Clémentine VITTE

Transposable elements evolutionary genomics and epigenomics

 CNRS, Principal Investigator

 clementine.vitte@inrae.fr —   +33 (0)1 69 33 23 57


 Genomics, Evolution and Adaptation of Domesticated plants

Implication de Clémentine Vitte dans axe1 80% axe1 Understanding and shedding light on evolutionary mecanisms Axe1 Implication de Clémentine Vitte dans axe2 20% axe2 Understanding and predicting the genetic bases of interactions Axe2 Implication de Clémentine Vitte dans axe3 0% axe3 Understanding and mobilizing cultivated diversity to provide solutions for agriculture and its actors Axe3
 Publications    

  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • IDEEV
  • 12 route 128
  • 91190 Gif-sur-Yvette
Clémentine VITTE

Research interests

My main research interest is to understand the contribution of transposable elements (TEs) to plant genome evolution. After analyzing the dynamics of transposable elements in diverse plant genomes and their impact on plant genome size variation in a phylogenetic perspective, I am now focusing on their functional impact. I am particularly interested in deciphering how they contribute to gene expression changes, at single genes but also at the level of gene regulatory networks. For this, I tackle the following questions: what is the contribution of TEs to cis-regulatory elements involved in gene expression regulation? Do they underlie particular functions, such as response to stress? What is the impact of TE structural variation on gene regulation? At what evolutionary scale do they provide useful novelty? In collaboration with Johann Joets, I also analyze the contribution of other structural variants, notably gene Presence/Absence Variants (PAVs), to expression variability of genes involved in development as well as in response to abiotic stresses. At the species level, I am investigating these questions using maize as a model system, with particular interest for the originality of the European germplasm. I also work on several monocot and dicot species to investigate these questions at a broader evolutionary scale. To tackle these questions, I use an integrative approach combining generation of genomic (full genome assemblies, resequencing), epigenomic (methylome, ATAC-seq and SAM-seq) and transcriptomic (mRNA-seq) resources and their integration through bioinformatics and biostatistics methodologies.

Current collaborations

  • Internal: Maud Fagny, Johann Joets, Karine Alix, Maud Tenaillon (GEvAD), Elodie Marchadier (BASE), Stéphane Nicolas (GQMS)
  • National: Leandro Quadrana (IPS2, Saclay), Angélique Déleris (I2BC, Gif-sur-Yvette), Hadi Quesneville & Johann Confais (URGI, Versailles), Yann Bourgeois & Julia Hengelhorn (DIADE, Montpellier), Randy Wisser (LEPSE, Montpellier);
  • International: Maike Stam (University of Amsterdam, The Netherlands), Thomas Hartwig (Max Planck Institute for Plant Breeding Research, Germany), Silvio Salvi (Bologna University, Italy)

Ongoing grants

  • 2025-2029 : SATURN (ANR, France). Coordinator
  • 2024: TEEM (SPS, France). Co-coordinator
  • 2023- 2026: EDin (ANR, France). Participant

Responsibilities and network animation

  • Member of the editorial board of PloS Genetics since 2024
  • Member of the editorial board of Mobile DNA since 2023
  • Member of the doctoral school SEVE council since 2023
  • Member of the scientific council of the GDR “Epigenetics in Ecology and Evolution” (2019 to 2023)
  • Member of the scientific council of the GDR 2157: “Evolution of Transposable elements: from genomes to populations" since 2009
  • Member of the GDR “Epiplant" since 2019
  • Co-organizer of the “Transposable Elements” workshop at the international congress “Plant and Animal Genome” since 2020
  • Co-organizer of the International Congress on Transposable Elements (ICTE) in 2024
  • Co-organizer of the National Congress on Transposable Elements (CNET) in 2022

Position and Education

  • CNRS researcher Section 23, GQE-Le Moulon (Gif-sur-Yvette, France), 2008-present
  • Postdoctoral fellow (Urgence FRM fellowship), Institut Jacques Monod (Paris, France), 2007
  • Postdoctoral fellow (Lavoisier Egide fellowship), Bennetzen laboratory (Athens, Georgia, USA), 2005-2006
  • PhD student (MENRT fellowship and teaching associate), ESE laboratory, Orsay (France), 2001-2004

Publications

  • Hure V., Piron-Prunier F., Yehouessi T., Vitte C. , Kornienko AE., Adam G., Nordborg M., Déléris A.. (2024) Alternative silencing states of Transposable Elements in Arabidopsis. Molecular Biology,
  • Leduque B., Edera A., Vitte C. , Quadrana L.. (2024) Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing. Nucleic Acids Research, gkae306
  • Desbiez-Piat A., Ressayre A., Marchadier E., Noly A., Remoue C., Vitte C. , Belcram H., Bourgais A., Galic N., Guilloux ML., Tenaillon MI., Dillmann C.. (2023) Pervasive GxE interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments. Genetics, (in press) 2023.01.13.523786
  • Moissiard G., Mirouze M., Carles CC., Vitte C. . (2023) Editorial: Plant epigenetics and chromatin dynamics - EPIPLANT 2021-2022. Front. Plant Sci., (14) 1260391
  • Fagny M., Kuijjer ML., Stam M., Joets J., Turc O., Rozière J., Pateyron S., Venon A., Vitte C. . (2021) Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks. Frontiers in Genetics, (11) 1703
  • Mabire C., Duarte J., Darracq A., Pirani A., Rimbert H., Madur D., Combes V., Vitte C. , Praud S., Rivière N., Joets J., Pichon JP., Nicolas SD.. (2019) High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array. BMC Genomics, 1 (20) 848
  • Bennetzen J., Flint-Garcia S., Hirsch C., Tuberosa R., Joets J., Vitte C. , Charcosset A.. (2018) Draft Assembly of the F2 European Maize Genome Sequence and Its Comparison to the B73 Genome Sequence: A Characterization of Genotype-Specific Regions. DOI.org (Crossref), 3-12
  • Darracq A., Vitte C. , Nicolas S., Duarte J., Pichon JP., Mary-Huard T., Chevalier C., Bérard A., Le Paslier MC., Rogowsky P., Charcosset A., Joets J.. (2018) Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics, 1 (19) 119
  • Brandenburg JT., Mary-Huard T., Rigaill G., Hearne SJ., Corti H., Joets J., Vitte C. , Charcosset A., Nicolas SD., Tenaillon MI.. (2017) Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts. PLOS Genetics, 3 (13) e1006666
  • Vitte C. , Fustier MA., Alix K., Tenaillon MI.. (2014) The bright side of transposons in crop evolution. Briefings in functional genomics, 4 (13) 276-95