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Daniel Jost (Laboratoire de Physique, ENS Lyon)
Modeling 3D genome organisation has been booming in the last years thanks to the availability of experimental datasets of genomic contacts. However, the field is currently missing the standardisation of methods and metrics to compare predictions and experiments. We present 3DGenBench, a web server available at https://inc-cost.eu/benchmarking/, that allows benchmarking computational models of...
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Ivan Junier (TIMC)
In bacteria, genetic context can have significant impact on gene expression but is currently not integrated in quantitative models of gene regulation despite known biophysical principles and quantitative in vitro measurements. Conceptually, the simplest genetic context consists of a single gene framed by two topological barriers, also known as the twin transcriptional-loop model, which...
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Prof. Angelo Rosa (Scuola Internazionale Superiore di Studi Avanzati (SISSA))
The spatial conformation of chromatin within the nucleus is of the uttermost importance for transcriptional regulation and therefore for phenomena such as cell differentiation. In particular, epigenetic modifications play a crucial role as they are believed to affect the spatial folding and the accessibility of the genome to transcription factors and proteins.
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Understanding and quantifying... -
Jose Gil Jr (Institut Curie - UMR3664)
The centromere’s primary role is to ensure chromosome segregation by catalyzing the formation of the kinetochore complex to promote attachment between spindle fibers and chromosomes during cellular division. In addition to this well-known function, centromeres are classic examples of chromosome regions known to impact the regulation and spatial architecture of the surrounding genome (Muller,...
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Kiran Padmanabhan (IGFL ENS Lyon)
Mammalian circadian oscillators are built on a feedback loop where the activity of the transcription factor CLOCK:BMAL1 is repressed by the PER-CRY complex. We found that Per deficient cells displayed altered nucleosome occupancy around transcription start sites (TSS) and at promoter-proximal and distal CTCF sites in the genome. This chromatin re-organization was coincident with a significant...
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Marc Joyeux (LIPHY (CNRS et Université Grenoble Alpes))
The mechanism responsible for the organization of bacterial DNA inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small fraction of the cell, although it is not separated from the rest of the cytoplasm by any membrane and would occupy a volume about thousand times larger outside from the cell....
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Prof. Mikhail Eltsov (Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC))
Folding of nucleosome chains influences DNA availability for functional interactions necessary for the regulation of transcription, DNA replication and repair. Despite the existing models based on studies in vitro, the nucleosome chain geometry within the crowded cell nucleus has remained elusive. Cryo-electron tomography (Cryo-ET) is the only method that provides a sufficient resolution to...
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Jiachuan BAI (Imaging and Modeling Unit, Institut Pasteur, Paris, France)
Single-molecule localization microscopy (SMLM) is a powerful super-resolution imaging technique that can image biological structures at near-molecular scales (resolutions down to ~20 nm or better), enabling broad applications in the life sciences. With standard reconstruction methods, SMLM typically requires ~10⁴-10⁵ low-resolution frames to generate a single super-resolution image, hence the...
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Jérémy Lebreton (ENS de Lyon, LBMC)
RNAs and transcription are emerging as important players in chromosome assembly and dynamics. Although the idea of a rigid and stable RNA scaffold has now been abandoned, several lines of evidence suggest that RNA form a dynamic mesh that controls chromatin structure. Moreover, transcription has been identified as a roadblock for SMC loop extruders such as Condensin, and the activity of RNA...
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Ànnia Carré Simon
The genome is susceptible to multiple damages, including DNA double-strand breaks (DSBs) and replication stress. Chromosome configuration of the Saccharomyces cerevisiae plays a critical role in maintaining genome integrity upon damage, as only DSBs near pericentromeres cause an increase in global mobility, protective for the genome (1). Here, we want to understand what makes the...
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Kévin Tartour (IGFL ENS Lyon)
In eukaryotes, DNA is wrapped around histones to form nucleosomes, the building blocks of chromatin. The condensation of the genome is not the only function of this organization and chromatin acts as a substrate of many processes: replication, transcription, DNA reparation. Even if most of the genome is thought to be covered by nucleosomes, physical modeling predicts some nucleosome...
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Pascal BERNARD (LBMC, CNRS & ENS-Lyon)
A conserved, yet incompletely understood, principle in living organisms is the folding of the genome into loops by DNA-translocases of the SMC family1. Upon mitotic entry, the condensin SMC complex binds DNA and shapes metaphase chromosomes by folding chromatin into loops, in preparation for genome segregation in anaphase. How condensin achieves this task remains unclear. The active extrusion...
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Kharerin Hungyo
The eukaryotic genome is packaged inside nucleus by histone octamers that bind with DNA forming a basic repeating structural unit called nucleosomes—about 147 base-pairs (bp) of DNA is wrapped around the histone octamer. Recent evidence suggests existence of stable sub-size nucleosomes < 147 bp. This may be due to the fact that the DNA ends of the nucleosomes can unwrap and rewrap. Indeed it...
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Jean-michel Arbona (ENS-Lyon)
The positioning and strength of origin of DNA replication in human are still poorly defined. Origins are licensed in G1 phase and fired in S phase of the cell cycle. Experiments can independently profile mean replication timing (MRT) and replication fork directionality (RFD) genome-wide. Such profiles contain information on multiple origins’ properties and on fork speed. Due to possible origin...
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Yasmina Djeghmoum
Homologous recombination is a template-dependent DNA double-strand break repair mechanism. A key step of HR is DNA strand invasion, which consists of the pairing of the single-stranded DNA flanking the break site to a complementary strand in a homologous double-stranded DNA (dsDNA) leading to the formation of a DNA joint molecule called a D-loop. D-loop metabolism is likely central in the...
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Dr Aurele Piazza (ENS Lyon)
Abstract
Homologous recombination (HR) templates DNA double-strand break (DSB) repair off an intact homologous dsDNA “donor” molecule, which can exist in the form of a sister chromatid, a homologous chromosome, or dispersed repeats. HR fidelity partly depends on this competitive donor selection process, which embeds homology sampling by the RecA/Rad51-ssDNA nucleoprotein filament...
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Fabian Erdel (CBI Toulouse)
Despite the tremendous progress in studying biomolecular condensates, it remains a challenge to reliably detect and quantify condensates produced by liquid-liquid phase separation (LLPS) in living cells. In particular, liquid droplets produced by LLPS and stretches of chromosomes decorated with nuclear proteins that do not undergo LLPS can share several properties, like an appearance as ‘foci’...
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hossein salari (Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon)
It is well known that the enhancer-promoter interactions are essential for gene expression, but the role of RNA Polymerase II (Pol II)-mediated activity on genome folding is remain controversial. Here by investigating Micro-C data for mESCs and Drosophila embryo, we show a significant correlation between gene compaction and Pol II occupancy inside the gene, independent of cohesin-dependent...
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Simon Grosse-Holz (Institut Curie & MIT)
The DNA in a cell’s nucleus is intricately structured across 4 orders of magnitude in space. Over the past decade, our understanding of these structures has advanced tremendously, but remains constrained to static snapshots. I will discuss two recent approaches that go beyond the static picture using fluorescence microscopy in live cells. By observing the interaction of two genomic loci on the...
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Maïwenn PINEAU
DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level is mainly regulated by topoisomerase I and DNA gyrase. Inhibiting either of these enzymes with antibiotics leads to global supercoiling modifications and subsequent changes in global gene expression. In previous studies, genes responding to DNA relaxation induced by gyrase inhibition were categorised as...
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