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Chromatin dynamics and signalling
 research groups

Keywords : Arabidopsis thaliana, Amaranthus, core, chromatin, transcription regulation, silencing, development, hormone, seed

Doctoral school affiliation : ED 567 Sciences du Végétal

Contacts :

Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech--ERL3559 CNRS
Bâtiment 7
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

tél : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19

Group Leader
Valérie Gaudin
Senior Scientist

Associate Group Leader
Enrico Magnani
Research Scientist


Associate Group Leader
Jeffrey Leung
Research Scientist CNRS


Marcela Gómez Páez


Jing Lu
PhD Student


Yann Sulio
DEUST Student



Summary :


Plants have uniquely acquired a remarkable degree of plasticity, established on multiple signalling pathways, to orchestrate developmental growth and responses to environmental fluctuations. However, a vital signalling dilemma consists in balancing the plant energy budget for adaptive growth in response to environmental cues. For example, in responding to various stresses, plant will slow growth by diverting energy demands to reinforce defence mechanisms.
This balance requires fine-tuning of the genome activity. Long-term adaptative responses will eventually impinge on chromatin organisation involving histone and/or DNA modifications and a wide range of associated proteins leading to changes of transcriptional output in specific genomic regions. Conversely, chromatin regulation is also known to function as a "memory", to propagate, maintain or reset specific genomic status in diverse cellular-environmental contexts.
The aim of the group is to better understand developmental and environmental signalling mechanisms, and their interplay with chromatin dynamics and nuclear architecture, to approach the delicate equilibrium between signalling pathways. To do so, we exploit different biological contexts.

Main Results :


Developmental signalling in seed tissue coordination
Project manager: Enrico Magnani

Angiosperm seed development is a paradigm of tissue cross-talk as it requires synchronous development of four maternal tissues (nucellus, seed coat, chalaza and funiculus) and two fertilization products (embryo and endosperm). We are characterizing the signaling pathways that coordinate the development of different seed structures and their evolutionary histories, from chromatin organisation to downstream signal propagation. We use Arabidopsis and Amaranthus as comparative models for the two most ancient seed structures and exploit an interdisciplinary approach that spans genetics, tissue three-dimensional reconstruction, cell-type-specific transcriptomic profiling, and gene network analysis.

Persons involved
Olivier Coen, PhD, Co-supervision E. Magnani & L. Lepinierc
Jing Li, PhD, Supervision E. Magnani
Valérie Gaudin

Coordinate regulation of metabolites and chromatin modification in responding to environmental stress
Project manager: Jeffrey Leung
Serving on Editorial Boards: Mol. Plant, Plant Mol. Biol., Advances in Bot.

Once considered as mere byproducts of cellular metabolism, many small metabolites are now recognized to have big influence on myriads of physiological processes. Key targets include chromatin modifying enzymes whose activities are regulated by the availability of specific metabolites, including acetyl-coenzyme A, S-adenosylmethionine, ?-ketoglutarate, nicotinamide adenine dinucleotide and polyamines. Metabolism and epigenetics interplay to synchronize gene expression patterns with the changing metabolic demand of the cell, like during stress. Our recent focus is on an acetylated metabolite that is found in plants and accumulates in human cancer. Our data indicate that the metabolite in plants is activated by covalent conjugates, which permits plants to maintain gas exchange for photosynthetic growth despite drought. We are reconstructing the signalling events by combining genetics, molecular biology, electrophysiology, chemistry, biochemistry, and eco-physiology.

Persons involved
Valérie Gaudin

Modelling chromatin dynamics
Project manager: Valérie Gaudin

Throughout its pleiotopic forms, from fiber to structures with higher orders of organisation in the cell nucleus, chromatin is a highly dynamic compartment formed by nucleic acids and a large repertoire of proteins. Its dynamics is central for life, and more specifically for genome activities, from replication, recombination, repair to regulation of genome transcription. Its dynamics participates to the control of development, the responses to environmental cues, and long-term adaptation.
We study chromatin dynamics at different scales in responses to various signalling events and question the organisational rules of the tri-dimensional nuclear architecture, exploiting the plant model Arabidopsis. We are particularly interested by Polycomb and trithorax proteins, which play critical dual roles in chromatin dynamics and transcriptional switches. We use an integrative approach based on molecular biology, microscopy and modelling approaches.

Persons involved
Philippe Andrey (IJPB-MIN team)
Jeffrey Leung
Enrico Magnani

former group

Selected Publications :

Coen, O., Fiume, E., Xu, W., De Vos, D., Lu, J., Pechoux, C., Lepiniec, L. and Magnani, E. (2017) Developmental patterning of the sub-epidermal integument cell layer in Arabidopsis seeds. Development, 144, 1490-1497.

Fiume, E., Coen, O., Xu, W., Lepiniec, L. and Magnani, E. (2017) Growth of the sub-epidermal integument cell layers might require an endosperm signal. Plant Signal Behav, 0.

Leung J (2017) The first broad-spectrum abscisic acid antagonist. Plant Physiol 173, 1939

Fendrych M, Leung J, Friml J (2016) TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife 5

Leung J, Benzihizina N, Mancuso S and Valon C (2016) Revisiting the plant's dilemma. Mol Plant 9, 7-9

Xu, W., Fiume, E., Coen, O., Pechoux, C., Lepiniec, L. and Magnani, E. (2016) Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds. Plant Cell, 28, 1343-1360.

del Prete S, Mikulski P, Schubert D, and Gaudin V (2015) One, Two, Three: Polycomb Proteins Hit All Dimensions of Gene Regulation. Genes 6: 520-542; doi:10.3390/genes6030520 (pdf)

Hecker A, Brand LH, Peter S, Simoncello N, Kilian J, Harter K, Gaudin V, Wanke D (2015) The Arabidopsis GAGA-Binding Factor BASIC PENTACYSTEINE6 Recruits the POLYCOMB-REPRESSIVE COMPLEX1 Component LIKE HETEROCHROMATIN PROTEIN1 to GAGA DNA Motifs. Plant Physiology 168:1013-24 (Pubmed)

Le Roux, C, Del Prete, S Boutet-Mercey S,Perreau F, Balague C, Roby D, Fagard M, Gaudin V (2014) The hnRNP-Q protein LIF2 participates in the plant immune response. PLoS One 9, e99343 (online)

Jarillo JA, Gaudin V, Hennig L, Kohler C, Pineiro M (2014) Plant chromatin warms up in Madrid: Meeting summary of the 3rd European Workshop on Plant Chromatin 2013, Madrid, Spain. Epigenetics 9: 644-52 (Pubmed)

Del Prete S, Arpon J, Sakai, K, Andrey P, Gaudin, V (2014) Nuclear Architecture and Chromatin Dynamics in Interphase Nuclei of Arabidopsis thaliana. Cytogenetic & Genome Research 143: 28-50 (Pubmed)

De Lucia F, Gaudin V (2013) Epigenetic control by plant Polycomb proteins: new perspectives and emerging roles in stress response. Chapter 3, Pp: 31-48.
In: P. Poltronieri, N. Burbulis,  C. Fogher, Editors: From Plant Genomics to Plant Biotechnology. Woodhead Publishing, Cambridge, UK,  Elsevier, 2013. ISBN-13: 978 1 907568 29 9

Chupeau MC, Granier F, Pichon O, Renou JP, Gaudin* V, Chupeau* Y (2013) Characterization of the early events leading to totipotency in an Arabidopsis protoplast liquid culture by temporal transcript profiling. Plant Cell 25: 2444-2463 (Pubmed)

Latrasse* D, Germann* S, Houba-Herin N, Dubois E, Bui-Prodhomme D, Hourcade D, Juul-Jensen T, Le Roux C, Majira A, Simoncello N, Granier F, Taconnat L, Renou JP, Gaudin V (2011) Control of flowering and cell fate by LIF2, an RNA binding partner of the polycomb complex component LHP1. PLoS One 6: e16592 (Pubmed)

Germann S, Gaudin V (2011) Mapping in vivo protein-DNA interactions in plants by DamID, a DNA adenine methylation-based method. In: Yuan L, Perry SE (eds) Plant Transcription Factors: Methods and Protocols. SPRINGER SCIENCE+BUSINESS MEDIA, LLC, New York, USA, pp 307-321 (Pubmed)

Andrey P, Kieu K, Kress C, Lehmann G, Tirichine L, Liu Z, Biot E, Adenot PG, Hue-Beauvais C, Houba-Herin N, Duranthon V, Devinoy E, Beaujean N, Gaudin V, Maurin Y, Debey P (2010) Statistical analysis of 3D images detects regular spatial distributions of centromeres and chromocenters in animal and plant nuclei. PLoS Comput Biol 6: e1000853 (Pubmed)

Tirichine L, Andrey P, Biot E, Maurin Y, Gaudin V (2009) 3D fluorescent in situ hybridization using Arabidopsis leaf cryosections and isolated nuclei. Plant Methods 5: 11 (Pubmed)

Gaudin V, Andrey P, Devinoy E, Kress C, Kieu K, Beaujean N, Maurin Y, Debey P (2009) Modeling the 3D functional architecture of the nucleus in animal and plant kingdoms. C.R.AS. 332: 937-946

Pouteau S, Carre I, Gaudin V, Ferret V, Lefebvre D, Wilson M (2008) Diversification of photoperiodic response patterns in a collection of early-flowering mutants of Arabidopsis. Plant Physiol 148: 1465-1473 (Pubmed)

Zhang* X, Germann* S, Blus BJ, Khorasanizadeh S, Gaudin V, Jacobsen SE (2007) The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat Struct Mol Biol 14: 869-871 (Pubmed)

Tessadori F, Chupeau MC, Chupeau Y, Knip M, Germann S, van Driel R, Fransz P, Gaudin V (2007) Large-scale dissociation and sequential reassembly of pericentric heterochromatin in dedifferentiated Arabidopsis cells. J Cell Sci 120: 1200-1208 (Pubmed)

Germann S, Juul-Jensen T, Letarnec B, Gaudin V (2006) DamID, a new tool for studying plant chromatin profiling in vivo, and its use to identify putative LHP1 target loci. The Plant J. 48: 153-163 (Pubmed)

Libault M, Tessadori F, Germann S, Snijder B, Fransz F, Gaudin V (2005) The Arabidopsis LHP1 protein is a component of euchromatin. Planta 222: 910-925 (Pubmed)

Pouteau S, Ferret V, Gaudin V, Lefebvre D, Sabar M, Zhao G, Prunus F (2004) Extensive phenotypic variation in early flowering mutants of Arabidopsis. Plant Physiol. 135: 201-211 (Pubmed)

Berger F, Gaudin V (2003) Chromatin dynamics and Arabidopsis development. Chromosome Research 11: 277-304 (Pubmed)

Pouteau S, Gaudin V, Ferret V, Lefebvre D, Libault M, Prunus F, Sabar M, Zhao G (2001) Analysis of the floral repression process in Arabidopsis. FNL 32: 3-9

Gaudin V, Libault M, Pouteau S, Juul T, Zhao G, Lefebvre D, Grandjean O (2001) Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development 128: 4847-4858 (Pubmed)

Autres productions
European Workshop Series on Plant Chromatin
Kohler C, Gaudin V, Hennig L (2010) Green chromatin dynamics in Zurich: meeting summary based on the European Workshop on Plant Chromatin 2009 in Zurich, Switzerland. Epigenetics 5: 80-83

Houba-Herin N, Hennig L, Kohler C, Gaudin V (2012) A fruitful chromatin harvest: meeting summary of the Second European Workshop on Plant Chromatin 2011 in Versailles, France. Epigenetics 7: 307-311

Pour en savoir plus sur les EWPC

Samouélian F, Gaudin V, Boccara M (2009) Génétique moléculaire des plantes. Editions Quae, p.208.

More information onDamID


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