GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Lerat Emmanuelle

Chargée de recherche

CNRS

Address: 69622 VILLEURBANNE cedex
69622 VILLEURBANNE cedex

Tel: 04 72 43 13 44

Email

My research concerns the study of the role of transposable elements (TEs) in the evolution of eukaryotic genomes using comparative genomics and bioinformatics approaches in different organisms. Since several years, I have developed expertise in the identification of TEs in sequenced genomes, the study of their effects on neighboring genes, but also in the evolutionary analysis of TE sequences.

 

Projects

• Detection of TE copies in whole genome sequences to analyze their dynamics and evolution. For this, we have developed several programs:

  • Genome-wide statistic method to detect horizontally transferred sequences without any a priori  (Modolo et al. 2014) available here.
  • Tool to parse RepeatMasker output file in order to obtain detailed information concerning the TE content in a genome at the family level (Bailly-Bechet et al. 2014) available at One-code-to-find-them-all.
  •  Tool to performe transcriptomic analysis of TEs  (Lerat et al. 2017) available here.
  •  In development: tool to simulate a distribution of polymorphic TE insertions.

• Study of the link between TE insertions, epigenetic modifications and gene expression under various conditions (for example: normal cells vs tumor) in mammals and Drosophila.
•  Influence of TEs on the evolution of duplicated genes .
• Participation in the development of a reference for the annotation of TEs in genomes with several international researchers (Hoen et al. 2015).


Short CV
    • 2005-present : CNRS researcher
    • 2010 : Accreditation to conduct research (HDR)
    • 2004-2005 : Post-doc at the LBBE (FRM funding)
    • 2002-2004 : Post-doc at the University of Arizona (Tucson, USA)
    • 2001-2002 : ATER  at University Lyon 1
    • 1998-2001 : PhD at University Lyon 1


Membership and expertise

  • Member of the "Society for Molecular Biology and Evolution" (SMBE)
  • Member of the French Society of Bioinformatics (SFBI)
  • Associate editor for  "Genome Biology and Evolution" (GBE) (2008-2023)
  • Recommender for PCI Genomics since 2020
  • ResearchGate.

  • Carène Rizzon (lab. Statistics and Genome, Université d’Evry, France)
  • Jocelyn Turpin and Caroline Leroux (UMR 754, INRAe, Univ Lyon)
  • Sandra Duharcourt (Institut Jacques Monod, Paris, France), Linda Sperling (I2BC, Gif sur Yvette, France), Eric Meyer (IBENS, Paris, France)
  • Anne Mey (CarMeN lab, France) et Jacques Samarut (IGFL, ENS Lyon, France)
  • Eric Peyretaillade, Nicolas Parisot, et Pierre Peyret (EA CIDAM, Université d’Auvergne, France)
  • Marc Bailly-Béchet (Institut Sophia Agrobiotech, Univ. Nice Sophia Antipolis)
  • Marie-Pierre Chapuis (Centre de Biologie et de Gestion des Populations, Montpellier)
  • Franck Picard (Lab. Biologie et Modélisation de la Cellule, ENS, Lyon)
  • Claudia Carareto (UNESP, Brazil)
  • Antoine Perasso (Lab. « Chrono-environnement », Université de Franche-Comté, France)
  • Christophe Guyeux (FEMTO-ST institute, Université de France-Comté, France)
  • Josefa Gonzalez (Institut de Biologie Evolutive (CSIC-Universitat Pompeu Fabra) Barcelone, Espagne)
  • Mohamed Makni (Lab. de Génomique des insectes ravageurs de cultures d’intérêt agronomique, Univ Tunis El Manar, Tunisie)
  • Gabriel da Luz Wallau (Department of Entomology, Aggeu Magalhães Institute (IAM), Recife, Brésil)

  • L3: A. Mula (2006), E. Ohanyan (2016 ; co-supervision M Bailly-Béchet)
  • M1: F. Giordano (2006), R. Kahoul (2007), C. Déchaud (2016), A. Benmehdia (2022; co-supervision C. Rizzon), C. Bompard (2022; co-supervision C. Rizzon),
  • M2: B. Cheaib (2007), H. Mortada (2008), L. Modolo (2011), L. Grégoire (2013 ; co-supervision A. Haudry), E. Saulnier (2013 ; co-supervision C. Rizzon), N. Bargues (2015), R. Lannes (2016), C. Déchaud (2017), V. A. Le (2019), M. Le Guet (2019 ; co-supervision G. da Luz Wallau), G. Pozo (2020; co-supervision C. Rizzon), T. Tesseraud (2021 ; co-supervision C. Rizzon), A. Benmehdia (2023; co-supervision C. Rizzon).
  • PhD: M. Deloger (2006-2009 ; co-direction C. Vieira et MF Sagot), A. Granzotto (2007-2011 ; co-direction C. Vieira et C. Carrareto), H. Mortada (2008-2011 ; co-direction C. Vieira), L. Modolo (2011-2014), S. Sedghiani (2016), M. Verneret (2022-2025; co-direction J. Turpin).

Publications

Display of 1 to 30 publications on 68 in total

Exploring endogenous retroviruses in ruminant genomes: They might not be all dead after all

Marie Verneret, Caroline Leroux, Thomas Faraut, Vincent Navratil, Emmanuelle Lerat, Jocelyn Turpin

Bioinformatics and Evolutionary Genomics (ALPHY = ALignments and PHYlogeny) .

Poster

see the publication

A genome-wide study of ruminants uncovers two endogenous retrovirus families recently active in goats

Marie Verneret, Caroline Leroux, Thomas Faraut, Vincent Navratil, Emmanuelle Lerat, Jocelyn Turpin

Mobile DNA . 16 ( 1 ) : 4

DOI: 10.1186/s13100-024-00337-6

Journal article

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Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Anthony B. Garza, Emmanuelle Lerat, Hani Z. Girgis

Mobile DNA . 15 ( 1 ) : 8

DOI: 10.1186/s13100-024-00317-w

Journal article

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Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions

Marie Verneret, van Anthony Le, Thomas Faraut, Jocelyn Turpin, Emmanuelle Lerat

DOI: 10.1101/2024.09.25.614865

Preprint

see the publication

Small ruminants versus endogenous retroviruses: an evolutive showdown still in progress in the domestic goat genome

Marie Verneret, Caroline Leroux, Vincent Navratil, Thomas Faraut, Jocelyn Turpin, Emmanuelle Lerat

International congress on transposable elements .

Poster

see the publication

Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Anthony B. Garza, Emmanuelle Lerat, Hani Z. Girgis

Mobile DNA . 15 ( 1 ) : 8

DOI: 10.1186/s13100-024-00317-w

Journal article

see the publication

A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats

Marie Verneret, Caroline Leroux, Thomas Faraut, Vincent Navratil, Emmanuelle Lerat, Jocelyn Turpin

DOI: 10.1101/2024.06.21.600049

Preprint

see the publication

MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation

Jérémy Tournayre, Valérie Polonais, Ivan Wawrzyniak, Reginald Florian Akossi, Nicolas Parisot, Emmanuelle Lerat...

International Journal of Molecular Sciences . 25 ( 2 ) : 880

DOI: 10.3390/ijms25020880

Journal article

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A first step towards the characterization of endogenous retroviruses’ evolutionary history and impact on small ruminant genomes

Marie Verneret, Caroline Leroux, Vincent Navratil, Thomas Faraut, Emmanuelle Lerat, Jocelyn Turpin

CNET 2023 : 24th National Congress on Transposable Elements 2023 .

Conference paper

see the publication

OVINE β-ENDOGENOUS RETROVIRUSES : FROM INTEGRATION TO COPY-SPECIFIC TRANSCRIPTION

Marie Verneret, Caroline Leroux, Emmanuelle Lerat, Vincent Navratil, Jocelyn Turpin

XXVèmes Journées Francophones de Virologie .

Poster

see the publication

Look4LTRs: A Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Anthony Garza, Emmanuelle Lerat, Hani Girgis

DOI: 10.1101/2023.07.28.551030

Preprint

see the publication

How genomics can help biodiversity conservation

Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul Berg, Christoph Bleidorn...

Trends in Genetics .

DOI: 10.1016/j.tig.2023.01.005

Journal article

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Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

Diamantis Sellis, Frédéric Guérin, Olivier Arnaiz, Walker Pett, Emmanuelle Lerat, Nicole Boggetto...

PLoS Biology . 19 ( 7 ) : e3001309

DOI: 10.1371/journal.pbio.3001309

Journal article

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The Transposable Element Environment of Human Genes Differs According to Their Duplication Status and Essentiality

Margot Correa, Emmanuelle Lerat, Etienne E. Birmelé, Franck Samson, Bérengère Bouillon, Kévin Normand...

Genome Biology and Evolution . 13 ( 5 )

DOI: 10.1093/gbe/evab062

Journal article

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An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

Tanguy Lallemand, Martin Leduc, Claudine Landès, Carène Rizzon, Emmanuelle Lerat

Genes . 11 ( 9 ) : 1046

DOI: 10.3390/genes11091046

Journal article

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Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

Romain Lannes, Carène Rizzon, Emmanuelle Lerat

Genes . 10 ( 3 ) : 249

DOI: 10.3390/genes10030249

Journal article

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On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Emmanuelle Lerat, Josep Casacuberta, Cristian Chaparro, Cristina Vieira

Genes . 10 ( 4 ) : 258

DOI: 10.3390/genes10040258

Journal article

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Population specific dynamics and selection patterns of transposable element insertions in European natural populations

Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira...

Molecular Ecology . : 1-17

DOI: 10.1111/mec.14963

Journal article

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Simulation-based estimation of branching models for LTR retrotransposons

Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat

Bioinformatics . 33 ( 3 ) : 320 - 326

DOI: 10.1093/bioinformatics/btw622

Journal article

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TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

Emmanuelle Lerat, Marie Fablet, Laurent Modolo, Hélène Lopez-Maestre, Cristina Vieira

Nucleic Acids Research . 45 : 13

DOI: 10.1093/nar/gkw953

Journal article

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The transposable element environment of human genes is associated with histone and expression changes in cancer

Laura Grégoire, Annabelle A. Haudry, Emmanuelle Lerat

BMC Genomics . 17 ( 1 )

DOI: 10.1186/s12864-016-2970-1

Journal article

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The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes

Abdel Belkorchia, Cyrielle Gasc, Valérie Polonais, Nicolas Parisot, Nicolas Gallois, Céline Ribière...

PLoS ONE . 10 ( 9 ) : 1-12

DOI: 10.1371/journal.pone.0139075

Journal article

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Subcellular Localization of ENS-1/ERNI in Chick Embryonic Stem Cells

Sophie Blanc, Florence Ruggiero, Anne-Marie Birot, Hervé Acloque, Didier Decimo, Emmanuelle Lerat...

PLoS ONE . 9 ( 3 ) : e92039

DOI: 10.1371/journal.pone.0092039

Journal article

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A call for benchmarking transposable element annotation methods.

Douglas R Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, Cédric Feschotte...

Mobile DNA . 6 : 13

DOI: 10.1186/s13100-015-0044-6

Journal article

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