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

Liste des abstracts

2. A Dynamic Single-Molecule Approach to Directly Visualize the Molecular Mechanisms of DNA-Binding Proteins.

kalthoum BEN MBAREK (LUMICKS)

Studying and validating the molecular mechanism of DNA processes often requires direct functional evidence. Here we present the C-Trap: a dynamic single-molecule microscope that allows researchers to directly visualize the dynamics and assembly of biological complexes under different conditions. All at the single-molecule level, providing direct proof of the biological mechanisms being...

13. Bacterial chromosome organization by condensins: functional analysis of MukBEF in E. coli

Mohammed SEBA

Abstract : Chromosome condensation and segregation are two essential processes for the transmission of genetic material in all living organisms. Indeed, chromosomes are composed of a DNA molecule and several families of proteins that perform various functions related to DNA. Ubiquitous SMC complexes in the living world are among these proteins that constitute the chromosome, and their study is...

3. Cell cycle dependent oscillations of gene expression in E. coli

Dr Bianca Sclavi (LCQB, UMR 7238, CNRS,)

A long-standing hypothesis sees DNA replication control in E. coli as a central cell cycle oscillator at whose core is the DnaA protein. The consensus is that the activity of the DnaA protein, which is dependent on its nucleotide bound state, is an effector of initiation of DNA replication and a sensor of cell size. However, while several processes are known to regulate the change in DnaA...

16. DNA supercoiling quantiatively regulates bacterial transcription by untwisting the promoter spacer

Sam Meyer (MAP, INSA Lyon)

DNA supercoiling acts as a global transcriptional regulator in bacteria, but the promoter sequence or structural determinants controlling its effect remain unclear. It was previously proposed to modulate the torsional angle between the −10 and −35 hexamers, and thereby regulate the formation of the closed-complex depending on the length of the ‘spacer’ between them. We develop a thermodynamic...

9. Genome stability: Interplay between Double Strand Break (DSB), chromatin mobility and SMC complexes.

Ànnia Carré Simon

Chromosome organization has recently emerged as essential for maintaining genome integrity. In the budding yeast, chromosomes follow a Rabl configuration where centromeres are clustered close to the nuclear envelope near the Microtubule Organization Center. The attachment of microtubules to kinetochores, multiprotein complexes associated with centromeres, ensures the faithful segregation of...

14. Modeling the coupling between epigenome regulation and 3D chromatin organization

Amith Zafal ABDULLA (École normale supérieure de Lyon)

The relation between the 3D chromosome organization and the epigenome (DNA methylation, histone modifications, etc.) has been long established. Several studies have demonstrated that epigenomic-driven interactions (mediated by architectural proteins like HP1 or PRC1) between loci sharing the same chromatin content are key drivers of the 4D Genome leading to (micro)phase separation and...

1. Multiple-scale polymer model of bacterial chromosomes

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

Supercoiled DNA often adopts tree-like double-folded branching configurations. In this context, we proposed a framework to generate expected bacterial chromosome structures at multiple scales. We built a coarse-grained model of bacterial DNA, which is known to adopt tree-like plectonemic structures due to negative DNA supercoiling. To this end, we extended our previous model of elastic polymer...

8. Poster: Exploring chromatin dynamics in Streptomyces, antibiotic-producing bacteria

Hoda Jaffal (I2BC)

Streptomyces are gram-positive, multicellular, filamentous aerobic bacteria characterized by a large linear chromosome divided into a central region harboring cores genes and two extremities enriched in genomic islands (GIs) such as the specialized metabolite biosynthetic gene clusters (SMBGCs) and prophage. Nevertheless, the majority of GIs remain transcriptionally silent over growth under...

12. Poster: Polymer modelling to investigate yeast’s 3D chromosome organization in S phase and Mitosis

Dario D'Asaro (ENS-lyon)

In Eukaryotes, DNA is tightly packed into a polymer-like structure called chromatin. Chromatin self-organization remains an elusive phenomenon whose impact is extensive in several cells' fundamental processes.
In our project, we focus on the specific problem of how chromatin folding couples with DNA replication dynamics. Taking into account chromosomes' conformation properties is in fact...

17. Poster: Revealing DNA’s topology : A spectral energy approach to loop detection

Michaël Liefsoens (Sorbonne Université)

Loop formation is a crucial aspect of understanding chromatin architecture and its functional role. However, detecting loops remains challenging due to cell population variability and conformation randomness. In this study, we propose a novel approach utilising spectral analysis to identify and quantify loops in experimental conformations obtained through super-resolution imaging. Applying our...

11. Poster: Salmonella chromatin reorganization upon SPI-1 expression

Dr Mounia Kortebi (Institute for Integrative Biology of the Cell (I2BC), Genome Biology Department, Gif-sur-Yvette, France)

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative intracellular bacterium that is a major cause of foodborne gastroenteritis in humans. It has the ability to infect numerous cell types, thanks to a broad arsenal of virulence genes. The majority of the genes encoding the most important virulence factors of S. Typhimurium are located within the highly conserved...

6. Poster: Targeting the 3D genomic and epigenetic changes in Mantle Cell Lymphoma

Anna Karpukhina (Université Paris-Saclay - Institut Gustave Roussy)

Recurrent chromosomal translocations found in most lymphomas frequently lead to overexpression of a certain oncogene, but in many cases, the expression of the oncogene alone does not suffice to produce a malignant phenotype. This is the case in mantle cell lymphoma (MCL), an aggressive B-cell non-Hodgkin lymphoma associated with the t(11;14)(q13;q32) translocation that results in the...

15. Quantitative insights into topoisomerase activity during gene transcription

Ivan Junier (TIMC, Grenoble)

While the feedback between transcription and DNA supercoiling is well understood theoretically and in vitro, it remains to be quantified in vivo. In this talk, I will present our work where we fill this gap by realizing, on a plasmid in Escherichia coli, the conceptual “twin transcriptional-loop model” [1] that is the basis of theoretical and in vitro studies. In particular, we...

7. Reconstitution in vitro of chromatin patterning

Maud Hertzog (CNRS)

Mammalian cells package their genomic DNA into a complex with proteins called chromatin. The assembly and compaction of chromatin are regulated by multiple molecular cues, including DNA modifications, histone post-translational modifications, and histone variants. The spatial partitioning of chromatin into active and inactive domains has also been proposed to be regulated by LLPS. The...

4. STRESSING CHROMATIN, FROM THE CELL TO THE NUCLEOSOME SCALE

Fabrizio CLERI (IEMN University of Lille I)

The physical impact of the nucleus on cellular function becomes evident during migration in 3-D environments. With its large volume and relative rigidity, governed by the nuclear envelope proteins and chromatin organization, the nucleus acts as physical barrier, particularly relevant to immune cells and invading cancer cells. These must move through tissue pores and clefts often smaller than...

10. TANGO II: an integrated framework for 3D bioimage analysis of cell nuclei

Christophe Escudé (Muséum National d'Histoire Naturelle)

The study of nuclear architecture has become an important field of cellular biology. Extracting quantitative data from large sets of 3D fluorescence images helps understanding how the genome is functionaly organized within different nuclear compartments. We present here Tango II, a new image analysis tool for studying nuclear architecture from fluorescence microscopy images. It is based on the...

5. Why chromosomal translocations are cell type-specific?

Yegor Vassetzky (CNRS UMR9018)

Most cancer-related chromosomal translocations appear to be cell type-specific. It is currently unknown why different chromosomal translocations occur in different cells. This can be either due to the occurrence of particular translocations in specific cell types or adaptive survival advantage conferred by translocations only in specific cells. We experimentally addressed this question by...