Montpellier Scientific Community



Plant Genome and Development Laboratory (LGDP)

Director: Jean-Marc Deragon
Research area
The LGDP Research Unit focuses on the following themes in Arabidopsis thaliana and rice, model plants: 1/ Organisation and evolution of plant genomes 2/ Study of gene regulation at the transcriptional and post-transcriptional level by genetic and epigenetic mechanisms 3/ Impact of the redox state on plant development
Research highlights
1. Plant genomics evolution
a. Wide genome characterisation of transposable retroelements and their impact in rice genome evolution (Roulin et al, Plant J 2009)
b. Study of genome duplications throughout the Oriza genus (Jacquemin et al. BMC Plant Biology 2009).
c. Annotation of transposable elements in diverse plant genomes (Argout et al Nat Genet, 2011)

2. Transcriptional and post-transcriptional gene regulation in Arabidopsis
a. The characterization of the new RNA polymerase system in plants and demonstration of its role in gene silencing (Pontier et al, Genes & Dev. 2007, Lahmy et al PNAS 2009).
b. The identification and characterisation of small nucleolar RNAs and RNA processing activities controlling processing and modification of ribosomal RNAs and other RNA targets (Pontvianne et al, Plos Genet 2010).
c. Identification and functional characterisation of RNA processing mechanisms and factors playing key roles in epigenetic, RNA modification and the biogenesis of small RNAs (siRNAS, snoRNAs, SINES, etc.) (Pouch-Pelissier et al, PloS Genet, 2008).
d. Regulation of mRNA metabolism in stress situation (Deragon and Bousquet-Antonelli, RNA, 2009)

3. Plant Development
a. Developmental control of meristem by the redox state (Bashandy, Plant Cell 2010).
Staff profile
Research org.
Researchers Professors Recherche eng.

Techn. and admin. staff

Doct.
CNRS, UPVD
9
11
1 (+2 CDD)

13

 5
Research teams
- Genome Analysis and Evolution
- Transcriptional Gene Silencing and RNAi in Plant
- Thiredoxin-Dependent Redox Regulation of Arabidopsis Development
- Biosynthesis of Ribosomal and Small Nucleolar RNAs in Arabidopsis
- Translational regulation in stress situation: Role of LAM-containing proteins
Platforms and other tools
LGDP laboratory has strong commitment to genomic programs for Genomes or EST libraries sequencing, as well as development of bioinformatics tools to annotate the plant genomes. It is currently part of the Genopôle Montpellier and is leading the DNA sequencing platform.
Most important international partnerships
OMAP project Arizona Genomic Institute and University of Purdue, Nagoya University, Japan; International Rice Research Institute (IRRI, Philippines)
Facts and figures
Publications in international ranking journals
2009: 21
2008: 50
2007: 31
2006: 27
2005: 34
Representative publications
1. Bashandy T, Guilleminot J, Vernoux T, Caparros-Ruiz D, Ljung K, Meyer Y, Reichheld JP. Interplay between the NADP-linked thioredoxin and glutathione systems in Arabidopsis auxin signalling. Plant Cell. 2010; 22(2):376-91.
2. Azevedo J, Garcia D, Pontier D, Ohnesorge S, Yu A, Garcia S, Braun L, Bergdoll M, Hakimi MA, Lagrange T, Voinnet O. Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein. Genes Dev. 2010; 24(9):904-15
3. Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJ, Matzke M, Pikaard CS, Zhu JK. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature. 2010; 465(7294):106-9.
4. Samaha H, Delorme V, Pontvianne F, Cooke R, Delalande F, Van Dorsselaer A, Echeverria M, Sáez-Vásquez J. Identification of protein factors and U3 snoRNAs from a Brassica oleracea RNP complex involved in the processing of pre-rRNA. Plant J. 2010; 61(3):383-98.
5. Karlowski WM, Zielezinski A, Carrère J, Pontier D, Lagrange T, Cooke R. Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis. Nucleic Acids Res. 2010 38(13) 4231-45.
6. Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science. 2009; 324(5924):268-72.
7. Bousquet-Antonelli C, Deragon JM. A comprehensive analysis of the La-motif protein superfamily. RNA. 2009: 15(5):750-64. Epub 2009 Mar 19
8. Meyer Y, Buchanan BB, Vignols F, Reichheld JP. Thioredoxins and glutaredoxins: unifying elements in redox biology. Annu Rev Genet. 2009 43:335-67.
9. Barbezier N, Canino G, Rodor J, Jobet E, Saez-Vasquez J, Marchfelder A, Echeverría M. Processing of a dicistronic tRNA-snoRNA precursor: combined analysis in vitro and in vivo reveals alternate pathways and coupling to assembly of snoRNP. Plant Physiol. 2009 150(3):1598-610.
10. Lahmy S, Pontier D, Cavel E, Vega D, El-Shami M, Kanno T, Lagrange T. PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit. Proc Natl Acad Sci U S A. 2009 106(3):941-6.
11. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. The B73 maize genome: complexity, diversity, and dynamics. Science. 2009 326(5956):1112-5.
12. Picault N, Chaparro C, Piegu B, Stenger W, Formey D, Llauro C, Descombin J, Sabot F, Lasserre E, Meynard D, Guiderdoni E, Panaud O. Identification of an active LTR retrotransposon in rice. Plant J. 2009 58(5):754-65.
13. Pouch-Pélissier MN, Pélissier T, Elmayan T, Vaucheret H, Boko D, Jantsch MF, Deragon JM. SINE RNA induces severe developmental defects in Arabidopsis thaliana and interacts with HYL1 (DRB1), a key member of the DCL1 complex. PLoS Genet. 2008 13;4(6):e1000096.
14. Fleurdépine S, Deragon JM, Devic M, Guilleminot J, Bousquet-Antonelli C. A bona fide La protein is required for embryogenesis in Arabidopsis thaliana. Nucleic Acids Res. 2007 35(10):3306-21.
15. El-Shami M, Pontier D, Lahmy S, Braun L, Picart C, Vega D, Hakimi MA, Jacobsen SE, Cooke R, Lagrange T. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 2007 21(20):2539-44.
Total annual budget
2010 :
Total annual budget (without equipment): 446 300
External contracts (2010): 221 500