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 31 to 60 publications on 66 in total

Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems

E Peyretaillade, D Boucher, N Parisot, C Gasc, R Butler, J-F Pombert...

Heredity . : 25182222

DOI: 10.1038/hdy.2014.78

Journal article

see the publication

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Marc Bailly-Bechet, Annabelle Haudry, Emmanuelle Lerat

Mobile DNA . 5 : 13

DOI: 10.1186/1759-8753-5-13

Journal article

see the publication

Identification and Analysis of Transposable Elements in Genomic Sequences

Laurent Modolo, Emmanuelle Lerat

Genome analysis, current procedures and applications . 978-1-908230-29-4

Book chapter

see the publication

Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids

Elias a G Carnelossi, Emmanuelle Lerat, Hélène Henri, Sonia Martinez, Claudia M A Carareto, Cristina Vieira

Genome Biology and Evolution . 6 : 1806 - 1817

DOI: 10.1093/gbe/evu141

Journal article

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The endogenous retrovirus ENS-1 provides active binding sites for transcription factors in embryonic stem cells that specify extra embryonic tissue

A. Mey, Hervé Acloque, Emmanuelle Lerat, S. Gounel, V. Tribollet, S. Blanc...

Retrovirology . 9 ( 1 ) : 21

DOI: 10.1186/1742-4690-9-21

Journal article

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A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans.

Cristina Vieira, Marie Fablet, Emmanuelle Lerat, Matthieu Boulesteix, Rita Rebollo, Nelly Burlet...

Journal of Environmental Radioactivity . 113 : 83-86

DOI: 10.1016/j.jenvrad.2012.04.001

Journal article

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Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes.

Emmanuelle Lerat, Nelly Burlet, Christian Biémont, Cristina Vieira

Gene . 473 ( 2 ) : 100-9

DOI: 10.1016/j.gene.2010.11.009

Journal article

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Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.

Hussein Mortada, Cristina Vieira, Emmanuelle Lerat

Journal of Molecular Evolution . 71 ( 3 ) : 180-91

DOI: 10.1007/s00239-010-9376-5

Journal article

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Identification of expressed transposable element insertions in the sequenced genome of Drosophila melanogaster

M. Deloger, F.M.G. Cavalli, E. Lerat, C. Biémont, M.-F. Sagot, Cristina Vieira

Gene . 439 : 55-62

Journal article

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Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs

E. Lerat

Heredity . -- : 1-14

Journal article

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Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila

M. Fablet, E. Lerat, R. Rebollo, B. Horard, N. Burlet, S. Martinez...

FASEB Journal . 23 : 54-62

Journal article

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Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements

Cristina Vieira, M. Fablet, E. Lerat

genome dyn stab . -- : 115-123

Journal article

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The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes.

Adriana Granzotto, Fabrício R Lopes, Emmanuelle Lerat, Cristina Vieira, Claudia M A Carareto

BMC Evolutionary Biology . 9 : 174

DOI: 10.1186/1471-2148-9-174

Journal article

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Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila.

Marie Fablet, Emmanuelle Lerat, Rita Rebollo, Béatrice Horard, Nelly Burlet, Sonia Martinez...

FASEB Journal . 23 ( 5 ) : 1482-9

DOI: 10.1096/fj.08-123513

Journal article

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Losing helena: The extinction of a drosophila line-like element

Rita Rebollo, Emmanuelle Lerat, Liliana Lopez Kleine, Christian Biémont, Cristina Vieira

BMC Genomics . 9 : 1-11

DOI: 10.1186/1471-2164-9-149

Journal article

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Influence of the transposable element neighborhood on human gene expression in normal and tumor tissues

E. Lerat, M. Sémon

Gene . 396 : 303-311

Journal article

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Maintenance in the chicken genome of the retroviral-like cENS gene family specifically expressed in early embryos

Emmanuelle Lerat, Anne-Marie Birot, Jacques Samarut, Anne Mey

Journal of Molecular Evolution . 65 ( 3 ) : 215-227

DOI: 10.1007/s00239-007-9001-4

Journal article

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Evolutionary origins of genomic repertoires in bacteria

E. Lerat, Vincent Daubin, H. Ochman, N.A. Moran

PLoS Biology . 3 : 0807-0814

Journal article

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Recognizing the pseudogenes in bacterial genomes

E. Lerat, H. Ochman

Nucleic Acids Research . 33 : 3125-3132

Journal article

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A bunch of fun-guys: the whole-genome view of yeast evolution

H. Ochman, Vincent Daubin, E. Lerat

Trends in Genetics . 21 : 1-3

Journal article

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Examining bacterial species under the specter of gene transfer and exchange

H. Ochman, E. Lerat, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 102 : 6595-6599

Journal article

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Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data

J.V. Earnest-Deyoung, E. Lerat, B.M.E. Moret

incollection . 3240 : 1-13

Journal article

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The evolutionary history of quorum-sensing in bacteria

E. Lerat, N.A. Moran

Molecular Biology and Evolution . 21 : 903-913

Journal article

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Ψ-Φ: Exploring the outer limits of bacterial pseudogenes

E. Lerat, H. Ochman

Genome Research . 14 : 2273--2278

Journal article

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Hypervariable and highly divergent intron/exon organizations in the chordate Oikopleura dioica

R. Edvardsen, E. Lerat, A.D. Maeland, M. Flat, R. Tewari, M.F. Jensen...

Journal of Molecular Biology . 59 : 448-457

Journal article

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$Psi$-$Phi$: Exploring the outer limits of bacterial pseudogenes

E. Lerat, H. Ochman

Genome Research . 14 : 2273-2278

Journal article

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Sequence divergence within transposable element families in the Drosophila melanogaster genome

E. Lerat, C. Rizzon, C. Biémont

Genome Research . 13 : 1889-1896

Journal article

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From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

Emmanuelle Lerat, Vincent Daubin, Nancy Moran

PLoS Biology . 1 ( 1 ) : 101-109

DOI: 10.1371/journal.pbio.0000019

Journal article

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The source of laterally transferred genes in bacterial genomes

Vincent Daubin, E. Lerat, G. Perrière

Genome Biology . 4 : R57.1-R57.12

Journal article

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The relative abundance of dinucleotides in transposable elements in five species

E. Lerat, P. Capy, C. Biémont

Molecular Biology and Evolution . 19 : 964-967

Journal article

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