A5091156775- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Developmental Biology and Gene Regulation
- dental development and anomalies
- RNA Research and Splicing
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genomics and Chromatin Dynamics
- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- Insect and Arachnid Ecology and Behavior
- RNA modifications and cancer
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Invertebrate Immune Response Mechanisms
- Animal Genetics and Reproduction
- Aquaculture disease management and microbiota
- Ichthyology and Marine Biology
- Morphological variations and asymmetry
- Genetics, Aging, and Longevity in Model Organisms
- Insect symbiosis and bacterial influences
- Animal Behavior and Reproduction
- Historical and Literary Analyses
- Retinoids in leukemia and cellular processes
- Protist diversity and phylogeny
Université Claude Bernard Lyon 1
2014-2025
École Normale Supérieure de Lyon
2015-2025
Centre National de la Recherche Scientifique
2012-2023
Inserm
2016-2023
Laboratoire de Biologie et Modélisation de la Cellule
2017-2023
Université de Lyon
2020
Uppsala University
2020
Institut de Génomique Fonctionnelle de Lyon
2009-2016
Structure Fédérative de Recherche Biosciences
2009
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2009
Hagfish and lampreys are the only living representatives of jawless vertebrates (agnathans), compared with jawed (gnathostomes), they provide insight into embryology, genomics, body plan ancestral vertebrate. However, this has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish relatives). Here, we show through deep...
Point mutations result from errors made during DNA replication or repair, so they are usually expected to be homogeneous across all regions of a genome. However, we have found region chloroplast in plants related sweetpea (Lathyrus) whose local point mutation rate is at least 20 times higher than elsewhere the same molecule. There very few precedents for such heterogeneity any genome, and suspect that hypermutable may subject an unusual process as repeated breakage repair. The 1.5 kb long...
Abstract To understand the origin and evolution of isochores—the peculiar spatial distribution GC content within mammalian genomes—we analyzed synonymous substitution pattern in coding sequences from closely related species different orders. In primate cetartiodactyls, GC-rich genes are undergoing a large excess → AT substitutions over substitutions: isochores slowly disappearing genome these two rodents, our analyses suggest both decrease an increase GC-poor isochores, but more data will be...
The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation all key signaling pathways, transcription factors, non-coding RNAs that will enhance ongoing functional studies. member Malacostraca clade, which includes food crop species. analysed immunity related genes as an important comparative these species, where aquaculture problems increased farming has...
Although numerous studies have emphasized the role of microRNAs (miRNAs) in control many different cellular processes, they might also exert a profound effect on macroevolution animal body plans. It has been hypothesized that, because miRNAs increase genic precision and are continuously being added to metazoan genomes through geologic time, be instrumental for canalization development morphological evolution. Nonetheless, an outstanding question remains: how new constantly evolving? To...
Gene order is not random with regard to gene expression in mammals: coexpressed genes, and particular housekeeping are clustered along chromosomes more often than expected by chance. To understand the origin of these clusters quantify impact this phenomenon on genome organization, we analyzed genes human mouse genomes. We show that neighboring experience continuous concerted changes during evolution, which leads formation clusters. The pattern within evolves slowly genomic average. Moreover,...
As paleopolyploid genomes evolve, the expression profiles of retained gene pairs are expected to diverge. To examine this divergence process on a large scale in vertebrate system, we compare Xenopus laevis, which has approximately 40% loci duplicate after recent whole-genome duplication (WGD), with its unduplicated relative Silurana (Xenopus) tropicalis. This comparison ingroup an outgroup allows direction change be inferred for set 1,300 X. laevis pairs, their single orthologs S....
In mouse embryonic cells, ligand-activated retinoic acid receptors (RARs) play a key role in inhibiting pluripotency-maintaining genes and activating some major actors of cell differentiation. To investigate the mechanism underlying this dual regulation, we performed joint RAR/RXR ChIP-seq mRNA-seq time series during first 48 h RA-induced Primitive Endoderm (PrE) differentiation process F9 embryonal carcinoma (EC) cells. We show here that regulation is associated with genomic redistribution...
Synonymous codon usage (SCU) varies widely among human genes. In particular, genes involved in different functional categories display a distinct usage, which was interpreted as evidence that SCU is adaptively constrained to optimize translation efficiency cellular states. We demonstrate here not driven by constraints on tRNA abundance, but large-scale variation GC-content, caused meiotic recombination, via the non-adaptive process of GC-biased gene conversion (gBGC). Expression cells...
Actinopterygian fishes harbor at least eight distinct pigment cell types, leading to a fascinating diversity of colors. Among this diversity, the cellular origin white color appears be linked several types such as iridophores or leucophores. We used clownfish Amphiprion ocellaris, which has pattern consisting bars over darker body, characterize cells that underlie hue. observe by electron microscopy in are similar iridophores. In addition, transcriptomic signature exhibits similarities with...
In the history of life, some phenotypes have been acquired several times independently, through convergent evolution. Recently, lots genome-scale studies devoted to identify nucleotides or amino acids that changed in a manner when evolved. These efforts had mixed results, probably because differences detection methods, and conceptual about definition substitution. Some methods contend substitutions are only if they occur on all branches where phenotype toward exact same state at given...
Regenerating animals have the ability to reproduce body parts that were originally made in embryo and subsequently lost due injury. Understanding whether regeneration mirrors development is an open question most regenerative species. Here, we take a transcriptomics approach examine leg shows similar temporal patterns of gene expression as embryo, crustacean Parhyale hawaiensis. We find stereotypic expression. In contrast, dynamics during show higher degree variation related physiology...
It is now clear that a whole-genome duplication (WGD) occurred at the base of teleost fish lineage. Like other anciently polyploid genomes investigated so far, behave like diploids with chromosomes forming pairs meiosis. The diploidization process currently poorly understood. associated many gene deletions, such one duplicates lost most loci and has also been proposed to coincide an increase in genomic instability. Here we ask whether WGD determinant rearrangement rate teleosts. We study...
Acquisition of new ecological opportunities is a major driver adaptation and species diversification [1Losos J.B. Lizards in an Evolutionary Tree: Ecology Adaptive Radiation Anoles. University California Press, 2009Crossref Google Scholar, 2Mayr E. Animal Species Evolution. Belknap Press Harvard 1963Crossref 3Schluter D. The Radiation. Oxford 2000Google 4Yoder Clancey Des Roches S. Eastman J.M. Gentry L. Godsoe W. Hagey T.J. Jochimsen Oswald B.P. Robertson J. et al.Ecological opportunity the...
Mammalian chromosomes are characterized by large-scale variations of DNA base composition (the so-called isochores). In contradiction with previous studies, Lercher et al. (Hum. Mol. Genet., 12, 2411, 2003) recently reported a strong correlation between gene expression breadth and GC-content, suggesting that there might be selective pressure favoring the concentration housekeeping genes in GC-rich isochores. We reassessed this issue examining human mouse using different measures (EST, SAGE...
It has been proposed that the synonymous codon usage of human tissue-specific genes was under selective pressure to modulate expression proteins by codon-mediated translational control (Plotkin, J. B., H. Robins, and A. Levine. 2004. Tissue-specific genes. Proc. Natl. Acad. Sci. USA 101:12588–12591.) To test this model, we analyzed internal correspondence analysis 2,126 expressed in 18 different tissues. We confirm differs significantly between However, effect is very weak: variability...
Both the monophyly and inter-relationships of major annelid groups have remained uncertain, despite intensive research on both morphology molecular sequences. Morphological cladistic analyses indicate that Annelida is monophyletic consists two groups, clitellates polychaetes, whereas phylogenetic suggest polychaetes are paraphyletic sipunculans crown-group annelids. placement within annelids in conflict with fossil record—the former because Cambrian stem taxa similar to modern possessing...
The fish order Cypriniformes is one of the most diverse ray-finned groups in world with more than 3000 recognized species. are characterized by a striking distribution their dentition: namely absence oral teeth and presence pharyngeal on last gill arch (fifth ceratobranchial). Despite this limited localisation, diversity tooth patterns astonishing. Here we provide further description using X-ray microtomography map resulting dental characters phylogenetic tree to explore evolutionary...
Mice have evolved a new dental plan with two additional cusps on the upper molar, while hamsters were retaining ancestral plan. By comparing dynamics of molar development transcriptome time series, we found at least three early changes in mouse development. Together, they redirect spatio-temporal to ultimately form cusps. The lower has undergone much more limited phenotypic evolution. Nevertheless, its developmental trajectory as that and co-evolved it. Among coevolving changes, some are...
ABSTRACT Although it is well established that certain stages of development are more conserved than others, the reasons for this phenomenon remain largely unknown. We study molecular conservation in an organ, molar, by comparing temporal profiles expression mice and hamsters. find molar characterized a rarely observed pattern level coding sequences forming inverse hourglass, with at beginning end morphogenesis intermediate stages. As rodent described, we were able to link properties...
Pleiotropy, which can occur when a gene affects multiple traits, is central property of living organisms, influencing their response to mutations and evolutionary trajectories. Despite many studies discussions, it remains very difficult reconcile molecular, developmental quantitative genetics viewpoints on pleiotropy appreciate how much puts constraints genetic evolution, phenotypic evolution adaptation. Here, we revisit this question by simulating in silico. Our model captures levels...