DNA break repair by homologous recombination (HR) entails a search for homology carried out by a specialized nucleoprotein filament (NPF). The search mechanism remains elusive, notably its interplay with the folding of chromatin in the nucleus. We show in the tractable model system S. cerevisiae that it takes place in the reorganized context of individualized metaphase-like chromosomes...
Chromosome conformation capture (3C/Hi-C)-based methods have been used extensively to probe the average 3D organization of genomes, revealing fundamental aspects of chromosome dynamics. However, when applied to prokaryotic and archaeal species the current protocols are expensive, inefficient, and limited in their resolution. We developed a cost-effective approach that allows the exploration of...
In E. coli, Topoisomerase IV is responsible for the untangling of catenanes that are formed during the replication of the chromosome and has been shown to play an essential role in nucleoid segregation. Previous studies have shown that alterations in Topo IV result in a prolonged interaction between sister chromosomes leading to poor chromosome segregation and a loss ...
Usual models of transcriptional regulation are centered on transcription factors, which recognize specific sequences in genes’ promoters. However, at a more global scale, the physical state of the double helix, embedded in the chromatin fibre, plays a crucial role in genes’ expression in vivo. In particular, torsional stress (or DNA supercoiling) is an ubiquitous feature in DNA transactions,...
The spatial configuration of the eukaryotic genome is organized and dynamic,
providing the structural basis for regulated gene expression in living cells. In Drosophila melanogaster , 3D genome organization is characterized by the phenomenon of somatic homolog pairing, where homologous chromosomes are intimately paired from end to end. While this organizational principle has been recognized...
In most eukaryotic cells, DNA is packed into the chromatin « bead on string » filament of nucleosomes, formed by 145–147 bp DNA wrapped into 1.65 turns of a left-handed superhelix around a histone octamer. Atomic resolution structures have been obtained from X-ray crystallography, and more recently from cryo-EM of identical, symmetric and highly stable engineered particles, which has led,...
Cellular identity is conferred by specific gene expression profiles that are regulated by transcription factors and chromatin. Combination of specific histone modifications characterize gene activity. Active genes typically display an enrichment in histone H3 lysine 4 trimethylation (H3K4me3) at their promoters, whereas SET Domain 2 (SETD2) trimethylates histone H3 lysine 36 (H3K36me3) in...
Past decade has shown that the cohesin is essential for the regulation of mammalian’s genomes 3D organization. Cohesin is a ring-shaped complex that interacts with three related hook-shaped proteins composed of HEAT repeats namely Pds5, Scc3/STAG and Scc2/Nipbl that regulate its functions. Cohesin shapes mammalian genomes by establishing chromatin loops along chromosomes, most likely through...
Chromosome conformation capture (3C) methods are a powerful tool for uncovering 3D genome organization. Short-read Illumina sequencing restricts 3C to the description of average conformations within large cell populations. Significant variation between individual cells within the same population may be present though. For instance, if different contacts happen simultaneously, exclusively, or...
Within the nucleus, heterochromatin domains segregate in particular compartments such as the chromocenters that contain pericentromeric heterochromatin (PCH) regions, or the lamina-associated domains (LADs) that localize at the periphery of the nucleus. In most cell types, DNA methylation is essential for heterochromatin formation, directly contributing to the transcriptional repression of DNA...
L’architecture tridimensionnelle des génomes eucaryotes joue un rôle important dans leur régulation fonctionnelle. Le développement de méthodes de capture de la conformation chromosomique, telles que le Hi-C, a mis en évidence l'existence de deux compartiments appelés A et B, séparés dans l'espace, qui correspondent respectivement à l'euchromatine (gènes exprimés) et à l'hétérochromatine...
