Research Team

Evolutionary Epigenomics and Genetic Conflicts

HomeTeamsEvolutionary Epigenomics and Genetic Conflicts
Access to genetic information is organized by epigenetic modifications and chromatin pathways. These mechanisms predate the last common ancestor to all eukaryotes and are hypothesized to perform conserved functions. Nevertheless, we find that they are subject to diversification in mammals (see publications). Genetic conflicts are well known to drive genome diversification, however their impact on epigenome evolution is poorly understood. Our team uses phylogenetics to identify chromatin pathways with evolutionary signatures of genetic conflicts, and test their function on the epigenome in vivo.




Currently, the Molaro Lab uses mouse models, mammalian cell culture and comparative epigenomics to answer 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?


Press and other highlights of our work


Unususal Histones Mediate Parental Conflicts in Mammals (Fragile Nucleosome Seminar Series, 2021, Youtube)

Jeune Chercheur Funding Highlight – Fondation pour la Recherche Médicale.

Tête-à-Tête with Antoine Molaro (14th NYRA meeting)

The Secret Role Histones Played in Complex Cell Evolution (Wired, 2021, by Viviane Callier)

Fundamental proteins that guide embryo development are co-opted by cancer (Fred Hutch News, 2021, by Sabrina Richards)


Team Pictures

February 2024

The “Evolutionary Epigenomics and Genetic Conflicts” studies the evolution of chromatin regulation in the context of genetic conflicts.


October 2022


Summer 2022


Summer 2021




19 publications

Recurrent Evolutionary Innovations in Rodent and Primate Schlafen Genes

Published on 13 Jan 2024 in bioRxiv

Joris Mordier , Marine Fraisse , Michel Cohen-Tannoudji , Antoine Molaro


Histone renegades: Unusual H2A histone variants in plants and animals.

Published on 15 Feb 2023 in Seminars in cell & developmental biology , vol. 135 - pp 35-42

Osakabe A, Molaro A


Distinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19.

Published on 30 Aug 2022 in Proceedings of the National Academy of Sciences of the United States of America , vol. 119 - pp e2206610119

Cariou M, Picard L, Guéguen L, Jacquet S, Cimarelli A, Fregoso OI, Molaro A , Navratil V, Etienne L

Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline.

Published on 03 Feb 2022 in Molecular biology and evolution , vol. 39

Raman P, Rominger MC, Young JM, Molaro A , Tsukiyama T, Malik HS


Short H2A histone variants are expressed in cancer.

Published on 20 Jan 2021 in Nature communications , vol. 12 - pp 490

Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A , Sarthy J


Biparental contributions of the H2A.B histone variant control embryonic development in mice.

Published on 04 Dec 2020 in PLoS biology , vol. 18 - pp e3001001

Molaro A , Wood AJ, Janssens D, Kindelay SM, Eickbush MT, Wu S, Singh P, Muller CH, Henikoff S, Malik HS

Dynamic Evolution of De Novo DNA Methyltransferases in Rodent and Primate Genomes.

Published on 01 Jul 2020 in Molecular biology and evolution , vol. 37 - pp 1882-1892

Molaro A , Malik HS, Bourc'his D

Sex and suicide: The curious case of Toll-like receptors.

Published on 04 Mar 2020 in PLoS biology , vol. 18 - pp e3000663

Navarro-Costa PA, Molaro A , Misra CS, Meiklejohn CD, Ellis PJ


Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals.

Published on 04 Apr 2018 in Genome research , vol. 28 - pp 460-473

Molaro A , Young JM, Malik HS

Evolutionary expansion of DNA hypomethylation in the mammalian germline genome.

Published on 04 Feb 2018 in Genome research , vol. 28 - pp 145-158

Qu J, Hodges E, Molaro A , Gagneux P, Dean MD, Hannon GJ, Smith AD

Studying the Evolution of Histone Variants Using Phylogeny.

Published on 01 Jan 2018 in Methods in molecular biology (Clifton, N.J.) , vol. 1832 - pp 273-291

Molaro A , Drinnenberg IA


Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline.

Published on 04 Apr 2016 in Current opinion in genetics & development , vol. 37 - pp 51-58

Molaro A , Malik HS


Two waves of de novo methylation during mouse germ cell development.

Published on 15 Jul 2014 in Genes & development , vol. 28 - pp 1544-9

Molaro A , Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD, Hannon GJ


Genomic landscape of human allele-specific DNA methylation.

Published on 08 May 2012 in Proceedings of the National Academy of Sciences of the United States of America , vol. 109 - pp 7332-7

Fang F, Hodges E, Molaro A , Dean M, Hannon GJ, Smith AD

Genomic landscape of human allele-specific DNA methylation.

Published on 08 May 2012 in Proceedings of the National Academy of Sciences of the United States of America , vol. 109 - pp 7332-7

Fang F, Hodges E, Molaro A , Dean M, Hannon GJ, Smith AD

Production of artificial piRNAs in flies and mice.

Published on 04 Jan 2012 in RNA (New York, N.Y.) , vol. 18 - pp 42-52

Muerdter F, Olovnikov I, Molaro A , Rozhkov NV, Czech B, Gordon A, Hannon GJ, Aravin AA


Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment.

Published on 07 Oct 2011 in Molecular cell , vol. 44 - pp 17-28

Hodges E, Molaro A , Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ

Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates.

Published on 16 Sep 2011 in Cell , vol. 146 - pp 1029-41

Molaro A , Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD

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