Antoine MOLARO



Antoine MOLAROprofile picture

Google Scholar


Twitter: @AntoineMolaro

Research Experience

Group Leader, iGReD - Team: Evolutionary Epigenomics and Genetic Conflicts

2013-2020       Postdoctoral Fellow, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. Advisor: Dr. Harmit S. Malik - Damon Runyon Cancer Research Foundation Fellow

2008-2012       Ph.D. thesis, Cold Spring Harbor Laboratory, NY, USA. Advisor: Prof. Gregory J. Hannon

2008    Master (II) internship, Cold Spring Harbor Laboratory, NY, USA. Advisor: Dr. Alexei Aravin and Prof. Gregory J. Hannon

2007    Master (I) internship, Pasteur Institute, Paris, France. Advisor: Dr. Philippe Clerc and Prof. Philip Avner



2012    Ph.D : Université Pierre et Marie Curie, Paris, France / Cold Spring Harbor Laboratory, NY, USA. Doctoral school: “Life Science Complexity” – ED515

2008    Master : Developmental Biology, Université Pierre et Marie Curie, Paris, France / École Normale Supérieure, Paris, France

2006    License : Biology, Université Pierre et Marie Curie, Paris, France / École Normale Supérieure, Paris, France


Fellowships and Scholarships

2014    Postdoctoral Fellowship, Damon Runyon Cancer Research Foundation.

2008    Scholarship for Excellence, awarded by Université Pierre et Marie Curie.



2020    « Amorçage de Jeunes Équipes », awarded by Fondation pour la Recherche Médicale.



I am broadly interested in understanding the function of the germline epigenome. In mammals, the germline epigenome is key to the inheritance of genetic and epigenetic information. It is also at the heart of intense evolutionary battles, known as genetic conflicts. These can arise between genetic elements within our genomes, whole chromosomes or between parents. In fact, these constant tugs of war shape fundamental aspect of reproduction and speciation and drive rapid evolutionary innovation. Thus, contrary to current paradigms that focus on evolutionary conservation, I study the rapid evolution of the epigenome to discover novel principles in reproduction and speciation. My research program interfaces epigenomics with evolutionary biology.


Some prior research

As a graduate student, I have uncovered some of the rules behind the co-evolution of the germline genome and epigenome in primates (Molaro, Hodges et al., 2011). I also identified the consequences of small RNA’s adaptive evolution on the establishment of the germ cell epigenome in mice (Molaro et al., 2014). During my postdoc, I have discovered adaptive evolution in germline DNA methyltransferases and in short H2A histone variants in mammals (Molaro et al., 2018 and 2019). Using mouse models, I have uncovered that some short H2As have parental-effect functions that are crucial for embryogenesis (Molaro et al., 2020). In collaboration with cancer biologists we have discovered that short H2As are ectopically expressed in many human cancer (Chew et al., 2021).


Current research

Currently, my team uses mouse models, mammalian cell culture and comparative epigenomics to answer some of the following questions:

1)    What are the functions of protein domains subject to diversification in chromatin modifying enzymes?

2)    Which evolutionary forces drive short histone H2A variants diversification in mammals?

3)    How do short H2As imprint parental epigenomes during mammalian reproduction?

4)    How does epigenome evolution shape normal development and disease progression in humans?


  • 2021
    • G. Chew, M. Bleakley, R. Bradley, H. Malik, S. Henikoff, A. Molaro and J. Sarthy, “Short H2A histone variants are expressed in cancer.”, Nature communications, vol. 12 (1) , pp. 490, 2021.
  • 2020
    • A. Molaro, A. Wood, D. Janssens, S. Kindelay, M. Eickbush, S. Wu, P. Singh, C. Muller, S. Henikoff and H. Malik, “Biparental contributions of the H2A.B histone variant control embryonic development in mice.”, PLoS biology, vol. 18 (12) , pp. e3001001, 2020.
    • P. Navarro-Costa, A. Molaro, C. Misra, C. Meiklejohn and P. Ellis, “Sex and suicide: The curious case of Toll-like receptors.”, PLoS biology, vol. 18 (3) , pp. e3000663, 2020.
    • A. Molaro, H. Malik and D. Bourc'his, “Dynamic evolution of de novo DNA methyltransferases in rodent and primate genomes.”, Molecular biology and evolution, 2020.
  • 2018
    • A. Molaro, J. Young and H. Malik, “Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals.”, Genome Res., vol. 28 (4) , pp. 460–473, 2018.
    • J. Qu, E. Hodges, A. Molaro, P. Gagneux, M. Dean, G. Hannon and A. Smith, “Evolutionary expansion of DNA hypomethylation in the mammalian germline genome.”, Genome Res., vol. 28 (2) , pp. 145–158, 2018.
    • A. Molaro and I. Drinnenberg, “Studying the Evolution of Histone Variants Using Phylogeny.”, Meth. Mol. Biol., vol. 1832 , pp. 273–291, 2018.
  • 2017
    • A. Molaro and H. Malik, “Culture shock.”, eLife, vol. 6 , 2017.
  • 2016
    • A. Molaro and H. Malik, “Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline.”, Current opinion in genetics & development, vol. 37 , pp. 51–58, 2016.
  • 2014
    • A. Molaro, I. Falciatori, E. Hodges, A. Aravin, K. Marran, S. Rafii, W. McCombie, A. Smith and G. Hannon, “Two waves of de novo methylation during mouse germ cell development.”, Genes Dev., vol. 28 (14) , pp. 1544–9, 2014.
  • 2013
    • L. Kaaij, M. van de Wetering, F. Fang, B. Decato, A. Molaro, H. van de Werken, J. van Es, J. Schuijers, E. de Wit, W. de Laat, G. Hannon, H. Clevers, A. Smith and R. Ketting, “DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus.”, Genome biology, vol. 14 (5) , pp. R50, 2013.
  • 2012
    • F. Fang, E. Hodges, A. Molaro, M. Dean, G. Hannon and A. Smith, “Genomic landscape of human allele-specific DNA methylation.”, Proc. Natl. Acad. Sci. U.S.A., vol. 109 (19) , pp. 7332–7, 2012.
    • F. Muerdter, I. Olovnikov, A. Molaro, N. Rozhkov, B. Czech, A. Gordon, G. Hannon and A. Aravin, “Production of artificial piRNAs in flies and mice.”, RNA, vol. 18 (1) , pp. 42–52, 2012.
  • 2011
    • E. Hodges, A. Molaro, C. Dos Santos, P. Thekkat, Q. Song, P. Uren, J. Park, J. Butler, S. Rafii, W. McCombie, A. Smith and G. Hannon, “Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment.”, Molecular cell, vol. 44 (1) , pp. 17–28, 2011.
    • A. Molaro, E. Hodges, F. Fang, Q. Song, W. McCombie, G. Hannon and A. Smith, “Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates.”, Cell, vol. 146 (6) , pp. 1029–41, 2011.