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.
Funders
Research
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.
Members
Publications
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
The TELOMERE REPEAT BINDING proteins TRB4 and TRB5 function as transcriptional activators of PRC2-controlled genes to regulate plant development.
Published on 01 Apr 2024 in Plant communications - pp 100890
Amiard S , Feit L , Vanrobays E , Simon L , Le Goff S , Loizeau L , Wolff L, Butter F, Bourbousse C, Barneche F, Tatout C , Probst AV
Evolutionarily conserved protein motifs drive interactions between the plant nucleoskeleton and nuclear pores
Published on 21 Sep 2023 in The Plant Cell
Mermet S , Voisin M , Mordier J , Dubos T , Tutois S , Tuffery P, Baroux C, Tamura K, Probst AV , Vanrobays E , Tatout C
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
Maintenance and dynamic reprogramming of chromatin organization during development.
Published on 26 Jan 2023 in The Plant Journal , vol. 118 - pp 657-670
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
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
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
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
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
Untangling chromatin interactions.
Published on 17 Aug 2020 in Journal of experimental botany , vol. 71 - pp 5115-5118
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
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
Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development.
Published on 30 Jan 2019 in The New phytologist , vol. 221 - pp 385-398
Benoit M , Simon L , Desset S , Duc C , Cotterell S , Poulet A , Le Goff S , Tatout C , Probst AV
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
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
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
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
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
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
The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants.
Published on 01 Feb 2017 in Journal of cell science , vol. 130 - pp 590-601
Poulet A , Duc C , Voisin M , Desset S , Tutois S , Vanrobays E , Benoit M , Evans DE, Probst AV , Tatout C
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
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
Structure and Function of Centromeric and Pericentromeric Heterochromatin in Arabidopsis thaliana.
Published on 30 Nov 2015 in Frontiers in plant science , vol. 6 - pp 1049
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
The histone chaperone complex HIR maintains nucleosome occupancy and counterbalances impaired histone deposition in CAF-1 complex mutants.
Published on 30 Mar 2015 in The Plant journal : for cell and molecular biology , vol. 81 - pp 707-22
Duc C , Benoit M , Le Goff S , Simon L , Poulet A , Cotterell S , Tatout C , Probst AV
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
Characterization of two distinct subfamilies of SUN-domain proteins in Arabidopsis and their interactions with the novel KASH-domain protein AtTIK.
Published on 30 Dec 2014 in Journal of experimental botany , vol. 65 - pp 6499-512
Graumann K, Vanrobays E , Tutois S , Probst AV , Evans DE, Tatout C
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
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
Heterochromatin dynamics during developmental transitions in Arabidopsis – a focus on ribosomal DNA loci.
Published on 15 Aug 2013 in Gene , vol. 526 - pp 39-45
Benoit M , Layat E , Tourmente S , Probst AV
Transcript levels, alternative splicing and proteolytic cleavage of TFIIIA control 5S rRNA accumulation during Arabidopsis thaliana development.
Published on 30 Jul 2012 in The Plant journal : for cell and molecular biology , vol. 71 - pp 35-44
Layat E , Cotterell S , Vaillant I , Yukawa Y, Tutois S , Tourmente S
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
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
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
A Pol V-mediated silencing, independent of RNA-directed DNA methylation, applies to 5S rDNA.
Published on 30 Oct 2009 in PLoS genetics , vol. 5 - pp e1000690
Douet J, Tutois S , Tourmente S
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
In Drosophila melanogaster the COM locus directs the somatic silencing of two retrotransposons through both Piwi-dependent and -independent pathways.
Published on 06 Feb 2008 in PloS one , vol. 3 - pp e1526
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