Team 03: ChrOmatin and 3D nuclEar Dynamics (CODED)

Our objective is to investigate the role of chromatin organization in the dynamic transcriptional regulation occurring during development and in response to environmental stimuli.


Eukaryotic genomes are organized into chromatin that packages the long DNA molecules and functions as carrier of epigenetic information. Chromatin organization affects all fundamental processes operating on DNA such as replication, repair and transcription. Indeed, genome structure and expression are determined both by local chromatin features at the level of the nucleosome, such as its composition in histone variants and their post-translational modifications, and by nuclear organization including the formation of higher-order chromatin domains such as the heterochromatic chromocenters. How these different aspects of chromatin organization are coordinated to allow a comprehensive transcriptional response during development and in response to external stimuli remains an unresolved question.

To comprehend these fundamental processes we study the epigenetic mechanisms involved in the establishment, maintenance and dynamics of chromatin organization using the plant Arabidopsis thaliana as a model system.

Our first objective is to characterize the processes that determine chromatin fiber organization and to analyze the consequences of deficient chromatin structure on gene transcription. We are concentrating on the impact of nucleosome composition, in particular the role of histone variants and their incorporation by histone chaperones. We also explore the role of chromatin dynamics via the study of the non-histone chromatin proteins, High Mobility Group A (HMGA).

The second objective is to study the chromatin organization in nuclear space by analyzing the interactions between chromatin, nucleoskeleton and nuclear envelope. We seek to characterize the network of proteins involved in these interactions and to understand the relationship between nuclear position and transcriptional activity.

We use epigenetics, genetics and molecular biology techniques and develop 3D-bioimaging approaches in collaboration with the GReD's microscopy platform CLIC and the Institut Pascal.

Our research group comprises CNRS researchers, an INSERM engineer, assistant professors belonging to the Clermont Auvergne University as well as students at the PhD and Master level. We are part of regional (CAP20-25 Challenge1 « Agro-écosystèmes durables dans un contexte de changement global »), national (GDR « EPIPLANT ») and European networks (COST Action « Impact of Nuclear Domains in Gene Expression and Plant Traits »; INDEPTH chaired par C. Tatout).


Contact us if you are interested to discuss with us or to join our team as future CNRS researcher, post-doc, PhD student or trainee.


Research thematics


Last Name First Name Position Contact
Simon AMIARD profile picture AMIARD Simon Research Fellow
Sylviane COTTERELL profile picture COTTERELL Sylviane Associate Professor
Cecilia DEFONTIS profile picture DEFONTIS Cecilia Intern
Sophie DESSET profile picture DESSET Sophie Research Engineer
Lea FEIT profile picture FEIT Lea Ph.D Student
Samuel LE GOFF profile picture LE GOFF Samuel Associate Professor
Guillaume MOUGEOT profile picture MOUGEOT Guillaume Ph.D Student
Stefania PALTRINIERI profile picture PALTRINIERI Stefania Ph.D Student
Aline PROBST profile picture PROBST Aline Principal Investigator
Lauriane SIMON profile picture SIMON Lauriane Assistant Professor
Gilles SIRETA profile picture SIRETA Gilles Ph.D Student
Aurelia STEVENS profile picture STEVENS Aurelia Associate Professor
Christophe TATOUT profile picture TATOUT Christophe Principal Investigator
Abderrahime TIZI profile picture TIZI Abderrahime Intern
Sylvie TUTOIS profile picture TUTOIS Sylvie Associate Professor
Emmanuel VANROBAYS profile picture VANROBAYS Emmanuel Associate Professor
Manon VERDIER profile picture VERDIER Manon Research Technician


  • 2022
    • R. Randall, C. Jourdain, A. Nowicka, K. Kaduchova, M. Kubova, M. Ayoub, V. Schubert, C. Tatout, I. Colas, Kalyanikrishna, S. Desset, S. Mermet, A. Boulaflous-Stevens, I. Kubalova, T. Mandakova, S. Heckmann, M. Lysak, M. Panatta, R. Santoro, D. Schubert, A. Pecinka, D. Routh and C. Baroux, “Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes.”, Nucleus, vol. 13 (1) , pp. 277–299, 2022.
    • A. Probst, “Deposition and eviction of histone variants define functional chromatin states in plants.”, Curr. Opin. Plant Biol., vol. 69 , pp. 102266, 2022.
    • T. Dubos, A. Poulet, G. Thomson, E. Pery, F. Chausse, C. Tatout, S. Desset, J. van Wolfswinkel and Y. Jacob, “NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects.”, BMC bioinformatics, vol. 23 (1) , pp. 216, 2022.
    • C. Tatout, G. Mougeot, G. Parry, C. Baroux, M. Pradillo and D. Evans, “The INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) Academy: a community resource for plant science.”, J. Exp. Bot., vol. 73 (7) , pp. 1926–1933, 2022.
    • G. Mougeot, T. Dubos, F. Chausse, E. Pery, K. Graumann, C. Tatout, D. Evans and S. Desset, “Deep learning -- promises for 3D nuclear imaging: a guide for biologists.”, Journal of cell science, vol. 135 (7) , 2022.
    • P. Pouchin, R. Zoghlami, R. Valarcher, M. Delannoy, M. Carvalho, C. Belle, M. Mongy, S. Desset and F. Brau, “Easing batch image processing from OMERO: a new toolbox for ImageJ.”, F1000Research, vol. 11 , pp. 392, 2022.
  • 2021
    • Y. Huang, S. Sicar, J. Ramirez-Prado, D. Manza-Mianza, J. Antunez-Sanchez, R. Brik-Chaouche, N. Rodriguez-Granados, J. An, C. Bergounioux, M. Mahfouz, H. Hirt, M. Crespi, L. Concia, F. Barneche, S. Amiard, A. Probst, J. Gutierrez-Marcos, F. Ariel, C. Raynaud, D. Latrasse and M. Benhamed, “Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis.”, Genome Res., 2021.
    • E. Layat, M. Bourcy, S. Cotterell, J. Zdzieszynska, S. Desset, C. Duc, C. Tatout, C. Bailly and A. Probst, “The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination.”, International journal of molecular sciences, vol. 22 (8) , 2021.
    • F. Lopez, A. Fort, L. Tadini, A. Probst, M. McHale, J. Friel, P. Ryder, F. Pontvianne, P. Pesaresi, R. Sulpice, P. McKeown, G. Brychkova and C. Spillane, “Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number.”, Plant Cell, 2021.
    • A. Meschichi, M. Ingouff, C. Picart, M. Mirouze, S. Desset, F. Gallardo, K. Bystricky, N. Picault, S. Rosa and F. Pontvianne, “ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization in Planta.”, Front Plant Sci, vol. 12 , pp. 677849, 2021.
  • 2020
  • 2019
    • T. Dumur, S. Duncan, K. Graumann, S. Desset, R. Randall, O. Scheid, D. Prodanov, C. Tatout and C. Baroux, “Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions.”, Nucleus, vol. 10 (1) , pp. 181–212, 2019.
    • S. Le Goff, B. Nur Keceli, H. Jerabkova, S. Heckmann, T. Rutten, S. Cotterell, V. Schubert, E. Roitinger, K. Mechtler, F. Franklin, C. Tatout, A. Houben, D. Geelen, A. Probst and I. Lermontova, “The H3 histone chaperone NASP(SIM) (3) escorts CenH3 in Arabidopsis.”, Plant J., 2019.
  • 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.
    • C. Charbonnel, O. Rymarenko, O. Da Ines, F. Benyahya, C. White, F. Butter and S. Amiard, “The Linker Histone GH1-HMGA1 Is Involved in Telomere Stability and DNA Damage Repair.”, Plant physiology, vol. 177 (1) , pp. 311–327, 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.
    • A. Poulet, X. Zhou, K. Tamura, I. Meier, C. Tatout, K. Graumann and D. Evans, “Computational Methods for Studying the Plant Nucleus.”, Meth. Mol. Biol., vol. 1840 , pp. 205–219, 2018.
    • M. Voisin, E. Vanrobays and C. Tatout, “Investigation of Nuclear Periphery Protein Interactions in Plants Using the Membrane Yeast Two-Hybrid (MbY2H) System.”, Meth. Mol. Biol., vol. 1840 , pp. 221–235, 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.
    • V. Muchova, S. Amiard, I. Mozgova, M. Dvorackova, M. Gallego, C. White and J. Fajkus, “Homology-dependent repair is involved in 45S rDNA loss in plant CAF-1 mutants.”, Plant J., vol. 81 (2) , pp. 198–209, 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.
    • P. Merle, M. Gueugneau, M. Teulade-Fichou, M. Muller-Barthelemy, S. Amiard, E. Chautard, C. Guetta, V. Dedieu, Y. Communal, J. Mergny, M. Gallego, C. White, P. Verrelle and A. Tchirkov, “Highly efficient radiosensitization of human glioblastoma and lung cancer cells by a G-quadruplex DNA binding compound.”, Scientific reports, vol. 5 , pp. 16255, 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.
    • P. Kalhorzadeh, Z. Hu, T. Cools, S. Amiard, E. Willing, N. De Winne, K. Gevaert, G. De Jaeger, K. Schneeberger, C. White and L. De Veylder, “Arabidopsis thaliana RNase H2 deficiency counteracts the needs for the WEE1 checkpoint kinase but triggers genome instability.”, Plant Cell, vol. 26 (9) , pp. 3680–92, 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.
    • W. Wei, Z. Ba, M. Gao, Y. Wu, Y. Ma, S. Amiard, C. White, J. Rendtlew Danielsen, Y. Yang and Y. Qi, “A role for small RNAs in DNA double-strand break repair.”, Cell, vol. 149 (1) , pp. 101–12, 2012.
    • A. Poulet, S. Pisano, C. Faivre-Moskalenko, B. Pei, Y. Tauran, Z. Haftek-Terreau, F. Brunet, Y. Le Bihan, M. Ledu, F. Montel, N. Hugo, S. Amiard, F. Argoul, A. Chaboud, E. Gilson and M. Giraud-Panis, “The N-terminal domains of TRF1 and TRF2 regulate their ability to condense telomeric DNA.”, Nucleic Acids Res., vol. 40 (6) , pp. 2566–76, 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.
    • J. Ye, C. Lenain, S. Bauwens, A. Rizzo, A. Saint-Leger, A. Poulet, D. Benarroch, F. Magdinier, J. Morere, S. Amiard, E. Verhoeyen, S. Britton, P. Calsou, B. Salles, A. Bizard, M. Nadal, E. Salvati, L. Sabatier, Y. Wu, A. Biroccio, A. Londono-Vallejo, M. Giraud-Panis and E. Gilson, “TRF2 and apollo cooperate with topoisomerase 2alpha to protect human telomeres from replicative damage.”, Cell, vol. 142 (2) , pp. 230–42, 2010.
    • I. Ourliac-Garnier, A. Poulet, R. Charif, S. Amiard, F. Magdinier, K. Rezai, E. Gilson, M. Giraud-Panis and S. Bombard, “Platination of telomeric DNA by cisplatin disrupts recognition by TRF2 and TRF1.”, Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, vol. 15 (5) , pp. 641–54, 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.
    • A. Poulet, R. Buisson, C. Faivre-Moskalenko, M. Koelblen, S. Amiard, F. Montel, S. Cuesta-Lopez, O. Bornet, F. Guerlesquin, T. Godet, J. Moukhtar, F. Argoul, A. Declais, D. Lilley, S. Ip, S. West, E. Gilson and M. Giraud-Panis, “TRF2 promotes, remodels and protects telomeric Holliday junctions.”, EMBO J., vol. 28 (6) , pp. 641–51, 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.