Biology subjects

Bignaud, A.

Publications and source records attributed to Bignaud, A..

5 recordsLinked to original sources

bioRxiv2025

Replication coordination marks the domestication of large extrachromosomal replicons in bacteria

Bacterial genomes often include extrachromosomal replicons (ERs), ranging from small plasmids to nearly chromosome-sized elements, that foster genome plasticity and adaptation. Despite their prevalence, the mechanisms underlying ER domestication and their long-term adaptation within bacterial hosts remain largely unexplored. By analyzing over 40,000 complete bacterial genomes, we identified two main ER categories: small ERs with diverse GC content and large ERs ([≥]10% the size of the main chromosome) that closely match the GC content of the chromosome. Across multiple phyla, marker frequency analyses showed that large ERs maintain a 1:1 copy number with the chromosome. Another key finding of this study is that large ERs terminate replication in synchrony with the chromosome. Hi-C contact maps revealed consistent ori-ori interactions between chromosomes and ERs. In large ERs, inter-replichore and ter-ter interactions, along with the recruitment of key chromosomal segregation motifs, suggest the co-option of chromosome-associated replication and segregation machineries. Together, our findings indicate that as ERs become larger, they become increasingly reliant on chromosome-driven processes for stable inheritance, potentially explaining why they do not exceed the size of the chromosome.

microbiology↗

bioRxiv2023

Chromosome-level genome assembly of the European Green woodpecker Picus viridis

The European Green Woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here we assembled a highly contiguous genome assembly for this species using a combination of short and long reads sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a [~]30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the Picus viridis genome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers.

genomics↗

bioRxiv2022

Exogenous chromosomes reveal how sequence composition drives chromatin assembly, activity, folding and compartmentalization

Genomic sequences co-evolve with DNA-associated proteins to ensure the multiscale folding of long DNA molecules into functional chromosomes. In eukaryotes, different molecular complexes organize the chromosomes hierarchical structure, ranging from nucleosomes and cohesin- mediated DNA loops to large scale chromatin compartments. To explore the relationships between the DNA sequence composition and the spontaneous loading and activity of these DNA-associated complexes in the absence of co-evolution, we characterized chromatin assembly and activity in yeast strains carrying exogenous bacterial chromosomes that diverged from eukaryotic sequences over 1.5 billion years ago. We show that nucleosome assembly, transcriptional activity, cohesin-mediated looping, and chromatin compartmentalization can occur in a bacterial chromosome with a largely divergent sequence integrated in a eukaryotic host, and that the chromatinization of bacterial chromosomes is highly correlated with their sequence composition. These results are a step forward in understanding how foreign sequences are interpreted by a host nuclear machinery during natural horizontal gene transfers, as well as in synthetic genomics projects.

genetics↗

bioRxiv2022

Transcriptional units form the elementary constraining building blocks of the bacterial chromosome

Transcription generates local topological and mechanical constraints along the DNA fiber, driving for instance the generation of supercoiled chromosomal domains in bacteria. However, the global impact of transcription-based regulation of chromosome organization remains elusive. Notably, the scale of genes and operons in bacteria remains well below the resolution of chromosomal contact maps generated using Hi-C (~ 5 - 10 kb), preventing to resolve the impact of transcription on genomic organization at the fine-scale. Here, we combined sub-kb Hi-C contact maps and chromosome engineering to visualize individual transcriptional units (TUs) while turning off transcription across the rest of the genome. We show that each TU forms a discrete, transcription-induced 3D domain (TIDs). These local structures impose mechanical and topological constraints on their neighboring sequences at larger scales, bringing them closer together and restricting their dynamics. These results show that the primary building blocks of bacteria chromosome folding consists of transcriptional domains that together shape the global genome structure.

microbiology↗

bioRxiv2022

Chromosome folding and prophage activation reveal gut-specific genome dynamics of bacteria in the OMM12 consortium

Bacteria and their viruses, bacteriophages, are the most abundant entities of the gut microbiota, a complex community of microorganisms associated with human health and disease. In this ecosystem the interactions between these two key components are still largely unknown. In particular, the impact of the gut environment on bacteria and their associated prophages is yet to be deciphered. To gain insight into the activity of lysogenic phages within the context of their host genomes, we performed Hi-C on the 12 strains of the OMM12 synthetic bacterial community stably associated within mice gut (gnotobiotic mouse line OMM12) in both in vitro and in vivo conditions. High-resolution contact maps of the chromosome 3D organization of the bacterial genomes revealed a wide diversity of architectures, differences between environments and an overall stability over time in the gut of mice. The DNA contacts also pointed at 3D signatures of prophages leading to predict 16 of them as functional. We identified circularization signals and observed different 3D patterns depending on the condition. Concurrent virome analysis showed that 11 of these prophages produced viral particles in vivo and/or in vitro, and that OMM12 mice do not carry other intestinal viruses. By predicting functional prophages, the Hi-C approach unlocks the study of phage-bacteria interaction dynamics.

microbiology↗