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Chromatin dynamics and gene regulation
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Keywords :Arabidopsis thaliana - nucleus -chromatin -transcription regulation - silencing - development

Doctoral school affiliation : ED 145 Sciences du Végétal, Paris XI Orsay

Contacts :

Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 2
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

 

Stefania Del Prete
PhD student
from 1/3/13 to 28/2/16


 


Summary :

Epigenetic mechanisms largely preside over the establishment, the maintenance, and the transmission of cell fates and, consequently, over the plant development, the responses to the environment and in the maintenance of the genome integrity. Major players in epigenetic controls are a large repertoire of post-translational histone modifications, histone variants, various chromatin-assocated complexes as well as DNA methylation and RNA components. A major goal for transcriptional regulation in plant biology is thus to unravel the chromatin structure and dynamics that orchestrate the control of gene expression in the nuclear space.
To address these questions, our team has developed two major research axes. The first axe concerns the study of the Polycomb Repressive Complex 1 (PRC1), especially one of its subunit, LHP1. The second axe focuses on the nuclear architecture and its relationship with the expression of the plant genome.



Main Results :


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LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is a PRC1 subunit in Arabidopsis thaliana, which recognizes and binds the H3K27me3 epigenetic mark (Gaudin et al 2001) , (Zhang, Germann et al 2007)

 

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Genome-wide distribution of the LHP1 binding sites by the DamID method (Germann et al 2007), (Germann et Gaudin 2011), (Zhang, Germann et al 2007). This was the first map of a chromatin-associated protein in plants.

 

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Identification of LIF2, an RNA binding protein, partner of LHP1 involved in the maintenance of cell fate and determination (Latrasse et al 2011)

 

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Large-scale reorganisation of the heterochromatin compartment (Tessadori et al 2007) during early events in the establishment of totipotency in protoplast-derived cells of A. thaliana. This extensive nuclear reorganisation is associated with marked changes in the expression of chromatin-associated genes and specific epigenetic status (Chupeau et al 2013).

 

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Development of methods and tools to investigate the A. thaliana 3D nuclear organisation (Tirichine et al 2009), (Andrey et al 2010).

 

 


Selected Publications :

 

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)
http://epigenomics.mcdb.ucla.edu/LHP1/index.html

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)

Other 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

To know more about EWPC

Samouélian F, Gaudin V, Boccara M (2009) Génétique moléculaire des plantes. Editions Quae, p.208.
http://www.quae.com/fr/r1147-genetique-moleculaire-des-plantes.html
http://prixroberval.utc.fr/genetique_moleculaire.html
http://www.inra.fr/Entreprises-Monde-agricole/Resultats-innovation-transfert/Toutes-les-actualites/Genetique-moleculaire-des-plantes

To know more DamID

 

 

  

 


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