Team 02: SILENT - Plant epigenetics

We study the molecular bases of epigenetic mechanisms controllng expression of genes and transposable elements. 

Gene silencing refers to various mechanisms of gene repression, which are epigenetic by nature and do not involve changes in the sequence of the DNA molecule. In both plants and animals, silencing is tightly associated with several epigenetic modifications of the chromatin, including cytosine DNA methylation and particular modification of histone proteins. Gene silencing does not only affect exogenous DNA entering the genome, but also endogenous genomic sequences such as certain protein-coding genes and most transposons. Efficient and accurate gene silencing is therefore essential for proper gene expression and genome stability. We combine genetic and genomic approaches to understand the mechanisms of gene silencing using the flowering plant Arabidopsis as a model.


In the cell nuclei of eukaryotic organisms, genomes are present in the molecular form of chromatin, which is formed by the association of DNA molecules and various proteins, notably histones. Chromatine structure, i.e. its chemical composition and physical state of compaction, plays an essential role in the control of gene expression. Chromatin structure largely depends, not only on the type of proteins that make it up (e.g. different histone variants), but also on the presence of chemical changes, called "epigenetic marks", that occur on both DNA and histones.

Using mainly the plant Arabidopsis thaliana as a model organism, we are implementing genetic and genomic approaches to characterize the molecular basis of epigenetic mechanisms. Our current projects aim at dissecting the pathways controlling the genomic profiles of different epigenetic marks and how these pathways are interconnected. We are also characterizing the molecular pathways involved in silencing of transposable elements and certain genes. We are particularly interested in silencing mechanisms independent of DNA methylation.

Research supported by:
Auvergne - RhôneAlpesRésultat de recherche d'images pour "embo young investigator"Résultat de recherche d'images pour "feder"

 Please do not hesitate to send your CV and research interest to Olivier if you are interested in joining us. 

Research thematics


Last Name First Name Position Contact
Olivier MATHIEU profile picture MATHIEU Olivier Principal Investigator
Margaux OLIVIER profile picture OLIVIER Margaux Post-doctoral Fellow
Marie-Noelle PELISSIER profile picture PELISSIER Marie-Noelle Research Engineer
Thierry PELISSIER profile picture PELISSIER Thierry Research Fellow


  • 2022
    • O. Mathieu, “Reaching the inaccessible DNA.”, Nat. Rev. Mol. Cell Biol., 2022.
  • 2021
    • A. Schmucker, B. Lei, Z. Lorkovic, M. Capella, S. Braun, P. Bourguet, O. Mathieu, K. Mechtler and F. Berger, “Crosstalk between H2A variant-specific modifications impacts vital cell functions.”, PLoS Genet., vol. 17 (6) , pp. e1009601, 2021.
    • P. Bourguet, C. Picard, R. Yelagandula, T. Pelissier, Z. Lorkovic, S. Feng, M. Pouch-Pelissier, A. Schmucker, S. Jacobsen, F. Berger and O. Mathieu, “The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation.”, Nature communications, vol. 12 (1) , pp. 2683, 2021.
  • 2020
  • 2019
    • C. Luxan-Hernandez, J. Lohmann, W. Hellmeyer, S. Seanpong, K. Woltje, Z. Magyar, A. Pettko-Szandtner, T. Pelissier, G. De Jaeger, S. Hoth, O. Mathieu and M. Weingartner, “PP7L is essential for MAIL1-mediated TE silencing and primary root growth.”, Plant J., 2019.
  • 2018
    • P. Bourguet, S. de Bossoreille, L. Lopez-Gonzalez, M. Pouch-Pelissier, A. Gomez-Zambrano, A. Devert, T. Pelissier, R. Pogorelcnik, I. Vaillant and O. Mathieu, “A role for MED14 and UVH6 in heterochromatin transcription upon destabilization of silencing.”, Life science alliance, vol. 1 (6) , pp. e201800197, 2018.
    • Y. Ikeda, R. Nishihama, S. Yamaoka, M. Arteaga-Vazquez, A. Aguilar-Cruz, D. Grimanelli, R. Pogorelcnik, R. Martienssen, K. Yamato, T. Kohchi, T. Hirayama and O. Mathieu, “Loss of CG methylation in Marchantia polymorpha causes disorganization of cell division and reveals unique DNA methylation regulatory mechanisms of non-CG methylation.”, Plant & cell physiology, 2018.
  • 2017
  • 2016
    • M. Rigal, C. Becker, T. Pelissier, R. Pogorelcnik, J. Devos, Y. Ikeda, D. Weigel and O. Mathieu, “Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids.”, Proc. Natl. Acad. Sci. U.S.A., 2016.
    • M. Clavel, T. Pelissier, T. Montavon, M. Tschopp, M. Pouch-Pelissier, J. Descombin, V. Jean, P. Dunoyer, C. Bousquet-Antonelli and J. Deragon, “Evolutionary history of double-stranded RNA binding proteins in plants: identification of new cofactors involved in easiRNA biogenesis.”, Plant molecular biology, 2016.
  • 2015
    • M. Clavel, T. Pelissier, J. Descombin, V. Jean, C. Picart, C. Charbonel, J. Saez-Vasquez, C. Bousquet-Antonelli and J. Deragon, “Parallel action of AtDRB2 and RdDM in the control of transposable element expression.”, BMC Plant Biol., vol. 15 , pp. 70, 2015.
  • 2014
    • O. Mathieu and N. Bouche, “Interplay between chromatin and RNA processing.”, Curr. Opin. Plant Biol., vol. 18C , pp. 60–65, 2014.
  • 2012
    • M. Rigal, Z. Kevei, T. Pelissier and O. Mathieu, “DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns.”, EMBO J., vol. 31 (13) , pp. 2981–93, 2012.
    • T. Pélissier and O. Mathieu, “Glue for Jumping Elements: Epigenetic Means for Controlling Transposable Elements in Plants”, Plant Transposable Elements, pp. 125–145, 2012.
  • 2011
    • C. Sarret, M. Rigal, C. Vaurs-Barriere, I. Dorboz, E. Eymard-Pierre, P. Combes, G. Giraud, R. Wanders, A. Afenjar, C. Francannet and O. Boespflug-Tanguy, “Sjogren-Larsson syndrome: novel mutations in the ALDH3A2 gene in a French cohort.”, J. Neurol. Sci., vol. 312 (1-2) , pp. 123–6, 2011.
    • T. Pelissier, M. Clavel, C. Chaparro, M. Pouch-Pelissier, H. Vaucheret and J. Deragon, “Double-stranded RNA binding proteins DRB2 and DRB4 have an antagonistic impact on polymerase IV-dependent siRNA levels in Arabidopsis.”, RNA, vol. 17 (8) , pp. 1502–10, 2011.
    • M. Rigal and O. Mathieu, “A "mille-feuille" of silencing: epigenetic control of transposable elements.”, Biochim. Biophys. Acta, vol. 1809 (8) , pp. 452–8, 2011.
    • Z. Kevei, M. Baloban, O. Da Ines, H. Tiricz, A. Kroll, K. Regulski, P. Mergaert and E. Kondorosi, “Conserved CDC20 cell cycle functions are carried out by two of the five isoforms in Arabidopsis thaliana.”, PLoS ONE, vol. 6 (6) , pp. e20618, 2011.
  • 2010
    • M. Tittel-Elmer, E. Bucher, L. Broger, O. Mathieu, J. Paszkowski and I. Vaillant, “Stress-induced activation of heterochromatic transcription.”, PLoS Genet., vol. 6 (10) , pp. e1001175, 2010.
  • 2009
    • S. Tsukahara, A. Kobayashi, A. Kawabe, O. Mathieu, A. Miura and T. Kakutani, “Bursts of retrotransposition reproduced in Arabidopsis.”, Nature, vol. 461 (7262) , pp. 423–6, 2009.
    • M. Mirouze, J. Reinders, E. Bucher, T. Nishimura, K. Schneeberger, S. Ossowski, J. Cao, D. Weigel, J. Paszkowski and O. Mathieu, “Selective epigenetic control of retrotransposition in Arabidopsis.”, Nature, vol. 461 (7262) , pp. 427–30, 2009.
  • 2008
    • S. Lageix, E. Lanet, M. Pouch-Pelissier, M. Espagnol, C. Robaglia, J. Deragon and T. Pelissier, “Arabidopsis eIF2alpha kinase GCN2 is essential for growth in stress conditions and is activated by wounding.”, BMC Plant Biol., vol. 8 , pp. 134, 2008.
    • M. Pouch-Pelissier, T. Pelissier, T. Elmayan, H. Vaucheret, D. Boko, M. Jantsch and J. Deragon, “SINE RNA induces severe developmental defects in Arabidopsis thaliana and interacts with HYL1 (DRB1), a key member of the DCL1 complex.”, PLoS Genet., vol. 4 (6) , pp. e1000096, 2008.
    • M. Caikovski, C. Yokthongwattana, Y. Habu, T. Nishimura, O. Mathieu and J. Paszkowski, “Divergent evolution of CHD3 proteins resulted in MOM1 refining epigenetic control in vascular plants.”, PLoS Genet., vol. 4 (8) , pp. e1000165, 2008.