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The LBBE supports the 12th Symposium de Morphométrie et Evolution des Formes, which will take place in Dijon on June 5-7, 2024.
The local protein composition of chromatin controls important processes such as transcription, replication and DNA repair, yet the diversity of chromatin and its distribution along chromosomes is still poorly characterized.Using DamID in Drosophila Kc cells, we generated high-resolution genome-wide binding maps of 53 chromatin proteins from a wide range of functional categories. For most of those proteins, no binding data was previously available.By constructing a non supervised classifier, we find that there are five principal chromatin types defined by unique yet overlapping combinations of proteins.Two types correspond to Polycomb and HP1-bound regions, respectively. The novel 'BLACK' chromatin type covers half of the genome and induces strong transcriptional repression on inserted transgenes. Remarkably, this chromatin type is devoid of the classic 'heterochromatin' proteins Polycomb and HP1. Thus, our data reveal the existence of a prominent repressive chromatin type that has largely been overlooked.Active genes are associated with one of the other two remaining combinations of proteins. H3K36 methylation is associated with only one of them, yet it was previously thought to mark every transcribed gene. In addition, active genes involved in growth and cell proliferation, and those involved in signal transduction are located in a distinct chromatin types.The five chromatin types modulate the interactions of transcription factors with DNA. We observe that most transcription factors bind their cognate motif only if it sits in the favored chromatin context. Our data rule out a simple exclusion mechanism but support a model whereby synergistic interactions target transcription factors to their binding site.Finally, genomic regions in the 5 chromatin types follow different evolutionary processes. The vast majority of synteny breaks with Drosophila pseudoobscura occurs in only one of the transcriptionally active types. Besides, the speed of evolution of genes located in that chromatin type is higher than for other types.In summary, our integrative approach identifies five major chromatin types, which are defined by unique combinations of proteins and have distinct functional properties.
The reduction of DNA sequencing costs over recent years has enabled whole genome sequencing to become relatively affordable for most organisms. However, sequencing many individuals, from multiple populations can still be financially limiting and require extensive computational power. Since its development in 2008, restriction-site associated DNA (RAD) sequencing has offered an effective method for sampling non-random, interspersed sequences across a genome. In brief, the approach involves digesting genomic DNA with a restriction enzyme, ligating adapters to these sites and sequencing the fragments with illumina technology. Publications based on the RAD method have addressed many biological questions ranging from population genetics to linkage mapping and phylogeography, using 10's or 100's of individuals from broods or wild collections. Here I will provide an overview of the RAD method, and highlight various approaches to analyze RAD datasets. Data generated by myself and colleagues, from tropical butterflies, pest moths and polymorphic ladybirds, will be presented to demonstrate our approach for assembling genetic linkage maps (with and without a reference genome), bulked segregant analysis, genome wide phylogenies and comparative genomics. Although there are both benefits and drawbacks to RAD sequencing, it is a universal genetic approach that could be considered for many organisms.
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Bumble bees are one of our most important wild pollinators, and populations are declining globally. Causes of decline appear to vary geographically. In Europe, for example, the proposed drivers are climate change, loss of floral resources and pesticides. In North America, however, a widely accepted hypothesis suggested that contact with an exotic European strain of fungal pathogen, Nosema bombi, was the sole cause of a precipitous decline. We have tested this exotic pathogen hypothesis using multiple genetic and genomic tools.
The study of predator-prey behavior is of primary importance to the field of ecology. However, few studies measure interactions between predators and their most dangerous prey. Our team used long-term datasets from Yellowstone National Park and Scandinavia to evaluate 1) the role of cooperative hunting in the ability of predators to hunt dangerous prey, 2) how predator preference for differentially dangerous prey species changes in relation to their relative abundance, and 3) how the kill rate of a top predator was affected by the presence of another. We found that 1) wolves (Canis lupus) were more cooperative when hunting bison (Bison bison), their most dangerous North American prey, than when hunting elk (Cervus elaphus). 2) Contrary to the prey switching hypothesis, wolves in northern Yellowstone attacked and killed disproportionately more of the rarer, but safer species; wolves maintained a strong preference against bison, even when this species was more than twice as abundant as elk. Analyses of wolf-bison behavioral interactions indicate that wolf preference against bison reflected an inability to consistently overcome bison antipredator defenses. 3) Finally, although brown bears (Ursus arctos) can monopolize wolf kills, we found no support in either Yellowstone or Scandinavia for the common assumption that brown bears cause wolves to kill more often. On the contrary, our results showed the opposite effect, suggesting that brown bear presence actually reduces wolf kill rate. One potential explanation for decreased wolf kill rate is the energetic costs associated with prematurely abandoning a kill to hunt dangerous prey. This research contributes to the current body of work addressing the effects of wolf reintroduction in Yellowstone, and sheds light on the behavioral relationships at play in a special type of predator-prey interaction: predators that hunt dangerous prey.