I am a postdoctoral researcher curious about the molecular processes that underlie the differences between species. I’m particularly interested in the study of the mechanisms driving variations in gene expression in vertebrates.
The aim of my PhD was to conjointly analyse the evolution of cis-regulatory elements, such enhancers, and the evolution of gene expression in several vertebrate species. A major challenge of this work was to identify the associations between cis-regulatory sequences and gene promoters. I achieved this using chromosome conformation capture data, which allows an experimental measurement of the structure of cis-regulatory landscapes. I compared regulatory sequences, their organisation in genomes and their physical contacts with genes between several cell types and different vertebrate species. I was able to link the evolution of cis-regulatory landscapes and gene expression patterns, using gene expression measurements taken at various stages of human and mouse development. I also took part in the development of a bioinformatic tool that predicts functions of cis-regulatory elements based on the genes they contact.
In my post-doc, I am currently working on the development of a method to systematically detect signatures of positive selection in cis-regulatory sequences. I am working with mammalian whole genome alignments, experimental data of transcription factor binding and substitution models of molecular evolution. The aim is to assess the contribution of positive selection on these non-coding sequences to the evolution of gene expression patterns leading to phenotypic adaptation.
Education
2018 - 2022: PhD in gene expression and genome evolution, Université Claude Bernard Lyon 1, Lyon, France
2016 - 2018: MSc in Biology, Ecology and Evolution, Université de Montpellier, France
2013 - 2016: BSc in Ecology and Biology of Organisms, Université de Montpellier, France
Research Experience
2022 - Now: Assistant professor, “Selection on gene expression at different time scales and vertebrates Evo-Devo”.
Robinson-Rechavi Group - Evolutionary Bioinformatics, Department of Ecology and Evolution, Université de Lausanne (UNIL), Switzerland.
Supervisors: Marc Robinson-Rechavi
2018 - 2022: PhD student, “Relationship between cis-regulatory landscapes evolution, gene expression evolution and phenotypic evolution in vertebrates”.
Laboratoire de Biométrie et Biologie Evolutive (LBBE), Equipe Bioinformatique, Phylogénie et Génomique Evolutive, Université de Lyon, France
Supervisors: Anamaria Necsulea and Éric Tannier
2018: MSs Internship (6 months), “Interplay between the regulatory landscape of gene expression and the large-scale evolution of mammal genomes”.
Laboratoire de Biométrie et Biologie Evolutive (LBBE), Equipe Bioinformatique, Phylogénie et Génomique Evolutive, Université de Lyon, France
Supervisors: Anamaria Necsulea and Éric Tannier
2017: MSs Internship (4 months), “Estimation of the adaptive substitution rate in the presence of biased gene conversion to GC in Galloanserae”.
Institut des Sciences de l'Évolution (ISEM), Phylogeny and Molecular Evolution Team, Montpellier, France
Supervisors: Nicolas Galtier and Marjolaine Rousselle
GOntact : using chromatin contacts to infer Gene Ontology enrichments for cis-regulatory elements, Alexandre Laverré, Eric Tannier, Philippe Veber, Anamaria Necsulea, bioRxiv, DOI:10.1101/2022.06.13.495495
Long-range promoter-enhancer contacts are conserved during evolution an contribute to gene expression robustness, Alexandre Laverré, Eric Tannier, Anamaria Necsulea, Genome research 32 (2), 280-296, DOI: 10.1101/gr.275901.121
Influence of recombination and GC-biased gene conversion on the adaptive and nonadaptive substitution rate in mammals versus birds, Marjolaine Rousselle, Alexandre Laverré, Emeric Figuet, Benoit Nabholz, Nicolas Galtier, Molecular biology and evolution 36 (3), 458-471, DOI:10.1093/molbev/msy243