Gonad Differentiation and its Perturbations (DGP)

Gonad Differentiation and its Perturbations (DGP)

Team leader : Béatrice Mandon-Pépin (beatrice.mandon-pepin@inrae.fr)

The DGP team includes INRAE staff from the "Animal Physiology and Livestock Systems" department (PhASE) and ELIANCE company. The team is composed of 12 tenured staff with expertise in reproductive physiology and endocrinology as well as skills in molecular biology, genetics and epigenetics of livestock. The team is developing functional genomics approaches in mammalian model species (mice) and farm animals (rabbits, small ruminants) and is implementing new technologies for targeted genome modifications (TALEN, CRISPR/cas9).

Composition : Béatrice Mandon-Pépin (CRHC), Eric Pailhoux (DR2, HDR), Dominique Thépot (CRCN), Eugénie Canon (IE), Aurélie Dewaele (AI), Elodie Poumerol (AI), Marjolaine André (TR), Emilie Dujardin (3ème année de thèse), Iris Barka (1ère année de thèse).


Our objectives

  1. To characterise the genes and mechanisms underlying the major stages of gonadal differentiation: sex-determination, germ cell differentiation, meiosis, formation and differentiation of ovarian follicles, oogenesis and spermatogenesis.
  2. To study how these developmental processes are influenced by (i) the maternal or perinatal environment (global warming, endocrine disruptors, plastic particles, diets), or (ii) genotypes (i.e., genetically modified animals).

These studies are carried out in both sexes and in different species of agronomic interest or model species.



Main question

Fertility and transmission of genetic and epigenetic information to offspring are intimately linked to proper germline differentiation. Within gonads, a harmonious cross-talk between germinal cells and their surrounding somatic cells is essential to determine their future fate and to differentiate quality gametes in sufficient quantity. During the first third of gestation in the mammalian foetus, these interactions are established very early as soon as the germ cells colonise the genital ridges. The proliferation of these primordial germ cells – which determine the gamete stock - is a key first step in the acquisition of fertility. A second step concerns their differentiation and entry into meiosis, which occur at different developmental stages and in different ways, depending on the sex of the individual. Throughout the process of germ cell differentiation, the somatic cells of the gonads (supporting cells, steroidogenic cells) will co-differentiate and play a key role in the development of future gametes and in the development of sexual dimorphisms. Many genes controlling these processes have already been identified, especially in mice. However, most often the mechanisms found in mice are not confirmed in other mammals, as rodents seem to have their own specificities. A better understanding of the mechanisms governing the fate of germ cells is therefore of interest not only in livestock, in order to identify the levers for improving animal husbandry conditions, but also in humans, where perturbations of gonad differentiation could cause infertility or cancer.

Scientific questions

Two main research axes are developed in the team.

Axis 1 – Molecular mechanisms involved in gonad differentiation

Characterisation of gene cascades involved in the determination and differentiation of ovary and testis.


Rabbit, goat, sheep, cattle, mouse, turtle

  • Phenotyping of wild type, natural mutants or genetically modified animals.
    • Histology, immunohistology, in situ hybridization
    • Transcriptome analyses: Bulk and Single-cell RNA-sequencing
  • Search for targets of transcription factors/ chromatin remodelers.
    • ChIP-Sequencing : FOXL2, SOX9, DMRT1, TRIM28 (in progress)
  • Characterisation of regulatory regions – histone marks
    • ChIP-qPCR on native chromatin and ChIP-seq (CUT&RUN in progress).

Axis 2 - Differentiation of the germline and fertility

  • Sexual determination of germ cells (« commitment »)
  • Epigenetic reprogramming of germ cells
  • Set up of female and male meiosis – Meiotic defects and fertility


Rabbit, goat, sheep cattle, mouse

Production of genetically modified animals

  • Knockout models (Mouse, Rabbit)  for Topaz1, long non-coding RNAs, Tex11, CYP19, DMRT1, DHX37 (ongoing)
    • Additive transgenesis: fluorescent tracers (rabbit): RARE-GFP line (retinoic acid signalling); OCT4-GFP/VASA-TOMATO line (cell sorting of germ cells).
  • Phenotyping of wild type or genetically modified animals.
    • Animal fertility analyses
    • Histological analyses, immunohistology, and in situ hybridization
    • Transcriptomic analyses: Bulk and Single-cell RNA-sequencing
    • Purification of germ cells
      • Laser Capture Microdissection (LCM) – platform INRAE @bridge
      • FACS  sorting of spermatogenic cells (Coll. CEA Fontenay)
      • FACS sorting with fluorescent tracers

DNA methylation analysis (LUMA and RRBS) – (Coll. MECP2 team within BREED unit)


Animal models

Biomedical models: rabbit, mouse, sheep, goat

Livestock models: bovine, ovine, caprine

Animal models make it possible to set up complex experiments (effects of pollutants, specific diets, treatment with hormones or analogues, etc.), but also to analyse the effects of over- or under-expression of genes in genetically modified animals. The team is also involved in the study of human mutations reproduced in animals (mice and rabbits) by allelic replacement (KI).  These animal models are produced at the Centre de Recherche Ile-de-France-Jouy-en-Josas - Antony within the animal experimental units: UE SAAJ (https://www.pluginlabs-universiteparissaclay.fr/fr/entity/915089-inra-unite-commune-dexperimentation-animale-ucea) and IERP (https://www6.jouy.inrae.fr/ierp/).

For ruminants, we also work in collaboration with other INRAE experimental units outside the Jouy-en-Josas centre: Le Pin experimental domain (https://www6.rennes.inrae.fr/domaine-experimental-du-pin/), UE 0332 at Bourges (https://www6.val-de-loire.inrae.fr/ue-bourges) or UE PAO at Tours-Nouzilly (https://www6.val-de-loire.inrae.fr/uepao/).

Methodological approaches

  • Cell culture : cell lines and primary cultures (granulosa)
  • Culture of ex-vivo gonadal explants
  • Histology, immunohisto/cytochemistry, in situ hybridization (RNA scope)
  • Transcriptomic analyses: RT-qPCR, microarray, bulk and single-cell RNA-sequencing
  • Epigenetic analyses: ChIP-qPCR and ChIP-sequencing (CUT&RUN)
  • Protein analyses: Western-blot.
  • Measure of enzymatic activity, hormone dosages
  • Cell sorting of spermatogenic or marked cells (FACS,  in collaboration)
  • Functional genomic and epigenomic
  • Micro-injection and bovine embryo culture (Allice)
  • Measures of spermatic parameters (CASA apparatus –Allice)


Collaborations et partenariats


  • Experimental units of INRAE Jouy-en-Josas : IERP and UE SAAJ
  • INRAE Platforms: @bridge, MIMA2, PAPSSO, Jouy en Josas
  • CNRS Platforms: I2BC Gif-sur-Yvette
  • Gabriel Livera, UMR SGCSR, Institut de Biologie François Jacob,  Fontenay-aux-roses
  • Reiner Vetia, Institut Jacques Monod, Paris-Diderot University
  • Anu Bashamboo, Ken McElreavey, CNRS UMR3738,  Institut Pasteur, Paris
  • Bertrand Bed’Hom, Norin Chai : MNHN, Paris
  • Charly Pignon, ENVA, Maisons-Alfort


  • INRAE URA, Nouzilly
  • INRAE, LPGP, Rennes
  • INRAE, SIGENAE UR875 BIA, Castanet-Tolosan
  • INRAE, GENPHySE, Castanet-Tolosan
  • INRAE, CNRGV, Toulouse
  • Allice
  • XENOTHERA, Nantes
  • Laurent Lagrost, Bourgogne University, INSERM UMR866, Lyon 
  • Marie Christine Chaboissier, INSERM U1091 / CNRS 7277, Nice
  • Francis Poulat, Brigitte Boizet-Bonhoure, CNRS UPR 1142, Montpellier
  • Norbert Ghyselinck, CNRS UMR7104, INSERM U964, Strasbourg University


  • COST action BM1308 SALAAM "Sharing Advances on Large Animal Models"
  • International Society for Transgenic Technologies (http://www.transtechsociety.org/)
  • Pr Paul Fowler, Institute of Medical Sciences, University of Aberdeen, UK
  • Richard G Lea, University of Nottingham, UK
  • Humphrey Yao, National Institute of Environmental Health Science, Durham N.C., USA
  • Serge Nef, Université de Genève, Suisse.
  • Tomer Avidor-Reiss, Toledo University, Ohio, USA


  • SAPS : Sciences Animales Paris Saclay. https://www6.inrae.fr/saps-paris
  • INRAE network on epigenetics : « EpiPhASE »
  •  « Gonad differentiation »
  • National  network on the reproduction function: « GDR 3606 repro ».  https://www6.inrae.fr/gdr-repro/
  • E. Poumerol is a member of the local Ethic commitee  for animal testing of the INRAE Jouy-en-Josas center, COMETHEA.
  • G. Jolivet is a member of  CELPHEDIA network. http://www.celphedia.eu/
  • E. Pailhoux is a founder member and organizer of ESSDV – European Symposium on Sex Determination in Vertebrates. https://symposium.inrae.fr/essdv-greenfield/

Publications (2014-2020)


FOXL2 is a Progesterone Target Gene in the Endometrium of Ruminants. Eozenou C, Lesage-Padilla A, Mauffré V, Healey GD, Camous S, Bolifraud P, Giraud-Delville C, Vaiman D, Shimizu T, Miyamoto A, Sheldon IM, Constant F, Pannetier M, Sandra O. Int J Mol Sci. 2020 Feb 21;21(4):1478.

Investigating the role of BCAR4 in ovarian physiology and female fertility by genome editing in rabbit. Peyny M, Jarrier-Gaillard P, Boulanger L, Daniel N, Lavillatte S, Cadoret V, Papillier P, Monniaux D, Peynot N, Duranthon V, Jolivet G, Dalbies-Tran R. Sci Rep. 2020 Mar 19;10(1):4992.

Retinoic acid synthesis by ALDH1A proteins is dispensable for meiosis initiation in the mouse fetal ovary.  Chassot AA, Le Rolle M, Jolivet G, Stevant I, Guigonis JM, Da Silva F, Nef S, Pailhoux E, Schedl A, Ghyselinck NB, Chaboissier MC. Sci Adv. 2020 May 22;6(21):eaaz1261. doi: 10.1126/sciadv.aaz1261. eCollection 2020 May. PMID: 32494737 .


RUNX1 maintains the identity of the fetal ovary through an interplay with FOXL2. Nicol B, Grimm SA, Chalmel F, Lecluze E, Pannetier M, Pailhoux E, Dupin-De-Beyssat E, Guiguen Y, Capel B, Yao HH. Nat Commun. 2019 Nov 11;10(1):5116

Transgenic short-QT syndrome 1 rabbits mimic the human disease phenotype with QT/APD shortening in the atria and ventricles and increased VT/VF inducibility. Odening, K. E., Bodi, I., Franke, G., Rieke, R., de Medeiros, A. R, Perez-Feliz, S, Fuerniss, H, Mettke, L, Michaelidis, K, Lang, C. N, Steinfurt, J, Pantulu, N, D, Ziupa, D, Menza, M, Zehender, M, Bugger, H, Peyronnet, R. Behrends, J, Doleschall, Z, zur Hausen, A, Bode, C, Jolivet, G, Brunner, M. Eur Heart J, 2019, 400 (10): 842-853

A novel evolutionary conserved mechanism of RNA stability regulates synexpression of primordial germ cell-specfic genes prior to the sex-determination stage.  Herpin, A, Schmidt, C, Kneitz, S, Gobé, C, Regensburger, M, Le Cam, A, Montfort, J, Lillesaar, C, Wilhlm, D, Kraeussling, M, Mourot, B, Porcon, B, Pannetier, M, Pailhoux, E, Etwiller, L, Dolle, DM, Guigen, Y, Schartl, M. Plos Biology, 2019, 17 (4): e3000185

Genetic defects in human azoospermia. Ghieh, F, Mitchell, V, Mandon-Pepin, B, Vialard, F. Basic Clin Androl, 2019, 29, 4 Review

Des souris et des femmes : une ovogenèse fœtale similaire ? Mandon-Pepin, B, Gobé, C. Médecine de la Reproduction, 2019, 21 (2), 111-126. Review

Long-term exposure to chemicals in sewage sludge fertilizer alters liver lipid content in females and cancer marker expression in males. Filis P, Walker N, Robertson L, Eaton-Turner E, Ramona L, Bellingham M, Amezaga MR, Zhang Z, Mandon-Pépin B, Evans NP, Sharpe RM, Cotinot C, Rees W.D, O’Shaughnessy P, Fowler PA. Environ Int, 2019, 124: 98-108  

Dual role of DMXL2 in olfactory information transmission and the first wave of spermatogenesisGobé C, Elzaiat M, Meunier N, André M, Sellem E, Congar P, Jouneau L, Allais-Bonnet A, Naciri I, Passet B, Pailhoux E, Pannetier M.  Plos Genetics, 2019, 15 (2): e1007909, 1-28 


The unusual rainbow trout sex determination gene hijacked the canonical vertebrate gonadal differentiation pathway. Bertho S, Herpin A, Branthonne A, Jouanno E, Yano A, Nicol B, Muller T, Pannetier M, Pailhoux E, Miwa M, Yoshizaki G, Schartl M, Guigen Y. PNAS, 2018, 115 (50): 12781-12786 

Impact of gestational exposure to diesel exhaust on offspring gonadal development: experimental study in the rabbit. Bourdon M, Torres L, Monniaux D, Faure C, Levy R, Tarrade A, Rousseau D, Chavatte-Palmer P, Jolivet G. J DOHaD, 2018, 9 (5): 519-529 

An initiator codon mutation in SD2 causes recessive embryonic lethality in Holstein cattle. Fritz S, Hoze C, Rebours E, Barbat M, Bizard M, Escouflaire C, Vander Jagt C, Boussaha M, Grohs C, Allais Bonet A, Philippe M, Vallée A, Amigues Y J, Hayes B, Boichard D, Capitan A. J Dairy Sci, 2018, 101 (7): 6220-6231


An assessment of fixed and native chromatin preparation methods to study histone post-translational modifications at a whole genome scale in skeletal muscle tissue. David SA, Hennecquet-Antier C, Pannetier M, Aguirre-Lavin T, Crochet S, Bordeau T, Couroussé N, Brionne A, Collin A, Coustham V. Biol Proced Online, 2017, 19: 10 

Amplification of R-spondin1 signaling induces granulosa cell fate defects and cancers in mouse adult ovary. De Cian MC, Pauper E, Bandiera R, Vidal VPI, Sacco S, Gregoire EP, Chassot AA, Panzolini C, Whilhelm D, Pailhoux E, Youssef SA, De Brui A, De Teerds K, Schedl A, Gillot I, Chaboissier MC. Oncogene, 2017, 36 (2): 208-218 

Recombinant human plasma phospolipid transfer protein (PLTP) to prevent bacterial growth and to treat sepsis. Deckert V, Lemaire S, Ripoll PJ, Pail de Barros JP, Labbé J, Chabert-Le Borgne C, Turquois V, Maquart G, Larose D, Desroche N, Ménétrier F, Le Guern N, Lebrun LJ, Desrumeaux C, Gautier T, Grober J, Thomas C, Masson D, Houdebine LM, Lagrost L. Sci Reports, 2017, 7 (1) 3053, 16 pages 

In mammalian fœtal testes, SOX9 regulates expression of its target genes by binding to genomic regions with conserved signatures. Rahmoun M, Lavery R, Laurent-Chaballier S, Bellora N, Philipp GK, Rossitto M, Pailhoux E, Cammas F, Chung J, Bagheri-Fam S, Murphy M, Bardwell V, Zarhower D, Boizet-Bonhoure B, Clair P, Harley VR, Poulat F. Nucleic Acids Res, 2017, 45 (12): 7191-7211 


A specific role for PRND in goat fetal Leydig cells is suggested by prion family gene expression during gonad development in goats and mice. Allais-Bonnet A, Castille J, Pannetier M, Passet B, Elzaïat M, André M, Montazer-Torbati F, Moazami-Goudarzi K, Vilotte JL, Pailhoux E. FEBS Open Bio, 2016, 6 (1): 4-15 

Foxl2 and its relatives are evolutionary conserved players in gonadal sex differentiation. Bertho S, Pasquier J, Pan Q, Le Trionnaire G, Bobe J, Postlewait J, Pailhoux E, Schartl M, Herpin A, Guigen Y. Sex Dev, 2016, 10 (3): 111-129 

Timing of maternal exposure and fetal sex determine the effects of low-level chemical mixture exposure on the fetal neuroendocrine system in sheep. Bellingham M, Fowler P A, MacDonald ES, Mandon-Pépin B, Cotinot C, Rhind S, Sharpe RM, Evans NP. J Neuroendocrinol, 2016, 28 (12) 

The fetal ovary exhibits temporal sensitivity to a ‘real-life’mixture of environmental chemicals. Lea RG, Amezaga MR, Loup B, Mandon-Pépin B, Stefansdottir A, Filis P, Kyle C, Zhang Z, Allen C, Purdie L, Jouneau L, Cotinot C, Rhind MS, Sinclair D. K, Fowler PA. Sci Reports, 2016, 6: 22279 

A reverse genetic approach identifies an ancestral frameshift mutation in RP1 causing recessive progessive retinal degeneration in European cattle Breeds. Michot P, Chahory S, Marete A, Grohs C, Dagios D, Donzel E, Aboukadiri A, Deloche MC, Allais-Bonnet A, Chambrial M, Barbey S, Genestout L, Boussaha M, Danchin-Burge C, Fritz S, Boichard D, Capitan A. Genet Sel Evol, 2016, 48 (1): 56 

Involvement of FOXL2 and RSPO1 in ovarian determination, development, and maintenance in mammals. Pannetier M, Chassot AA, Chaboissier MC, Pailhoux E. Sex Dev, 2016, 10 (4): 167-184 

Sex reversal in non-human placental mammals.  Parma P, Veyrunes F, Pailhoux E. Sex Dev, 2016, 10 (5-6): 326-344  

Analysis of STAT1 expression and biological activity reveals interferon-tau-dependent STAT1-regulated SOC genes in the bovine endometrium. Vitorino Carvalho A, Eozenou C, Healey GD, Forde N, Reinaud P, Chebrout M, Gall L, Rodde N, Lesage-Padilla A, Giraud-Delville C, Leveugle M, Richard C, Sheldon IM, Lonergan P, Jolivet G, Sandra O. Reprod Fertil Dev, 2016, 28 (4): 459-474 

Preface. In Sex Reversal in vertebratesPailhoux, E., 2016. Eds Karger , Sex Dev, 10 (5-6): 221-222 (chapitre d’ouvrage)

Sex Reversal in vertebratesPailhoux, E., 2016. Eds Karger in Sex Dev, 10 (5-6): 217-346 (direction d’ouvrage)


Spatio-temporal gene expression profiling during in vivo early ovarian folliculogenesis: integrated transcriptomic study and molecular signature of early follicular growth. Bonnet A, Servin B, Mulsant P, Mandon-Pépin B. Plos One, 2015, 10 (11): e141482

TOPAZ1, a germ cell specific fator, is essential for male meiotic progession. Luangpraseuth-Prosper A, Lesueur E, Jouneau L, Pailhoux E, Cotinot C, Mandon-Pépin B. Dev Biol, 2015, 406 (2): 158-171 

Whole-genome sequencing identifies a homozygous deletion encompassing exons 17 to 23 of the integrin beta 4 gene in a Charolais calf with junctional epidermolysis bullosa. Michot P, Fantini O, Braque R, Allais-Bonnet A, Saintilan R, Grohs C, Barbieri J, Genestout L, Danchin-Burge C, Gourreau J-M, Boichard D, Pin D, Capitan A. Genet Sel Evol, 2015, 47 (37): 1-7 

Transgenic rabbits expressing ovine PrP are susceptible to scrapie. Sarradin P, Viglietta C, Limouzin C, Andréoletti O, Daniel-Carlier N, Barc C, Leroux-Coyau M, Berthon P, Chapuis J, Rossignol C, Gatti J-L, Belghazi M, Labas V, Vilotte J-L, Beringue V, Lantier F, Laude H, Houdebine LM. Plos Pathogens, 2015, 11 (8), e1005077 

Genome-wide next generation DNA and RNA sequencing reveals a mutation that perturbs splicing of the phosphatidylinositol glycan anchor biosynthesis class H gene (PIGH) and causes arthrogryposis in Belgian Blue cattle. Sartelet A, Wanbo L, Pailhoux E, Richard C, Tamma N, Karim L, Fasquelle C, Druet T, Coppieters W, Georges M, Charlier C. BMC Genomics, 2015, 16: 316 


Role of the prion protein family in the gonads. Allais-Bonnet A, Pailhoux E. Frontiers in Cell Dev Biol, 2014, 2: 56 

FOXL2 is a female sex–determining gene in the goat. Boulanger L, Pannetier M, Gall L, Allais-Bonnet A, Elzaiat M, Le Bourhis D, Daniel N, Richard C, Cotinot C, Ghyselinck NB, Pailhoux E. Curr Biol, 2014, 24 (4): 404-408

High-Throughout sequencing analyses of XX genital ridges lacking FOXL2 reveal DMRT1 Up-regulation before SOX9 expression during the sex-reversal process in goatsElzaiat M, Jouneau L, Thépot D, Klopp C, Allais-Bonnet A, Cabau C, André M, Chaffaux S, Cribiu EP, Pailhoux E, Pannetier M. Biol Reprod, 2014, 91 (6): 153, 1-14  

Does grazing on biosolids treated pasture pose a pathophysiological risk associated with increased exposure to endocrine disrupting compounds. Evans NP, Bellingham M, Sharpe RM, Cotinot C, Rhind SM, Kyle C, Erhard H, Hombach-Klonisch S, Lind PM, Fowler PA. J Anim Sci, 2014, 92 (8): 3185-3198 

Attitudes towards genetically modified animals in food production. Frewer LJ, Coles D, Houdebine LM, Kleter GA. British food journal, 2014, 116 (8): 1291-1313 

Induction of body weight loss through RNAi-knocdown of APOBEC1 gene expression in transgenic rabbits. Jolivet G, Braud S, Da Silva B, Passet B, Harscoët E, Viglietta C, Gautier T, Lagrost L, Daniel-Carlier N, Houdebine LM, Harosh I. PLos One, 2014, 9 (9): e106655

Maternal high-fat diet induces follicular atresia but does not affect fertility in adult rabbit offspring. Leveillé P, Tarrade A, Dupont C, Larcher T, Dahirel M, Poumerol E, Cordier A-G, Picone O, Mandon-Pépin B, Jolivet G, Lévy R, Chavatte-Palmer P. J Dev Orig Hlth Dis, 2014, 5 (2): 88-97 

DNA methylation and transcription in a distal region Upstream from the bovine AlphaS1 casein gene after once or twice daily milking. Nguyen M, Boutinaud M, Pétridou B, Gabory A, Pannetier M, Chat S, Bouet S, Jouneau L, Jaffrezic F, Laloë D, Klopp C, Brun N, Kress C, Jammes H, Charlier M, Devinoy E. Plos One, 2014, 9 (11): e111556 

The Proto-MHC of Placozoans, a Region Specialized in Cellular Stress and Ubiquitination/Proteasome Pathways. Suurväli J, Jouneau L, Thépot D, Grusea S, Pontarotti P, Du Pasquier L, Boudinot SR, Boudinot P. J Immunol, 2014, 193: 2891-2901 

Design and Characterization of a 52K SNP Chip for Goats. Tosser-Klopp G, Bardou P, Bouchez O, Cabau C, Crooijmans R, Dong Y, Donnadieu-Tonon C, Eggen A, Heuven HC, Jamli S, Jiken AJ, Klopp C, Lawley CT, McEwan J, Martin P, Moreno CR, Mulsant P, Nabilhoudine I, Pailhoux E, Palhière I, Rupp R, Sarry J, Savre BL, Tircazes A, Jun Wang Wang W, Zhang W. Plos One, 2014, 22 (9): e86227 

La différenciation sexuelle des gonades et de l’appareil génital. Pailhoux, E., Pannetier, M., Mandon-Pépin, B., 2014. In: Chastant-Maillard, S., Saint-Dizier, M. (coord), La reproduction animale et humaine, Editions Quae, 2014, chapitre 1 : 19-39 (chapitre d'ouvrage)

Modification date : 06 May 2024 | Publication date : 19 April 2010 | Redactor : Laurent M.