Research Team

Chromatin and 3D Nuclear Dynamics (CODED)

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HomeTeamsChromatin and 3D Nuclear Dynamics (CODED)
In eukaryotes, genomic DNA is packaged with histone proteins into nucleosomes, the basic building blocks of chromatin. Chromatin organization is central to epigenetic regulation and influences all DNA-based processes, including transcription. Chromatin is a dynamic structure that is constantly modified through post-translational modifications of histones, the incorporation of histone variants, or changes in higher-order chromatin folding that may facilitate or prevent interaction of distant DNA sequences and the formation of chromatin domains. Our team studies how these different mechanisms affect the regulation of gene expression during development or in response to environmental stimuli.

To address this question, we mainly use Arabidopsis thaliana as a model system and combine molecular biology, genetic, epigenomic, biochemistry, imaging and bioinformatics approaches.

Networks: Our research is integrated into local initiatives such as the CAP20-25 project International research Centre 1 (CIR1) on Sustainable Agro-ecosystems and CIR3 on mobility, national networks such as the GDRs (Groupements de Recherche) EPIPLANT, the ADN&G, the IMABIO, or the RtmFM network, European projects such as Marie Curie Doctoral Networks, and international networks through our involvement in the Society of Experimental Biology (SEB).

Teaching and Outreach: We contribute actively to the life of Clermont Auvergne University through our implication in the Unité de Formation et de Recherche (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 are also engaged in the dissemination of scientific culture through our participation in outreach events through the local association astu’science.

Our research is supported by EU MSCA DN EpiSeedLink and AGILE, 4D-Heat [ANR-21-CE20-0036], SeedChrom [ANR-22-CE20-0028], EpiLinks [ANR-22-CE20-0001], NUCLINV [ANR-24-CE20-5404] and His2AVar and through funding from the CAP20-25 CIR1 and CIR3.

Funders

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Research

We currently focus on three research areas:

 

Histone variants and chaperones

Precise dynamics of histone proteins is critical for all DNA-template based processes that take place in the context of chromatin. A network of histone chaperone proteins therefore tightly coordinates the incorporation of histone variants into the nucleosomes. We study how the incorporation of different histone variants changes nucleosome properties, influences higher-order chromatin organization and affects gene activity. We focus on the transition from seed to seedling, a key developmental transition in plants that involves major changes in gene expression and chromatin organization.

A. Probst, S. Cotterell, S. Le Goff, L. Simon, R. Kaur, S. Paltrinieri, G. Sireta. M. Verdier

 

Coordinating Polycomb activity through GH1 domain proteins

Polycomb group (PcG) proteins play a central role in controlling developmental genes that govern growth, differentiation, and morphogenesis in eukaryotes. Proteins with a globular histone H1 (GH1) domain contribute to H3K27me3 homeostasis either by favoring the establishment of a repressive chromatin structure or through direct recruitment of the Polycomb Repressive 2 (PRC2) complexes. We aim to understand how Telomere Repeat Binding (TRB) proteins, GH1-High mobility group proteins (GH1-HMGA) and the linker histone H1 work together to fine-tune Polycomb activity and to regulate gene expression.

S. Amiard, E. Vanrobays, S. Tutois, L. Feit, H. El Idrissi Moubtassim

 

Assessing variability in chromatin organization at single cell level

Precise and quantitative evaluation of chromatin and nuclear organization at the level of a single cell single is a prerequisite for uncovering structural and functional principles at unprecedented spatial and temporal scale. To assess chromatin organization at the single-cell level, we develop advanced imaging methods combined with deep-learning image analysis tools for 3D image segmentation and cell tracking in different model systems.

C. Tatout, C. Desset, S. Safarbati

 

 

Former Team Members

 

Shimlal Ayilalath, PhD, 2022-25
Aurelia Stevens, Assistant Professor, 2018-24
Guillaume Mougeot, PhD, 2021-23
Sarah Mermet, PhD, 2019-22
Tristan Dubos, PhD, 2018-21
Gwénaëlle Détourné, PhD, 2015-19
Maxime Voisin, PhD, 2013-17
Céline Duc, Postdoc, 2010-14
Lauriane Simon, PhD, 2012-16
Axel Poulet, PhD, 2012-16
Mélanie Thomas, PhD, 2011-14
Matthias Benoit, PhD, 2010-14

Members

Publications

70 publications
2025

New three-dimensional nuclear morphometry tool quantifies impact of slow freezing on sperm hypercondensed chromatin.

Published on 04 Jul 2025 in Andrology

Carcy O, Desset S , Dubos T , Puceat C, Andrieux M, Compagnon M, Sireta G , Pereira B, Cachin F, Probst AV , Tatout C , Brugnon F, Pons-Rejraji H

Ubiquitin-dependent proteolysis of KNL2 driven by APC/CCDC20 is critical for centromere integrity and mitotic fidelity

Published on 25 Jun 2025 in The Plant Cell , vol. koaf164

Kalidass M Jarubula VG, Ratnikava M, Chandra JR, Le Goff S , Probst AV , Esposito S, Grasser KD, Bruckmann A, Gagneux JF, Prosée RF, Rutten T, Schubert V, Demidov D, Lechner E, Steiner FA, Genschik P, Lermontova I

Plant epigenetics: controlling genome expression to integrate developmental and environmental cues

Published on 17 Jun 2025 in J Exp Bot , vol. 76 - pp 2389-2393

Catoni M, Lechon Gomez T, Probst AV

Characterizations of Nuclear Organization and Chromatin Modifications in Mature Embryos from Arabidopsis Dry Seeds.

Published on 01 Jan 2025 in Methods in molecular biology (Clifton, N.J.) , vol. 2873 - pp 247-262

Simon L , Verdier M , Probst AV

2024

The dual trxG/PcG protein ULTRAPETALA1 modulates H3K27me3 and directly enhances POLYCOMB REPRESSIVE COMPLEX 2 activity for fine-tuned reproductive transitions

Published on 24 Oct 2024 in bioRxiv

Geshkovski V, Engelhorn J, Izquierdo JB, Laroussi H, Thouly C, Turchi L, Le Masson M, Thévenon E, Petitalot A, Simon L , Desset S , Michl-Holzinger P, Parrinello H, Grasser KD, Probst AV , Margueron R, Vachon G, Kadlec J, Carles CC

The histone chaperones ASF1 and HIRA are required for telomere length and 45S rDNA copy number homeostasis

Published on 14 Oct 2024 in The Plant Journal , vol. 120 - pp 1125-1141

Machelová A, Dadejová MN, Franek M, Mougeot G , Simon L , Le Goff S , Duc C , Bassler J, Demko M, Schwarzerová J, Desset S , Probst AV , Dvořáčková M

Biom3d, a modular framework to host and develop 3D segmentation methods

Published on 25 Jul 2024

Mougeot G , Safarbati S , Alégot H , Pouchin P , Field N, Almagro S, Pery E, Probst AV , Tatout C , Evans DE, Graumann K, Chausse F, Desset S

Maintenance and dynamic reprogramming of chromatin organization during development.

Published on 01 May 2024 in The Plant journal , vol. 118 - pp 657-670

Simon L , Probst AV

2023

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

Published on 17 Aug 2023 in bioRxiv 2023.08.16.553498

Amiard S , Feit L , Simon L , Le Goff S , Loizeau L, Wolff L, Butter F, Bourbousse C, Barneche F, Tatout C , Probst AV

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

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

Teano G, Concia L, Wolff L, Carron L, Biocanin I, Adamusová K, Miloslava Fojtová, Michael Bourge, Amira Kramdi, Vincent Colot, Ueli Grossniklaus, Bowler C, Baroux C, Carbone A, Probst AV , Procházková Schrumpfová P, Fajkus J, Amiard S , Grob S, Bourbousse C, Barneche F

HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions

Published on 28 Jan 2023 in Nat. Comm. , vol. 14 - pp 469

Huang Y, An J, Sircar S, Bergis C, Lopes CD, He X, Da Costa B, Tan FQ, Bazin J, Antunez-Sanchez J, Mammarella MF, Devani RS, Brik-Chaouche R, Bendahmane A, Frugier F, Xia C, Rothan C, Probst AV , Mohamed Z, Bergounioux C, Delarue M, Zhang Y, Zheng S, Crespi M, Fragkostefanakis S, Mahfouz MM, Ariel F, Gutierrez-Marcos J, Raynaud C, Latrasse D, Benhamed M

2022

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

Teano G, Concia L, Wolff L, Carron L, Biocanin I, Adamusová K, Fojtová M, Bourge M, Kramdi A, Colot V, Grossniklaus U, Bowler C, Baroux C, Carbone A, Probst AV , Procházková Schrumpfová P, Fajkus J, Amiard S , Grob S, Bourbousse C, Barneche F

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

Deposition and eviction of histone variants define functional chromatin states in plants.

Published on 30 Oct 2022 in Current opinion in plant biology , vol. 69 - pp 102266

Probst AV

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

2021

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

Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number

Published on 31 May 2021 in The Plant Cell , vol. 33 - pp 1135-1150

Lopez FB, Fort A, Tadini L, Probst AV , McHale M, Friel J, Ryder P, Pontvianne FDR, Pesaresi P, Sulpice R, McKeown P, Brychkova G, Spillane C

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

2020

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

Similar yet critically different: the distribution, dynamics and function of histone variants.

Published on 17 Aug 2020 in Journal of experimental botany , vol. 71 - pp 5191-5204

Probst AV , Desvoyes B, Gutierrez C

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

Published on 30 Jan 2020 in The Plant Journal , 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

2019

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

Looking At the Past and Heading to the Future: Meeting Summary of the 6(th) European Workshop on Plant Chromatin 2019 in Cologne, Germany.

Published on 07 Feb 2019 in Frontiers in plant science , vol. 10 - pp 1795

Moreno-Romero J, Probst AV , Trindade I, Kalyanikrishna, Engelhorn J, Farrona S

2018

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

A Compendium of Methods to Analyze the Spatial Organization of Plant Chromatin.

Published on 01 Jan 2018 in Methods in molecular biology (Clifton, N.J.) , vol. 1675 - pp 397-418

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

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

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

2017

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

2016

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

2015

Stress-induced structural changes in plant chromatin.

Published on 30 Oct 2015 in Current opinion in plant biology , vol. 27 - pp 8-16

Probst AV , Mittelsten Scheid O

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

2014

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 , vol. 22 - pp 241-52

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

2013

Heterochromatin reorganization during early mouse development requires a single-stranded noncoding transcript.

Published on 26 Sep 2013 in Cell reports , vol. 4 - pp 1156-67

Casanova M, Pasternak M, El Marjou F, Le Baccon P, Probst AV , Almouzni G

2012

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

2011

Heterochromatin maintenance and establishment: lessons from the mouse pericentromere.

Published on 01 Sep 2011 in Nucleus (Austin, Tex.) , vol. 2 - pp 332-8

Almouzni G, Probst AV

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

Heterochromatin establishment in the context of genome-wide epigenetic reprogramming.

Published on 30 May 2011 in Trends in genetics : TIG , vol. 27 - pp 177-85

Probst AV , Almouzni G

SUMOylation promotes de novo targeting of HP1α to pericentric heterochromatin.

Published on 30 Mar 2011 in Nature genetics , vol. 43 - pp 220-7

Maison C, Bailly D, Roche D, Montes de Oca R, Probst AV , Vassias I, Dingli F, Lombard B, Loew D, Quivy JP, Almouzni G

2010

A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development.

Published on 19 Oct 2010 in Developmental cell , vol. 19 - pp 625-38

Probst AV , Okamoto I, Casanova M, El Marjou F, Le Baccon P, Almouzni G

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

Heterochromatin at mouse pericentromeres: a model for de novo heterochromatin formation and duplication during replication.

Published on 01 Jan 2010 in Cold Spring Harbor symposia on quantitative biology , vol. 75 - pp 155-65

Maison C, Quivy JP, Probst AV , Almouzni G

2009

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

2008

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

Pericentric heterochromatin: dynamic organization during early development in mammals.

Published on 30 Jan 2008 in Differentiation; research in biological diversity , vol. 76 - pp 15-23

Probst AV , Almouzni G

Theses

9 theses
2019
Realized by :
Gwénaëlle Détourné
Defense date:
29/05/2019
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