Meiosis is the specialized, highly regulated process at the basis of the sexual reproduction of eukaryotes. During this process, a diploid cell undergoes a single round of DNA replication and two successive rounds of chromosome segregation, halving the chromosome set to generate four haploid products (gametes). Homologous (i.e. paternal and maternal) chromosomes during the prophase of the first division of meiosis undergo a highly regulated succession of events that include recognition, pairing, and synapsis along their length. An important aspect of chromosome organization, besides pairing and synapsis, consist in the condensation step: axial elements form between sister chromatids, bridging distant axis sites comprising cohesins, and resulting in the extrusion of chromatin loops away from the axis. The precise organization of these chromatin loops remain unclear, and is notably impaired by the sequence similarities of the two homologs. Our aim is to characterize the fine organization of chromatin on both homologs during meiotic prophase, and how this organization is functionally related to a recombination event.

Our aim is to characterize the fine organization of chromatin on homologs during meiotic prophase, and how this organization is functionally related to recombination.

Hi-C contact maps reflect the relative contact frequencies between pairs of genomic loci, quantified through deep-sequencing. Differential analyses of these maps facilitate downstream biological interpretations. However, the multi-fractal nature of the DNA polymer inside the cellular envelope results in frequency values spanning several orders of magnitude: contacts involving loci pairs at large genomic distance are much sparser compared to closer pairs. The same is true for poorly covered regions such as telomeres and repeated sequences. Poor coverage translates into low signal-to-noise ratios. There is no clear consensus to address this limitation. We present a fast, flexible procedure operating on simple data that takes into account the contacts in each region of a contact map. Binning is performed only when necessary on noisy regions, preserving informative ones. This results in high-quality, low-noise contact maps that can be conveniently visualized for rigorous comparative analyses.

With an estimated 1031 particles on earth, bacteriophages are the most abundant genomic entities across all habitats and important drivers of microbial communities. Growing evidence suggest that they play roles in intestinal human microbiota homeostasis, and recent metagenomics studies on the viral fraction of this ecosystem have provided crucial information about their diversity and specificity. However, the bacterial hosts of this viral fraction, a necessary information to characterize further the balance of these ecosystems, remain poorly characterized. Here we unveil, using an enhanced metagenomic Hi-C approach, a large network of 6,651 host-phage relationships in the healthy human gut allowing to study in situ phage-host ratio. We notably found that half of these contigs appear to be sleeping prophages whereas ¼ exhibit a higher coverage than their associated MAG representing potentially active phages impacting the ecosystem. We also detect different candidate members of the crAss-like phage family as well as their bacterial hosts showing that these elusive phages infect different genus of Bacteroidetes. This work opens the door to single sample analysis and concomitant study of phages and bacteria in complex communities.

New mouse genetic reference populations obtained from 8 distinct founder strains, including 3 wild-derived strains, have been developped since the 2000s and are now available. These populations captured around 95% of the existing murine genetic diversity and constitute a better model than standard inbred laboratory mouse strains. These populations constitute tools to identify new phenotypes and to map the causative genetic variants (QTL mapping) behind these phenotypes. These populations include : i) Collaborative Cross (CC) inbred strains; ii) Recombinant inbred between CCs (CC-RIXs) and iii) Diversity Outbred. These populations are specifically used in the Mouse Genetics Laboratory to identify new variants involved in host susceptiblity differences to pathogens.