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Epigenetic variation
 research groups

Keywords : Arabidopsis thaliana, phénotype, régulation épigénétique, stress abiotique

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
Nicolas Bouché
Senior Scientist

Sébastien Beaubiat

Yassir Idir
PhD Student




Summary :

Epigenetic is defined as the study of heritable modifications in gene expression without changes in DNA sequence. Behind this very straightforward definition, the complex mechanisms underlying epigenetic modifications and chromatin dynamic are now very widely studied, in particular in plant models such as Arabidopsis. Recent high-throughput analyses revealed the epigenetic landscapes of Arabidopsis like variations in DNA methylation, histone modifications and small RNAs abundance, as well as epigenetic polymorphisms in transcribed regions of different accessions. Studies of plant natural variation have been focused mainly on sequence variation, and little is known about the role of epigenetic machinery in these processes. We now clearly need to isolate and study more epialleles to understand the significance of inherited epigenetic alterations in natural populations.

In the Institut Jean Pierre Bourgin, several groups (VAST) are interested in the analysis of Arabidopsis natural variation as a source of biodiversity. Many different quantitative trait loci (QTL) responsible for these variations were determined and the genes underlying these QTLs revealed. Interestingly, genes for which the polymorphism observed at the nucleotide level in the parental accessions cannot explain the phenotype of certain recombinant inbred lines (RILs), were also identified.

Our objective is to characterize natural epivariants with phenotypic consequences and investigate the mechanisms underlying them.

Main Results :

Selected Publications :

Corem S, Doron-Faigenboim A, Jouffroy O, Maumus F, Arazi T, Bouché N. (2018) Redistribution of CHH methylation and small interfering RNAs across the genome of tomato ddm1 mutants. The Plant Cell. 10.1105/tpc.18.00167

Agorio A, Durand S, Fiume E, Brousse C, Gy I, Simon M, Anava S, Rechavi O, Loudet O, Camilleri C, Bouché N. (2016) An Arabidopsis Natural Epiallele Maintained by a Feed-Forward Silencing Loop between Histone and DNA. PLoS Genet. 13(1):e1006551.

Brousse C, Liu Q, Beauclair L, Deremetz A, Axtell M.J. and Bouché N. (2014). A non-canonical plant microRNA target site. Nucleic Acids Research, 42 (8) : 5270-9. (pdf)

Mathieu O and Bouché N. (2014). Interplay between chromatin and RNA processing. Current Opinion in Plant Biology, 18:60-5 (pubmed)

Coustham V, Vlad D, Deremetz A, Gy I, Cubillos F, Kerdarec E, Loudet O and Bouché N. (2014). SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1. PLoS ONE, 9 (1) : e84687. doi:10.1371/journal.pone.0084687 (online)

Durand S, Bouché N, Perez Strand E, Loudet O and Camilleri C. (2012). Rapid establishment of genetic incompatibility through natural epigenetic variation. Current Biology, 22 (4) :326-31. (pubmed)

Galon Y, Aloni R, Nachmias D, Snir O, Feldmesser E, Scrase-Field S, Boyce J, Bouché N, Knight M and Fromm H (2010). Calmodulin binding Transcription Activator (CAMTA) 1 mediates auxin signaling and responds to stresses in Arabidopsis. Planta, 232(1):165-78. (pubmed)

Bouché N (2010). New insights into miR398 functions in Arabidopsis. Plant Signaling & Behavior, 5(6):684-6. (pubmed)

Beauclair L, Yu A and Bouché N (2010). MicroRNA-directed cleavage and translational repression of the copper chaperone for superoxide dismutase mRNA in Arabidopsis. The Plant Journal, 62(3):454-62. (pubmed)

Mallory A, Hinze A, Tucker M, Bouché N, Gasciolli G, Elmayan T, Lauressergues D, Jauvion V, Vaucheret H and Laux T (2009). Redundant and specific roles of the ARGONAUTE proteins AGO1 and ZLL in development and small RNA-directed gene silencing. PLoS Genetics, 5 (9) : e1000646.doi:10.1371/journal.pgen.1000646. (on-line)

Perez-Hormaeche J, Potet F, Beauclair L, Le Masson I, Courtial B, Bouché N and Lucas H (2008). Invasion of the Arabidopsis genome by the tobacco retrotransposon Tnt1 is controlled by reversible transcriptional gene silencing. Plant Physiol, 147 (3) : 1264-78. (pubmed)

Mallory AC and Bouché N (2008). MicroRNA-directed regulation: to cleave or not to cleave Trends Plant Sci, 13 (7) : 359-67. 2008 (pubmed)

Ülker B, Peiter E, Dixon DP, Moffat C, Capper R, Bouché N, Edwards R, Sanders D, Knight H and Knight MR (2008). Getting the most out of publicly available T-DNA insertion lines. The Plant Journal, 26 (9) :1015-1017. (pubmed)

Ludewig F, Hüser A, Fromm H, Beauclair L and Bouché N (2008). Mutants of GABA transaminase (POP2) suppress the severe phenotype of succinic semialdehyde dehydrogenase (ssadh) mutants in Arabidopsis. PLoS ONE, 3(10): e3383 doi:10.1371/journal.pone.0003383. (pubmed)

Adenot X, Elmayan T, Lauressergues D, Boutet S, Bouché N, Gasciolli V and Vaucheret H (2006). Uncoupled production of ta-siRNAs in hypomorphic rdr6 and sgs3 mutants uncovers a role for TAS3 in AGO7- DCL4-DRB4-mediated control of leaf morphology. Current Biol, 16: 927-932. (pubmed)

Bouché N, Lauressergues D, Gasciolli V and Vaucheret H (2006). An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J, 26;25 (14) : 3347-3356. (pubmed)

Bouché N, Yellin A, Snedden W and Fromm H (2005). Calmodulin-binding proteins in plants. Ann Rev Plant Biol, 56: 435-466. (pubmed)

Bouché N and Fromm H (2004). GABA in plants : just a metabolite ? Trends in Plant Science, Vol. 9, 3: 110-115. (pubmed)

Bouché N, Fait A, Zik M and Fromm H (2004). The root-specific glutamate decarboxylase (GAD1) is essential for sustaining normal GABA evels in Arabidopsis.Plant Mol Biol, 55(3) : 315-325. (pubmed)

Bouché N, Lacombe B and Fromm H (2003). GABA signalling: a conserved and ubiquitous mechanism. Trends Cell Biol, 13, 12: 607-610. (pubmed)

Bouché N, Fait A, Bouchez D, Møller SG and Fromm H (2003). Mitochondrial succinic-semialdehyde dehydrogenase of the gamma-aminobutyrate shunt is required to restrict levels of reactive oxygen intermediates in plants. PNAS, 100 (11) : 6843-6848. (pubmed)

Bouché N, Scharlat A, Snedden W, Bouchez D and Fromm H (2002). A novel family of calmodulin-binding transcription activators in multicellular organisms. J Biol Chem, 277 (24) : 21851-21861. (pubmed)

Bouché N and Bouchez D (2001). Arabidopsis gene knockout: phenotypes wanted.Curr Opin Plant Biol, 4 (2) : 111-117. (pubmed)

Sunkar R, Kaplan K, Bouché N, Arazi T, Dolev D, Talke I N, Maathuis F J M, Sanders D, Bouchez D and Fromm H (2000). Expression of a truncated tobacco NtCBP4 channel in transgenic plants, and disruption of the homologous Arabidopsis CNGC1 gene confer Pb2+ tolerance, The Plant Journal, 24: 533-542. (pubmed)



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