Huitième réunion annuelle du GdR Architecture et Dynamique Nucléaires (ADN)

Liste des abstracts

30. Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps

M. Léopold Carron (LPTMC)

Abstract
Motivation

Genome-wide chromosomal contact maps are widely used to uncover the 3D organization of genomes. They rely on collecting millions of contacting pairs of genomic loci. Contacts at short range are usually well measured in experiments, while there is a lot of missing information about long-range contacts.
Results

We propose to use the sparse information contained in raw...

32. Chromosome structuring versus genome organisation in bacteria

M. Ivan Junier (TIMC-IMAG, Grenoble)

I will present results about the relationship between the hierarchical structuring of bacterial chromosomes observed in HiC experiments and the 1D functional partitioning of genomes obtained from comparative genomics.

42. CTCF binding controls the expression of imprinted Dlk1-Dio3 and Igf2-H19 loci by structuring allele-specific sub-domains

Benoît Moindrot (I2BC / Université Paris-Sud)

Mammalian genome are organized into structural units known as Topological Associating Domains (TADs), with CTCF protein being enriched at their borders. Mammalian genomic imprinting provides a unique paradigm to explore intra-cellular differences in chromatin 3D-structuration.
In this presentation, I will focus on the two conserved paternally-imprinted domains in mammals, the Igf2-H19 and...

34. Emergence of the spatio-temporal replication program: from 1D signals to 3D chromatin structures

Jean-michel Arbona (ENS-Lyon)

In the last few years, several models of the spatio-temporal replication program in eukaryotic cells were proposed in the literature. We proposed a simpler model with natural hypothesis that reproduces the frequency of new replication origin firing per length of unreplicated DNA along the S-phase, I(t), a fundamental quantity which present a universal bell shape in eukaryotes. Our model also...

33. From open large image datasets to scientific insights in developmental biology

Paul Villoutreix (Turing Center for Living Systems - LIS)

Embryogenesis is the process by which a single fertilized cell is turned into a multi-cellular organism. It is a process involving coordinated dynamics at multiple scales, from single molecules, to cells, to tissues, to organs. Dynamical processes in biology are studied using an ever-increasing number of microscopy techniques, each of which brings out unique features of the system. To learn...

36. Global and ancestral regulation of bacterial transcription by DNA supercoiling

Sam Meyer (MAP, INSA Lyon)

DNA supercoiling acts as a global and ancestral transcriptional regulator in bacteria, that plays an important role in adapting their expression program to environmental changes, but for which no quantitative or even qualitative regulatory model is available. I will present two quantitative thermodynamic models of (1) promoter binding by the RNA Polymerase and (2) promoter opening during...

40. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

Yad Ghavi-Helm (CNRS)

Chromatin topology is intricately linked to gene expression, yet its functional requirement remains unclear. We comprehensively assessed the interplay between genome topology and gene expression using highly rearranged chromosomes (balancers) spanning ~75% of the Drosophila genome. Using transheterozyte (balancer/wild-type) embryos, we measured allele-specific changes in genome topology and...

27. Modeling heterochromatin reorganization during senescence

Dr Daniel Jost

I will present our last results regarding the reorganization of heterochromatin during oncogene-induced senescence. Using polymer physics models in addition to microscopy and Hi-C data from the Cavalli's lab, we show that the formation of heterochromatic foci during senescence may be interpreted as a general screening of of HP1-mediated interactions.

37. Molecular dynamics insights for DNA lesions in oligonucleotides and nucleosomal DNA

Elise Dumont (LCH, UMR 5182, ENS de Lyon)

The identification of complex oxidatively-generated DNA lesions involving not only a single-nucleobase but two proximal nucleotides has recieved much attention over the last years since such lesions are formed with a very low occurrence (typically a few lesions per 10^9 nucleotides) but turn out to be highly mutagenic. The structural elucidation of such complex lesions is extremely...

29. Nuclear Beta-Actin and Nuclear Myosin I are required for rDNA/RNAP1 repositioning within the nucleolus after rDNA repair.

Ambra Giglia-Mari (CNRS)

During DNA Repair, ribosomal DNA and RNA polymerase I (rDNA/RNAP1) are reorganised within the nucleolus and undergo relatively long-distance movements that are normally not observed except when cells are in mitosis.

UV lesions trigger the DNA repair reaction, blocking RNAP1 transcription and displacing the rDNA/RNAP1 complex at the periphery of the nucleolus. Because most repair proteins are...

35. Probing genome organization with intra-nuclear mechanical micro-manipulation

Antoine Coulon (Institut Curie)

Over the past decades, our understanding of the physical organization of the genome has improved tremendously. Developments in imaging and chromatin conformation capture have uncovered how eukaryotic chromosomes are structured at different scales (territories, compartments, TADs, loops) and how each level of organization relates to genome functions. A lot of effort is currently put on...

39. Studying the effects of single mutations on nucleosome positioning with deep neural network.

Etienne Routhier (LPTMC Sorbonne Université)

The MNase protocol makes it possible to experimentally study the positioning of the nucleosomes along the genome. Studying the effects of point mutations on this positioning can help us to understand how the DNA sequence encodes nucleosomes positions.
We propose to use deep neural networks to provide a tool to study the effect of single mutations at a genome wide scale . We trained a deep...

31. Séparation de phase de protéines liées à l’ADN

Gabriel David (Laboratoire Charles Coulomb, Université de Montpellier)

Le confinement des espèces chimiques à l’intérieur du cytoplasme est capital pour l’organisation spatio-temporelle de l’activité cellulaire. Les cellules compartementalisent en effet l’espace cytoplasmique en utilisant soit des vésicules membranaires soit des organelles sans membranes. Pour ces dernières, les cellules peuvent utiliser la séparation de phase pour créer des régions localisées à...

28. Viral transactivators shape the nucleus of human B-cells for oncogenesis

Dr Yegor Vassetzky (CNRS UMR8126)

Recently we discovered a novel mechanism explaining how B-cell lymphomas might be induced in HIV-infected persons. HIV-positive subjects have an increased risk to develop specific lymphoma subtypes including Burkitt lymphoma (BL). We found that the viral transactivator of transcription (Tat) protein, which is released by infected cells into the blood stream, could remodel the B-cell nucleus...