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profil pic RougeulleClaire

Claire Rougeulle

Team Leader | Deputy Director (CNRS)



Claire is a Research Director (DR1) at the CNRS. She joined the Epigenetics and Cell Fate Centre as a founding member in 2009 and is the Deputy Director of the center since 2019. Claire received her Ph.D. in 1996 from Université Pierre et Marie Curie in Paris, focusing on the genetic mapping of the region controlling X chromosome inactivation in mice and humans. She was recruited to the CNRS in 1999 after her post-doctoral studies at the Harvard Medical School in Boston, during which she investigated imprinted gene expression in Angelman Syndrome. She was awarded the Bronze and Silver Medals of the CNRS in 2007 and 2019, respectively. Claire is an EMBO member since 2016. She is also Professor at the Ecole Polytechnique, Université Paris-Saclay.


  • Huret C., Ferrayé L., David A. Mohamed M., Valentin N., Charlotte F., Savignac M., Goodhardt M., Guéry J-C.,Rougeulle C. and Morey C. Altered X-chromosome inactivation predisposes to autoimmunity . Science Advances, 2024 May
  • Rosspopoff O,  Cazottes E, Huret C, Loda A, Collier A, Casanova M, Rugg-Gunn P, Heard E, Ouimette JF, Rougeulle C. Species-specific regulation of XIST by the JPX/FTX orthologs. Nucleic Acids Research, 2023 Feb
  • Mahadik K, Rougeulle C.  Study of X Chromosome Activity Status in Human Naive Pluripotent Stem Cells Using RNA-FISH Methods Mol Biol. 2022;2416:239-255
  • Heard E, Rougeulle C. Digging into X chromosome inactivation. Science. 2021 Nov 19;374(6570):942-943.
  • Ouimette JF, Rougeulle C. Many XCI-ting routes to reach the eXACT dose. Nat Cell Biol. 2020 Dec;22(12):1397-1398
  • Cazottes E., Rougeulle C. Straight to the X: Modeling Human X Chromosome Inactivation in hESCs by FGF Signal Blockade.Cell Stem Cell. 2020 Sep 3;27(3):352-353
  • Patrat C, Ouimette JF, Rougeulle C. X chromosome inactivation in human development. Development. 2020 Jan 3;147(1).
  • Casanova M, Moscatelli M, Chauvière LÉ, Huret C, Samson J, Liyakat Ali TM, Rosspopoff O, Rougeulle C. A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans. Nat Commun. 2019 Dec 11;10(1):5652.
  • Furlan G, Gutierrez Hernandez N, Huret C, Galupa R, van Bemmel JG, Romito A, Heard E, Morey C, Rougeulle C. The Ftx Noncoding Locus Controls X Chromosome Inactivation Independently of Its RNA Products. Mol Cell. 2018 Apr 20.
  • Ouimette JF, Rougeulle C, Veitia RA. Three-dimensional genome architecture in health and disease. Clin Genet. 2018 Jan 29.
  • Kilens S, Meistermann D, Moreno D, Chariau C, Gaignerie A, Reignier A, Lelièvre Y, Casanova M, Vallot C, Nedellec S, Flippe L, Firmin J, Song J, Charpentier E, Lammers J, Donnart A, Marec N, Deb W, Bihouée A, Le Caignec C, Pecqueur C, Redon R, Barrière P, Bourdon J, Pasque V, Soumillon M, Mikkelsen TS, Rougeulle C, Fréour T, David L. Parallel derivation of isogenic human primed and naive induced pluripotent stem cells. Nat Commun. 2018 Jan 24;9(1):360
  • Sahakyan A, Plath K, Rougeulle C. Regulation of X-chromosome dosage compensation in human: mechanisms and model systems. Philos Trans R Soc Lond B Biol Sci. 2017 Nov 5;372(1733).
  • Vallot C., Patrat C., Collier AJ., Huret C., Casanova M., Liyakat Ali TM., Tosolini M., Frydman N., Heard E., Rugg-Gunn P.J.and Rougeulle C. Competing action of XIST and XACT noncoding RNAs in the control of X chromosome activity during human early development. Cell Stem Cell. 2017 Jan 5;20(1):102-111.
  • Cantone I., Bagci H., Dormann D., Dharmalingam G., Nesterova T., Brockdorff N., Rougeulle C., Vallot C., Heard E., Chaligne R., Merkenschlager M., Fisher A.G. Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming. Nat Commun. 2016 Aug 10;7:12354.
  • Vallot C., Ouimette JF., Rougeulle C. Establishment of X chromosome inactivation and epigenomic features of the inactive X depend on cellular contexts. Bioessays. 2016 Jul 8.
  • Casanova M., Liyakat Ali T.M., Rougeulle C. Enlightening the contribution of the dark matter to the X chromosome inactivation process in mammals. Semin Cell Dev Biol. 2016 May 9.
  • Furlan G., Rougeulle C. Function and evolution of the long noncoding RNA circuitry orchestrating X-chromosome inactivation in mammals. Wiley Interdiscip Rev RNA. 2016 May 13.
  • Nguyen LS, Lepleux M, Makhlouf M, Martin C, Fregeac J, Siquier-Pernet K, Philippe A, Feron F, Gepner B, Rougeulle C, Humeau Y, Colleaux L. Profiling olfactory stem cells from living patients identifies miRNAs relevant for autism pathophysiology. Mol Autism. 2016 Jan 8;7:1
  • Ouimette JF, Rougeulle C. How Many Non-coding RNAs Does It Take to Compensate Male/Female Genetic Imbalance? (2016) Adv Exp Med Biol. 886:33-49.
  • Lazorthes S., Briois S., Vallot C., Aguirrebengoa M., Thuret JY., St. Laurent G., Rougeulle, C., Kapranov P., Mann C., Trouche D., and Nicolas E. A vlincRNA participates in senescence maintenance by relieving H2AZ mediated repression at the INK4 locus. (2015) Nature Com. 6 : 5971.
  • Chen H., Aksoy I., Gonnot F., Osteil P., Aubry M., Hamela C., Rognard C., Hochard A., Voisin S., Fontaine E., Mure M., Afanassieff M., Cleroux E., Guibert S., Chen J., Vallot C., Acloque H., Genthon C., Donnadieu C., De Vos J., Sanlaville D., Guérin JF., Weber M., Stanton LW., Rougeulle, C., Pain B., Bourillot PY., and Savatier P. Reinforcement of STAT3 activity reprograms human embryonic stem cells to naïve-like pluripotency. (2015) Nature Com. 6: 7095.
  • Vallot C, Ouimette JF, Makhlouf M, Féraud O, Pontis J, Côme J, Martinat C, Bennaceur-Griscelli A, Lalande M, Rougeulle C. Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape. Cell Stem Cell. (2015) Apr 21. pii : S1934-5909(15)00127-7.
  • Makhlouf M, Ouimette JF, Oldfield A, Navarro P, Neuillet D, Rougeulle, C. A prominent and conserved role for YY1 in Xist transcriptional activation. (2014) Nat Commun. Sep 11;5:4878.
  • Vallot C. and Rougeulle, C. Long non-coding RNAs and human X-chromosome regulation: a coat for the active X chromosome. (2013) RNA Biol. 10(8):1262-5.
  • Vallot C. and Rougeulle, C. X chromosome inactivation in human: XACT and XIST, a non coding RNA for each X. (2013) Med Sci. 29(2):223-5.
  • Vallot C., Huret C, Lesecque Y., Resch A., Oudrhiri N., Bennaceur-Griscelli A., Duret L. and Rougeulle, C. XACT, a long non-coding transcript coating the active X chromosome in human pluripotent cells. (2013) Nat. Genet. 45(3):239-41
  • Vallot C. and Rougeulle, C. Epigenetic stability of human pluripotent stem cells. (2012) Epigenomics: From Chromatin Biology to Therapeutics. 118-133.
  • Romito, A. and Rougeulle, C. Origin and evolution of the long non-coding genes in the X-inactivation center. (2011). Biochimie. 93(11):1935-42.
  • Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C. (2011) Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. Hum Mol Genet. 20(4):705-18.
  • P. Navarro, A. Oldfield, J. Legoupi, N. Festuccia, A.Dubois, M. Attia, C. Rougeulle, I. Chambers, and P. Avner. (2010) Molecular coupling of Tsix regulation and pluripotency. Nature. 468(7322):457-60.
  • Mitjavila-Garcia, M.-T.; Bonnet, M.L.; Yates, F.; Haddad, R.; Oudrhiri, N.; Feraud, O.; Magniez, A.; Makhlouf, M.; Vallot, C.; Rougeulle C.; Bennaceur-Griscelli, A.; Turhan, A.G. (2010) Partial reversal of the methylation pattern of the X-linked gene HUMARA during hematopoietic differentiation of human embryonic stem cells. J Mol Cell Biol. 2(5): 291-298.
  • Navarro, P., Chamber, I., Karwacki-Neisius, V., Chureau, C., Morey, C., Rougeulle, C. and Avner, P. (2008) Molecular coupling of Xist regulation and pluripotency. Science. 321: 1693-1695.