Research Team

Chromatin and 3D Nuclear Dynamics (CODED)

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HomeTeamsChromatin and 3D Nuclear Dynamics (CODED)
Eukaryotic genomic DNA is organized together with histones into nucleosomes, the basic subunits of chromatin. Chromatin organization is at the heart of epigenetic regulation and affects all fundamental processes operating on DNA, such as replication, repair and transcription. In order to regulate chromatin organization, nucleosome structure can be modified through post-translational modifications of histones or incorporation of histone variants, but also at the level of higher order chromatin organization by facilitating or preventing interaction of distant DNA sequences and the formation of chromatin domains.

Using the plant Arabidopsis thaliana as a model organism, our team studies how these different aspects of chromatin organization allow an adequate transcriptional response during development or in response to environmental stimuli.




To better understand the contribution of these epigenetic mechanisms in transcriptional regulation, we characterize the composition of nucleosomes in histone variants and study how these histone variants are stored, transported and incorporated into chromatin by histone chaperones (Le Goff et al, 2019, Probst, 2022). We further investigate the influence of chromatin structure on transcription via the study of GH1-domain chromatin proteins that include linker histone H1 and non-histone proteins of the TRB and GH1-HMGA type (Charbonnel et al, 2018, Teano et al, 2022). Finally, our studies of the interactions between chromatin, lamina and the nuclear envelope have led us to better understand the relationship between chromatin position in nuclear space and transcriptional activity (Poulet et al, 2017, Mermet et al, 2021).

We use molecular biology, genetics, epigenetics and bioinformatics approaches and develop new bio-imaging tools including artificial intelligence to monitor chromatin dynamics imaged by confocal microscopy (Dubos et al, 2020, 2022, Mougeot et al, 2022).

Our team is composed of two CNRS researchers, an INSERM engineer, six Associate Professors from the Clermont Auvergne University and several Master and PhD students. Our research is integrated into local networks including the CAP20-25 project International research Centre 1 (CIR1) on Sustainable Agro-ecosystems and CIR3 on mobility, national networks such as the GDR EPIPLANT, the GDR ADN&G, the GDR IMABIO, or the RtmFM network, European networks such as the Marie Curie Doctoral Network EpiSeedLink and international networks through our involvement in the Society of Experimental Biology (SEB).

We are strongly involved in the life of Clermont Auvergne University through our implication in the UFR Biology and our contribution to courses in genetics in the Bachelor of Life Sciences, epigenetics in the Master of Health Biology and in the Master of Plant Biology, and bioinformatics in the Master of Bioinformatics. We also contribute to dissemination of scientific culture through our participation in the astu’science association.



46 publications

Distinct clades of TELOMERE REPEAT BINDING transcriptional regulators interplay to regulate plant development

Published on 17 Aug 2023 in bioRxiv 2023.08.16.553498

Simon Amiard , Léa Feit , Lauriane Simon , Samuel Le Goff , Loriane Loizeau, Léa Wolff, Falk Butter, Clara Bourbousse, Fredy Barneche, Christophe Tatout , Aline. V. Probst

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

Published on 28 Jul 2023 in Cell Reports , vol. 42 - pp 112894

Gianluca Teano, Lorenzo Concia, Léa Wolff, Léopold Carron, Ivona Biocanin, Kateřina Adamusová, Miloslava Fojtová, Michael Bourge, Amira Kramdi, Vincent Colot, Ueli Grossniklaus, Chris Bowler, Célia Baroux, Alessandra Carbone, Aline V Probst , Petra Procházková Schrumpfová, Jiří Fajkus, Simon Amiard , Stefan Grob, Clara Bourbousse, Fredy Barneche

Maintenance and dynamic reprogramming of chromatin organization during development.

Published on 26 Jan 2023 in The Plant journal : for cell and molecular biology

Simon L , Probst AV


Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes.

Published on 30 Dec 2022 in Nucleus (Austin, Tex.) , vol. 13 - pp 277-299

Randall RS, Jourdain C, Nowicka A, Kaduchová K, Kubová M, Ayoub MA, Schubert V, Tatout C , Colas I, Kalyanikrishna, Desset S , Mermet S , Boulaflous-Stevens A, Kubalová I, Mandáková T, Heckmann S, Lysak MA, Panatta M, Santoro R, Schubert D, Pecinka A, Routh D, Baroux C

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

Published on 06 Dec 2022 in bioRxiv

Gianluca Teano, Lorenzo Concia, Léa Wolff, Léopold Carron, Ivona Biocanin, Kateřina Adamusová, Miloslava Fojtová, Michael Bourge, Amira Kramdi, Vincent Colot, Ueli Grossniklaus, Chris Bowler, Célia Baroux, Alessandra Carbone, Aline V. Probst , Petra Procházková Schrumpfová, Jiří Fajkus, Simon Amiard , Stefan Grob, Clara Bourbousse, Fredy Barneche

Easing batch image processing from OMERO: a new toolbox for ImageJ.

Published on 24 Nov 2022 in F1000Research , vol. 11 - pp 392

Pouchin P , Zoghlami R, Valarcher R , Delannoy M, Carvalho M, Belle C, Mongy M, Desset S , Brau F

Deep learning — promises for 3D nuclear imaging: a guide for biologists.

Published on 01 Apr 2022 in Journal of cell science , vol. 135

Mougeot G , Dubos T , Chausse F, Péry E, Graumann K, Tatout C , Evans DE, Desset S


ANCHOR: A Technical Approach to Monitor Single-Copy Locus Localization in Planta.

Published on 06 Jul 2021 in Frontiers in plant science , vol. 12 - pp 677849

Meschichi A, Ingouff M, Picart C, Mirouze M, Desset S , Gallardo F, Bystricky K, Picault N, Rosa S, Pontvianne F

Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis.

Published on 03 Jun 2021 in Genome research , vol. 31 - pp 1230-44

Huang Y, Sicar S, Ramirez-Prado JS, Manza-Mianza D, Antunez-Sanchez J, Brik-Chaouche R, Rodriguez-Granados NY, An J, Bergounioux C, Mahfouz MM, Hirt H, Crespi M, Concia L, Barneche F, Amiard S , Probst AV , Gutierrez-Marcos J, Ariel F, Raynaud C, Latrasse D, Benhamed M

The Histone Chaperone HIRA Is a Positive Regulator of Seed Germination.

Published on 14 Apr 2021 in International journal of molecular sciences , vol. 22

Layat E , Bourcy M, Cotterell S , Zdzieszyńska J, Desset S , Duc C , Tatout C , Bailly C, Probst AV


Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0.

Published on 30 Dec 2020 in Nucleus (Austin, Tex.) , vol. 11 - pp 315-329

Dubos T , Poulet A , Gonthier-Gueret C, Mougeot G , Vanrobays E , Li Y , Tutois S , Pery E, Chausse F, Probst AV, Tatout C , Desset S

Untangling chromatin interactions.

Published on 17 Aug 2020 in Journal of experimental botany , vol. 71 - pp 5115-5118

Parry G, Pradillo M, Probst AV , Tatout C

The H3 histone chaperone NASP(SIM3) escorts CenH3 in Arabidopsis.

Published on 30 Jan 2020 in The Plant journal : for cell and molecular biology , vol. 101 - pp 71-86

Le Goff S , Keçeli BN, Jeřábková H, Heckmann S, Rutten T, Cotterell S , Schubert V, Roitinger E, Mechtler K, Franklin FCH, Tatout C , Houben A, Geelen D, Probst AV , Lermontova I


Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions.

Published on 30 Dec 2019 in Nucleus (Austin, Tex.) , vol. 10 - pp 181-212

Dumur T, Duncan S, Graumann K, Desset S , Randall RS, Scheid OM, Prodanov D, Tatout C , Baroux C


Spatial organization of chromosome territories in the interphase nucleus of trisomy 21 cells.

Published on 30 Jun 2018 in Chromosoma , vol. 127 - pp 247-259

Kemeny S, Tatout C , Salaun G, Pebrel-Richard C, Goumy C, Ollier N, Maurin E, Pereira B, Vago P, Gouas L

Meeting report – INDEPTH kick-off meeting.

Published on 25 Jun 2018 in Journal of cell science , vol. 131

Parry G, Probst AV, Baroux C, Tatout C

The Linker Histone GH1-HMGA1 Is Involved in Telomere Stability and DNA Damage Repair.

Published on 30 May 2018 in Plant physiology , vol. 177 - pp 311-327

Charbonnel C , Rymarenko O, Da Ines O , Benyahya F, White CI , Butter F, Amiard S

Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana.

Published on 06 Apr 2018 in Nucleic acids research , vol. 46 - pp 3019-3033

Simon L , Rabanal FA, Dubos T , Oliver C, Lauber D , Poulet A , Vogt A, Mandlbauer A, Le Goff S , Sommer A, Duborjal H, Tatout C , Probst AV

High-Affinity LNA-DNA Mixmer Probes for Detection of Chromosome-Specific Polymorphisms of 5S rDNA Repeats in Arabidopsis thaliana.

Published on 01 Jan 2018 in Methods in molecular biology (Clifton, N.J.) , vol. 1675 - pp 481-491

Simon L , Probst AV

Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ.

Published on 01 Jan 2018 in Methods in molecular biology (Clifton, N.J.) , vol. 1675 - pp 615-632

Desset S , Poulet A , Tatout C

Computational Methods for Studying the Plant Nucleus.

Published on 01 Jan 2018 in Methods in molecular biology (Clifton, N.J.) , vol. 1840 - pp 205-219

Poulet A , Zhou X, Tamura K, Meier I, Tatout C , Graumann K, Evans DE

Investigation of Nuclear Periphery Protein Interactions in Plants Using the Membrane Yeast Two-Hybrid (MbY2H) System.

Published on 01 Jan 2018 in Methods in molecular biology (Clifton, N.J.) , vol. 1840 - pp 221-235

Voisin M , Vanrobays E , Tatout C


Arabidopsis ATRX Modulates H3.3 Occupancy and Fine-Tunes Gene Expression.

Published on 30 Jul 2017 in The Plant cell , vol. 29 - pp 1773-1793

Duc C , Benoit M , Détourné G , Simon L , Poulet A , Jung M, Veluchamy A, Latrasse D, Le Goff S , Cotterell S , Tatout C , Benhamed M, Probst AV

Exploring the evolution of the proteins of the plant nuclear envelope.

Published on 02 Jan 2017 in Nucleus (Austin, Tex.) , vol. 8 - pp 46-59

Poulet A , Probst AV, Graumann K, Tatout C , Evans D


A novel family of plant nuclear envelope-associated proteins.

Published on 30 Oct 2016 in Journal of experimental botany , vol. 67 - pp 5699-5710

Pawar V, Poulet A , Détourné G , Tatout C , Vanrobays E , Evans DE, Graumann K


NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei.

Published on 01 Apr 2015 in Bioinformatics (Oxford, England) , vol. 31 - pp 1144-6

Poulet A , Arganda-Carreras I, Legland D, Probst AV, Andrey P, Tatout C

Marker gene tethering by nucleoporins affects gene expression in plants.

Published on 01 Jan 2015 in Nucleus (Austin, Tex.) , vol. 6 - pp 471-8

Smith S, Galinha C, Desset S , Tolmie F, Evans D, Tatout C , Graumann K


Evolutionary history of Methyltransferase 1 genes in hexaploid wheat.

Published on 23 Oct 2014 in BMC genomics , vol. 15 - pp 922

Thomas M, Pingault L, Poulet A , Duarte J, Throude M, Faure S, Pichon JP, Paux E, Probst AV, Tatout C

The plant LINC complex at the nuclear envelope.

Published on 30 Jun 2014 in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology , vol. 22 - pp 241-52

Tatout C , Evans DE, Vanrobays E , Probst AV, Graumann K


The N-terminal domains of TRF1 and TRF2 regulate their ability to condense telomeric DNA.

Published on 30 Mar 2012 in Nucleic acids research , vol. 40 - pp 2566-76

Poulet A , Pisano S, Faivre-Moskalenko C, Pei B, Tauran Y, Haftek-Terreau Z, Brunet F, Le Bihan YV, Ledu MH, Montel F, Hugo N, Amiard S , Argoul F, Chaboud A, Gilson E, Giraud-Panis MJ


Characterization of a cinnamoyl-CoA reductase 1 (CCR1) mutant in maize: effects on lignification, fibre development, and global gene expression.

Published on 30 Jul 2011 in Journal of experimental botany , vol. 62 - pp 3837-48

Tamasloukht B, Wong Quai Lam MS, Martinez Y, Tozo K, Barbier O, Jourda C, Jauneau A, Borderies G, Balzergue S, Renou JP, Huguet S, Martinant JP, Tatout C , Lapierre C, Barrière Y, Goffner D, Pichon M


TRF2 and apollo cooperate with topoisomerase 2alpha to protect human telomeres from replicative damage.

Published on 23 Jul 2010 in Cell , vol. 142 - pp 230-42

Ye J, Lenain C, Bauwens S, Rizzo A, Saint-Léger A, Poulet A , Benarroch D, Magdinier F, Morere J, Amiard S , Verhoeyen E, Britton S, Calsou P, Salles B, Bizard A, Nadal M, Salvati E, Sabatier L, Wu Y, Biroccio A, Londoño-Vallejo A, Giraud-Panis MJ, Gilson E

Platination of telomeric DNA by cisplatin disrupts recognition by TRF2 and TRF1.

Published on 30 Jun 2010 in Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry , vol. 15 - pp 641-54

Ourliac-Garnier I, Poulet A , Charif R, Amiard S , Magdinier F, Rezaï K, Gilson E, Giraud-Panis MJ, Bombard S

Identification and mapping of induced chromosomal deletions using sequence polymorphisms.

Published on 30 Jan 2010 in BioTechniques , vol. 48 - pp 53-60

Vanrobays E , Jennings BH, Ish-Horowicz D


TRF2 promotes, remodels and protects telomeric Holliday junctions.

Published on 18 Mar 2009 in The EMBO journal , vol. 28 - pp 641-51

Poulet A , Buisson R, Faivre-Moskalenko C, Koelblen M, Amiard S , Montel F, Cuesta-Lopez S, Bornet O, Guerlesquin F, Godet T, Moukhtar J, Argoul F, Déclais AC, Lilley DM, Ip SC, West SC, Gilson E, Giraud-Panis MJ


TOR regulates the subcellular distribution of DIM2, a KH domain protein required for cotranscriptional ribosome assembly and pre-40S ribosome export.

Published on 30 Oct 2008 in RNA (New York, N.Y.) , vol. 14 - pp 2061-73

Vanrobays E , Leplus A, Osheim YN, Beyer AL, Wacheul L, Lafontaine DL

Hypomethylation and hypermethylation of the tandem repetitive 5S rRNA genes in Arabidopsis.

Published on 30 Apr 2008 in The Plant journal : for cell and molecular biology , vol. 54 - pp 299-309

Vaillant I , Tutois S , Jasencakova Z, Douet J, Schubert I, Tourmente S


8 theses
Organisation de la périphérie nucléaire et son influence sur l’expression des gènes chez Arabidopsis thaliana
Realized by :
Sarah Mermet
Defense date:
Realized by :
Gwénaëlle Détourné
Defense date:
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