Team 03: Histone variants and the nuclear envelope in heterochromatin organization

Our group is interested in the molecular mechanisms implicated in maintenance and developmental dynamics of heterochromatin organization in the model system Arabidopsis. We study heterochromatin composition in histone variants, heterochromatin position within the nucleus in respect to the nuclear envelope and the transcriptional regulation occurring at heterochromatic loci.


Historically, our laboratory was one of the pioneers in the discovery of a specific class of repeated sequences in the Arabidopsis genome, the clusters of 5S ribosomal RNA (rRNA) genes that encode a critical RNA component of the ribosome. Despite being situated within the transcriptionally repressive environment of pericentromeric heterochromatin, part of the 5S rRNA genes is highly transcribed. Our work showed that 5S rRNA expression is controlled through the availability of its specific transcription factor TFIIIA, and epigenetic mechanisms such as the RNA directed DNA methylation pathway. Together, these different modes of regulation allow fine-tuning of 5S rRNA transcription during development and overcome the repressive effect of the heterochromatic environment.

While we continue studying 5S rDNA clusters as model genes situated within heterochromatin, we now concentrate our efforts on better defining intrinsic features of heterochromatin organization and its dynamics. For that purpose we pursue two complementary approaches, which aim to identify the critical players involved in establishment and maintenance of heterochromatin in Arabidopsis:

We study histone variants and their mode of incorporation into chromatin, which is controlled by specific histone chaperone proteins. Our aim is to understand how the different variants together with their specific post-translational modifications impact heterochromatin organization and function.

We further investigate the molecular structures implicated in the nuclear-cytoplasmic crosstalk and focus on identifying complexes that link chromatin to the nuclear periphery. Indeed, the periphery of the nucleus has emerged as an anchoring point for certain chromatin domains and to impact their expression. Using reverse genetic approaches and specifically developed 3D imaging tools in collaboration with bio-mathematicians, we aim to understand the interrelationship between nuclear position, chromatin organization and gene expression. 

Research thematics


Last Name First Name Position Contact
Cindy CHAUVET profile picture CHAUVET Cindy Intern
Nicolas CORRE profile picture CORRE Nicolas Intern
Sylviane COTTERELL profile picture COTTERELL Sylviane Associate Professor
Nicolas DESFORGES-DESAMIN profile picture DESFORGES-DESAMIN Nicolas Intern
Sophie DESSET profile picture DESSET Sophie Research Engineer
Gwenaelle DETOURNE profile picture DETOURNE Gwenaelle Ph.D Student
Tristan DUBOS profile picture DUBOS Tristan Ph.D Student
Celine GONTHIER profile picture GONTHIER Celine Engineer
Samuel LE GOFF profile picture LE GOFF Samuel Associate Professor
Yanru LI profile picture LI Yanru Intern
Jeremy MEZHOUD profile picture MEZHOUD Jeremy Intern
Vincent PAILLER profile picture PAILLER Vincent Intern
Claire PELISSIER profile picture PELISSIER Claire Technical Assistant
Aline PROBST profile picture PROBST Aline Principal Investigator
Christophe TATOUT profile picture TATOUT Christophe Professor
Sylvie TUTOIS profile picture TUTOIS Sylvie Associate Professor
Emmanuel VANROBAYS profile picture VANROBAYS Emmanuel Associate Professor


  • 2018
    • S. Kemeny, C. Tatout, G. Salaun, C. Pebrel-Richard, C. Goumy, N. Ollier, E. Maurin, B. Pereira, P. Vago and L. Gouas, “Spatial organization of chromosome territories in the interphase nucleus of trisomy 21 cells.”, Chromosoma, vol. 127 (2) , pp. 247–259, 2018.
    • M. Benoit, L. Simon, S. Desset, C. Duc, S. Cotterell, A. Poulet, S. Le Goff, C. Tatout and A. Probst, “Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development.”, The New phytologist, 2018.
    • G. Parry, A. Probst, C. Baroux and C. Tatout, “Meeting report - INDEPTH kick-off meeting.”, Journal of cell science, vol. 131 (12) , 2018.
    • L. Simon, F. Rabanal, T. Dubos, C. Oliver, D. Lauber, A. Poulet, A. Vogt, A. Mandlbauer, S. Le Goff, A. Sommer, H. Duborjal, C. Tatout and A. Probst, “Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.”, Nucleic Acids Res., 2018.
    • A. Probst, “A Compendium of Methods to Analyze the Spatial Organization of Plant Chromatin.”, Meth. Mol. Biol., vol. 1675 , pp. 397–418, 2018.
    • L. Simon and A. Probst, “High-Affinity LNA-DNA Mixmer Probes for Detection of Chromosome-Specific Polymorphisms of 5S rDNA Repeats in Arabidopsis thaliana.”, Meth. Mol. Biol., vol. 1675 , pp. 481–491, 2018.
    • S. Desset, A. Poulet and C. Tatout, “Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ.”, Meth. Mol. Biol., vol. 1675 , pp. 615–632, 2018.
  • 2017
  • 2016
  • 2015
    • S. Smith, C. Galinha, S. Desset, F. Tolmie, D. Evans, C. Tatout and K. Graumann, “Marker gene tethering by nucleoporins affects gene expression in plants.”, Nucleus, vol. 6 (6) , pp. 471–8, 2015.
    • A. Probst and O. Mittelsten Scheid, “Stress-induced structural changes in plant chromatin.”, Curr. Opin. Plant Biol., vol. 27 , pp. 8–16, 2015.
    • C. Duc, M. Benoit, S. Goff, L. Simon, A. Poulet, S. Cotterell, C. Tatout and A. Probst, “The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF-1 complex mutants.”, Plant J., 2015.
    • L. Simon, M. Voisin, C. Tatout and A. Probst, “Structure and Function of Centromeric and Pericentromeric Heterochromatin in Arabidopsis thaliana.”, Front Plant Sci, vol. 6 , pp. 1049, 2015.
  • 2014
    • K. Graumann, E. Vanrobays, S. Tutois, A. Probst, D. Evans and C. Tatout, “Characterization of two distinct subfamilies of SUN-domain proteins in Arabidopsis and their interactions with the novel KASH-domain protein AtTIK.”, J. Exp. Bot., vol. 65 (22) , pp. 6499–512, 2014.
    • A. Poulet, I. Arganda-Carreras, D. Legland, A. Probst, P. Andrey and C. Tatout, “NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei.”, Bioinformatics (Oxford, England), 2014.
    • C. Tatout, D. Evans, E. Vanrobays, A. Probst and K. Graumann, “The plant LINC complex at the nuclear envelope.”, Chromosome Res., 2014.
    • M. Thomas, L. Pingault, A. Poulet, J. Duarte, M. Throude, S. Faure, J. Pichon, E. Paux, A. Probst and C. Tatout, “Evolutionary history of Methyltransferase 1 genes in hexaploid wheat.”, BMC genomics, vol. 15 , pp. 922, 2014.
  • 2013
    • M. Casanova, M. Pasternak, F. El Marjou, P. Le Baccon, A. Probst and G. Almouzni, “Heterochromatin reorganization during early mouse development requires a single-stranded noncoding transcript.”, Cell Rep, vol. 4 (6) , pp. 1156–67, 2013.
    • M. Benoit, E. Layat, S. Tourmente and A. Probst, “Heterochromatin dynamics during developmental transitions in Arabidopsis - a focus on ribosomal DNA loci.”, Gene, vol. 526 (1) , pp. 39–45, 2013.
  • 2012
    • E. Layat, A. Probst and S. Tourmente, “Structure, function and regulation of Transcription Factor IIIA: From Xenopus to Arabidopsis.”, Biochim. Biophys. Acta, vol. 1829 (3-4) , pp. 274–82, 2012.
    • A. Ayar, S. Wehrkamp-Richter, J. Laffaire, S. Le Goff, J. Levy, S. Chaignon, H. Salmi, A. Lepicard, C. Sallaud, M. Gallego, C. White and W. Paul, “Gene targeting in maize by somatic ectopic recombination.”, Plant Biotechnol. J., vol. 11 (3) , pp. 305–14, 2012.
  • 2011
    • G. Almouzni and A. Probst, “Heterochromatin maintenance and establishment: lessons from the mouse pericentromere.”, Nucleus, vol. 2 (5) , pp. 332–8, 2011.
    • B. Tamasloukht, M. Wong Quai Lam, Y. Martinez, K. Tozo, O. Barbier, C. Jourda, A. Jauneau, G. Borderies, S. Balzergue, J. Renou, S. Huguet, J. Martinant, C. Tatout, C. Lapierre, Y. Barriere, D. Goffner and M. Pichon, “Characterization of a cinnamoyl-CoA reductase 1 (CCR1) mutant in maize: effects on lignification, fibre development, and global gene expression.”, J. Exp. Bot., vol. 62 (11) , pp. 3837–48, 2011.
    • A. Probst and G. Almouzni, “Heterochromatin establishment in the context of genome-wide epigenetic reprogramming.”, Trends Genet., vol. 27 (5) , pp. 177–85, 2011.
    • C. Maison, D. Bailly, D. Roche, R. Montes de Oca, A. Probst, I. Vassias, F. Dingli, B. Lombard, D. Loew, J. Quivy and G. Almouzni, “SUMOylation promotes de novo targeting of HP1alpha to pericentric heterochromatin.”, Nat. Genet., vol. 43 (3) , pp. 220–7, 2011.
    • C. Maison, J. Quivy, A. Probst and G. Almouzni, “Heterochromatin at mouse pericentromeres: a model for de novo heterochromatin formation and duplication during replication.”, Cold Spring Harb. Symp. Quant. Biol., vol. 75 , pp. 155–65, 2011.
  • 2010
    • A. Probst, I. Okamoto, M. Casanova, F. El Marjou, P. Le Baccon and G. Almouzni, “A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development.”, Dev. Cell, vol. 19 (4) , pp. 625–38, 2010.
    • E. Vanrobays, B. Jennings and D. Ish-Horowicz, “Identification and mapping of induced chromosomal deletions using sequence polymorphisms.”, BioTechniques, vol. 48 (1) , pp. 53–60, 2010.
  • 2009
    • A. Probst, E. Dunleavy and G. Almouzni, “Epigenetic inheritance during the cell cycle.”, Nat. Rev. Mol. Cell Biol., vol. 10 (3) , pp. 192–206, 2009.
    • Y. Barriere, V. Mechin, F. Lafargette, D. Manicacci, F. Guillon, H. Wang, D. Lauressergues, M. Pichon, M. Bosio and C. Tatout, “Towards the discovery of maize cell wall genes involved in silage quality and capacity to biofuel production”, Maydica, pp. 161–198, 2009.
  • 2008
    • E. Vanrobays, A. Leplus, Y. Osheim, A. Beyer, L. Wacheul and D. Lafontaine, “TOR regulates the subcellular distribution of DIM2, a KH domain protein required for cotranscriptional ribosome assembly and pre-40S ribosome export.”, RNA, vol. 14 (10) , pp. 2061–73, 2008.