs (CFMs) using standard Latent...

18. Poster : Characterization of PARP1 dynamics during the DNA damage response by Single Particle Tracking

fabiola garcia fernandez (INSERM)

19. Poster : Mechanism of bacterial DNA segregation: LLPS behavior, beyond trend and reality.

Perrine Revoil (Université Toulpuse III Paul Sabatier - Laboratoire de Microbiologie et Génétique Moléculaires)

In bacteria, low-copy-number replicons carry self-specific partition systems to ensure their faithful segregation. Among these systems, ParABS partition systems, consisting of a Walker-type ATPase (ParA) and a DNA-binding protein (ParB) along with parS centromere sites, are the most prevalent on plasmids and the only one present on chromosomes. ParB proteins, recently shown to belong to a...

10. Poster : RNA profiling of nuclear micro-environments with high molecular crowding

Nathan Lecouvreur (IGMM)

Studying nuclear micro-environments with high molecular crowding, particularly membrane-less organelles (MLOs) such as Cajal bodies, PML bodies, speckles or paraspeckles, has always been a challenge. Indeed, such MLOs typically result from liquid-liquid phase separation and thus behave as liquid-like droplets that are particularly difficult to isolate. The characterization of internal...

1. Poster : SUMO RNAi-mediated hyper-clustering of PRC1 results in the re-wiring of genome-wide TADs.

Nazli AKILLI

Polycomb group complexes (PcGs) are crucial regulators of genome organization in Drosophila, with PRC1—comprised of the subunits Pc, Ph, Psc, and Sce—playing an important role. PRC1 is integral to three-dimensional (3D) chromatin architecture and interacts with PRC2, which mediates the H3K27me3 mark. The clustering of PRC1 into foci, measuring 100 to 200 nm, is closely linked to its functional...

16. Poster: Role of the Nuclear Periphery in Epithelial to Mesenchymal Transition

Nouhaila Laabas (CNRS-IGH)

The positioning of genomic loci on the center-to-periphery nuclear radius, called radial nuclear positioning, is neither fixed nor random. In particular, association of genomic loci with the nuclear lamina is usually associated with cell-type specific gene repression, while association with the nuclear pores has been proposed to facilitate super-enhancers activation of cell-type specific...

9. PRC1 nano-structures compact Hox chromatin during Drosophila embryogenesis

Thierry Cheutin (CNRS)

Polycomb machinery is required to maintain silencing of key developmental genes during development. In Drosophila, its genomic landscape is composed of discrete element named PREs, where Polycomb group (PcG) proteins bind, and large domains covered with H3K27me3 marks. Inside the cell nucleus, Polycomb foci are the place where PcG subunits and its associated chromatin localize. To connect the...

15. Role of the H3.3 histone variant in establishment of mammalian circadian rhythms.

Mlle Dominika LETKOVA

Circadian clocks are an important feature that allow organisms to adapt and to anticipate daily changes in their environment. Almost every cell has its own circadian clock and such timekeeping system is orchestrated by transcriptional-translational feedback loops. In mammals, robust circadian oscillators coordinate gene-expression programs in a tissue-specific manner, being critical for...

6. The ParB-CTP Cycle Activates Phase Separation in Bacterial DNA Segregation

Mlle Linda Delimi (Laboratoire Charles Coulomb)

Cell function relies on liquid-like organelles formed through phase transitions, yet the mechanisms ensuring their specificity and rapid assembly remain poorly understood. In bacterial chromosome segregation via the ParABS system, hundreds of ParB proteins are recruited around the centromere-like parS sequence forming the partition complex. Recent studies have shown that ParB binds CTP and...

12. Uncovering a New Function of Cis-Regulatory Elements in Alternative Splicing

Andrew Oldfield (IGH)

Cis-regulatory elements have recently been shown to play a much broader range of functional roles beyond simple gene expression regulation. In this work, we uncover a novel role for cis-regulatory elements in alternative splicing regulation. By studying the regulatory interplay between chromatin architecture and alternative splicing during the epithelial-to-mesenchymal transition (EMT)—a key...