Christophe TATOUT

Professor in Genetics & epigenetics

Resume

Christophe TATOUTprofile picture
  • 2013: Professor of Genetics, Principal Investigator
  • 2009: Professor of Genetics, Blaise Pascal University, (S. Tourmente's Team)
  • 1997-2009: Group leader of the maize genetics and genomics team at Biogemma, France.
  • 1999-2007: Member of the maize genetics and genomics team at Biogemma, France.
  • 1997-1999:  Postdoc, UMR CNRS 6457, Pr  Jean-Marc Deragon's team
  • 1994-1997: Postdoc, Department of Zoology and Animal Biology, Geneva, Dr Vincenzo Pirrotta's team 
  • 1990-1993: PhD, URA360, Blaise Pascal University, France, Pr Hubert Pinon's team

Research

Role of the nuclear periphery in chromatin organization

Sophie DESSET (IR INSERM), Tristan DUBOS (PhD), Sarah MERMET (PhD), Christophe TATOUT (PR), Sylvie TUTOIS (MC) and Emmanuel VANROBAYS (MC)

It is becoming increasingly clear that the 3D organization of the genome within the nucleus has a profound influence on gene expression and several functional nuclear domains have been defined including the nuclear periphery.  Many proteins components have described over the 10 last years (left side of the figure) and mutants affecting these proteins impact nuclear size and shape (right side of the figure) with for some of them significant alterations of transcription. Despite the fact that the protein composition differs between animals and plants, the concept that the nuclear periphery is a functional interface influencing gene expression is conserved. Yet, the protein composition of the nuclear periphery in plants is still poorly documented and this motivated our research efforts to better understand the impact of the nuclear periphery on chromatin organization and transcription regulation.

See reviews (Tatout et al, Chromosome Res, 2014, and Parry et al, J. Cell Science, 2018) and research articles (Graumann et al, J. Exp. Bot., 2014, and Pawar et al 2016).

 

Evolutionary origin of the components of the plant nuclear periphery

Much of the work describing novel proteins of the plant nuclear periphery has been carried out in Arabidopsis. We took advantage of the genome sequencing of Amborella trichopoda to perform a new evolutionary survey of components of the nuclear periphery in the plant lineage. Amborella is the most primitive basal Angiosperm (the flowering plants) to be described and shows very limited evidence of transposon activity and no recent genome duplication event. Analyzing the genes expressing components of the nuclear envelope and nuclear periphery from the most basic unicellular to Arabidopsis provided opportunities to explore function as well as to speculate on origins of this protein network and was inspiring future research collaborations. This work identified the mid-SUN proteins as the most conserved component of the plant nuclear periphery (Figure) and showed that plants have developed their own protein network with similar function but distinct proteins (non-homologous) from animal species.

This work involved collaboration with the team of D. Evans and K. Graumann (Oxford Brookes University, UK) and gave rise to 1 scientific article (Poulet et al, Nucleus, 2016).

 

Discovery and characterization of components of the plant nuclear periphery

The linker of nucleoskeleton and cytoskeleton (LINC) complex is an evolutionary well-conserved protein bridge connecting the cytoplasmic and nuclear compartments across the nuclear membrane.  When we started this project very few proteins of the nuclear envelope and its periphery were known. Therefore we aimed to identify and characterize components of the plant nuclear envelope known to be involved in chromatin organization in other species. In collaboration with the Oxford Brookes team, Emmanuel Vanrobays and Sylvie Tutois identified three new orthologs of SAD1/UNC84 (SUN) that we called midSUN and one new KLARSICHT/ANC1/SYNE1 homology (KASH) proteins in Arabidopsis demonstrating the existence of a plant Linker of Nucleoskeleton and Cytoskeleton (LINC) complex that bridges the nuclear envelope. We used classical Yeast two Hybrid and Membrane Yeast Two Hybrid (MYTH, Figure) to describe SUN-SUN and SUN-KASH interactions, but also to discover new partners of SUN proteins. We further established combinations of sun and kash mutants to evaluate their impact on heterochromatin organization and nuclear morphology.

 

The linker of nucleoskeleton and cytoskeleton (LINC) complex is an evolutionary well-conserved protein bridge connecting the cytoplasmic and nuclear compartments across the nuclear membrane. While recent data support its function in nuclear morphology and meiosis, its implication in chromatin organization has been less studied in plants. Our quantitative measurements of 3D position of chromocenters in the nucleus indicated that most chromocenters are situated in close proximity to the nuclear periphery but that this distance varies with nuclear volume, ploidy or in mutants with a defective LINC complex. Axel Poulet a co-tutelle PhD student between Oxford Brookes and our University (2013-16) demonstrated that LINC complex mutants release transcriptional silencing (Figure) and show decompaction of heterochromatic sequences suggesting that the LINC complex contributes to proper heterochromatin organization, positioning and function.

Furthermore, using Seh1 and Nup50a nucleoporins anchored at the nuclear envelope and the Lac Operator / Lac Repressor (LacI-LacO) bacterial system, we induced tethering of a specific LacO array to the nuclear periphery, which modified transcription of the reporter gene supporting again a functional role of the nuclear periphery in transcription regulation.

Gwenaelle Detourne, a PhD student in co-tutelle between Oxford Brookes and Université Clermont Auvergne (2015-19) also discovered and characterized a novel family of Nuclear Envelope Associated Proteins (NEAPs), which are proposed to be interacting with the putative plant lamina, a structure underneath the nuclear envelope. This small gene family is composed of three genes encoding proteins, which are anchored at the inner nuclear membrane through their C-terminal transmembrane domains (Figure). NEAPs also possess several long coiled-coil domains reminiscent to the structure of animal lamin proteins. Finally, NEAPs interact with the bZIP18 transcription factor, a potential repressor of transcription. We suggest that NEAPs are part of an envelope sensor transmitting signals across the nuclear envelope and connected to chromatin by the bZIP18 transcription factor.

This work involved collaboration with the team of D. Evans and K. Graumann (Oxford Brookes University, UK) and gave rise to 3 scientific articles (Smith, Nucleus, 2015; Pawar, J. Exp. Bot, 2016; Poulet, J. Cell Science, 2017). The project now focused on the plant nucleoskeleton in the frame of the PhD of Sarah Mermet in collaboration with Kentaro Tamura (Shizuoka,Japan).

 

3D Image Analysis and applications

We envisage multidisciplinary research and technological innovations as a mean for translational research (here across plant and animal kingdoms). In our case, we have been focusing on 3D bio-image analysis.

First, NucleusJ, an ImageJ plugin, has been developed by Axel Poulet in collaboration with Philippe Andrey (INRA, Versailles)  to meet the needs of researchers investigating nuclear structure and function. NucleusJ was designed to use image stacks from widefield (MMAF, Leica) and confocal microscopy (LSM800, Zeiss) to measure nuclear morphology and chromatin organization in 3D. New bio-imaging methods were developed to delineate the nucleus as well as chromatin domains by partitioning the nucleus. NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects such as chromatin domains and compute their position in respect to the nuclear periphery (Figure). NucleusJ was successfully used for several applications including the characterization of chromocenter formation during seedling development in WT and histone chaperone mutants, nuclear envelope mutants and a cell model for human trisomy. Our bio-imaging work is now continued in collaboration with the Institut Pascal and a Tristan Dubos, a new PhD student in Bio-imaging (2018-2021) to include new break-through methods derived from Artificial Intelligence.

Second, Sophie Desset, strongly involved in the GReD microscopy platform (CLIC), was trained in 3D DNA-Fluorescent in situ Hybridization (FiSH) (Amsterdam, 2013) and then in 3D RNA-FiSH (Uppsala, 2018). Sophie organized two training schools in Clermont-Ferrand (2014 and 2018) in 3D FiSH and image analysis. We also organized an OMERO workshop (Lisbon 2019) to develop a repository for 3D images of Plant nucleus. The team is now recognized for its 3D-FiSH, Microscopy and image analysis expertise (Figure).

This work involved collaboration with P. Andrey (INRA, Versailles) during the initial steps of NucleusJ development (Poulet et al, Bioinformatics, 2015) and gave rise to an additional scientific article (Kemeny et al, Chromosome Research, 2018), 2 Method Papers (Poulet et al, Methods in Molecular Biology, 2018, Desset et al, Methods in Molecular Biology, 2018 and a review in the frame of WG1 INDEPTH COST-Action (Dumur et al , Nucleus, 2019). in collaboration with Frederic Chausse and Emilie Pery from the Institut Pascal to explore new segmentation procedures using Artificial Intelligence methods such as convolution neural network (deep learning).

Publications

  • 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.
    • 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.
    • 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
  • 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.
  • 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.
  • 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.
  • 2007
    • J. Gutierrez-Marcos, M. Dal Pra, A. Giulini, L. Costa, G. Gavazzi, S. Cordelier, O. Sellam, C. Tatout, W. Paul, P. Perez, H. Dickinson and G. Consonni, “empty pericarp4 encodes a mitochondrion-targeted pentatricopeptide repeat protein necessary for seed development and plant growth in maize.”, Plant Cell, vol. 19 (1) , pp. 196–210, 2007.
  • 2006
    • A. Martin, J. Lee, T. Kichey, D. Gerentes, M. Zivy, C. Tatout, F. Dubois, T. Balliau, B. Valot, M. Davanture, T. Terce-Laforgue, I. Quillere, M. Coque, A. Gallais, M. Gonzalez-Moro, L. Bethencourt, D. Habash, P. Lea, A. Charcosset, P. Perez, A. Murigneux, H. Sakakibara, K. Edwards and B. Hirel, “Two cytosolic glutamine synthetase isoforms of maize are specifically involved in the control of grain production.”, Plant Cell, vol. 18 (11) , pp. 3252–74, 2006.
  • 2005
    • A. Karkonen, A. Murigneux, J. Martinant, E. Pepey, C. Tatout, B. Dudley and S. Fry, “UDP-glucose dehydrogenases of maize: a role in cell wall pentose biosynthesis.”, The Biochemical journal, vol. 391 (Pt 2) , pp. 409–15, 2005.
  • 2002
    • T. Pelissier, C. Tatout, J. Lavige, I. Busseau, A. Bucheton and J. Deragon, “Utilization of the IR hybrid dysgenesis system in Drosophila to test in vivo mobilization of synthetic SINEs sharing 3' homology with the I factor.”, Gene, vol. 285 (1-2) , pp. 239–45, 2002.
    • G. Dellino, C. Tatout and V. Pirrotta, “Extensive conservation of sequences and chromatin structures in the bxd polycomb response element among Drosophilid species.”, The International journal of developmental biology, vol. 46 (1) , pp. 133–41, 2002.
  • 2001
    • A. Tikhonov, L. Lavie, C. Tatout, J. Bennetzen, Z. Avramova and J. Deragon, “Target sites for SINE integration in Brassica genomes display nuclear matrix binding activity.”, Chromosome Res., vol. 9 (4) , pp. 325–37, 2001.
  • 2000
    • E. Gauthier, C. Tatout and H. Pinon, “Artificial and epigenetic regulation of the I factor, a nonviral retrotransposon of Drosophila melanogaster.”, Genetics, vol. 156 (4) , pp. 1867–78, 2000.
    • B. Horard, C. Tatout, S. Poux and V. Pirrotta, “Structure of a polycomb response element and in vitro binding of polycomb group complexes containing GAGA factor.”, Molecular and cellular biology, vol. 20 (9) , pp. 3187–97, 2000.
    • M. Delattre, C. Tatout and D. Coen, “P-element transposition in Drosophila melanogaster: influence of size and arrangement in pairs.”, Molecular & general genetics : MGG, vol. 263 (3) , pp. 445–54, 2000.
  • 1999
    • C. Goubely, P. Arnaud, C. Tatout, J. Heslop-Harrison and J. Deragon, “S1 SINE retroposons are methylated at symmetrical and non-symmetrical positions in Brassica napus: identification of a preferred target site for asymmetrical methylation.”, Plant molecular biology, vol. 39 (2) , pp. 243–55, 1999.
  • 1998
    • C. Tatout, E. Gauthier and H. Pinon, “Rapid evaluation in Escherichia coli of antisense RNAs and ribozymes.”, Letters in applied microbiology, vol. 27 (5) , pp. 297–301, 1998.
    • C. Tatout, L. Lavie and J. Deragon, “Similar target site selection occurs in integration of plant and mammalian retroposons.”, Journal of molecular evolution, vol. 47 (4) , pp. 463–70, 1998.
  • 1994
    • C. Tatout, M. Docquier, P. Lachaume, M. Mesure, P. Lecher and H. Pinon, “Germ-line expression of a functional LINE from Drosophila melanogaster: fine characterization allows for potential investigations of trans-regulators.”, The International journal of developmental biology, vol. 38 (1) , pp. 27–33, 1994.