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DNA repair and genome editing
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Keywords :Arabidopsis thaliana, Physcomitrella patens, meiosis, meiotic recombination, mitotic recombination, mismatch repair, gene targeting, mutants

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
Fabien Nogué

Senior Scientist

Anouchka Guyon-Debast
Assistant Engineer



Florence Charlot
Assistant Engineer





Summary :

Mechanisms of the targeted integration of transgenes.
The frequency of recombination found into the moss P. patens makes this organism a good model for the analysis of the mechanisms of mitotic homologous recombination and gene targeting in plants. The main interest of our group is to determine what are the elements of the machinery of homologous recombination that allow such a high rate of gene targeting compared to what is possible in higher eukaryotes in general and especially in plants . We have isolated loss of function mutants for a large number of genes representing different pathways of DNA repair in eukaryotes. The following genes have been deleted: RAD50, MRE11, LigIV, RAD1, RAD10, RAD51, RAD51B, RAD51C, RAD51D, RAD54, their respective roles in gene targeting is under study.

Using Physcomitrella patens as a tool for functional analysis.
The frequency of recombination found in P. patens permits, as in yeast, targeted mutagenesis of genes of interest. In this framework we have set up a platform for obtaining mutants by gene targeting. We have many tools for functional analysis: Knock-out, constitutive expression, inducible expression, GUS, GFP and TAP-TAG fusions


Main Results :

We have shown the importance of RAD51 and of the MRN DSB detection pathway for gene targeting in P. patens. We are currently working on the involvement of the others RAD51 paralogs in homologous recombination and gene targeting.

Selected Publications :

Collonnier C, Epert A, Mara K, Maclot F, Guyon Debast A, Charlot F, White C, Schaefer DG, Nogué F (2017) CRISPR-Cas9-mediated efficient directed mutagenesis and RAD51-dependent and RAD51-independent gene targeting in the moss Physcomitrella patens. Plant Biotechnology Journal 15: 122-131

Alburquerque N, Baldacci-cresp F, Baucher M, et al (2016) New transformation technologies for trees. In: Vettori C, Fladung M, Häggman. H, et al. (eds) Biosafety of Forest Transgenic Trees, Springer.

Collonnier C, Nogué F, Casacuberta JM (2016) Targeted Genetic Modification in Crops Using Site-Directed Nucleases. In: Watson RR, Preedy VR (eds) Genetically Modified Organisms in Food. Elsevier, London, pp 133–145

Casacuberta JM, Devos Y, du Jardin P, et al (2015) Biotechnological uses of RNAi in plants: risk assessment considerations. Trends Biotechnol 33:145–147. doi: 10.1016/j.tibtech.2014.12.003 (abstract)

von Schwartzenberg K, Lindner A-C, Gruhn N, et al (2015) CHASE domain-containing receptors play an essential role in the cytokinin response of the moss Physcomitrella patens. J Exp Bot erv479. doi: 10.1093/jxb/erv479 (pubmed)

Charlot F, Chelysheva L, Kamisugi Y, et al (2014) RAD51B plays an essential role during somatic and meiotic recombination in Physcomitrella. Nucleic Acids Res 1–14. doi: 10.1093/nar/gku890 (pubmed)

Maumus F, Epert A, Nogué F, Blanc G (2014) Plant genomes enclose footprints of past infections by giant virus relatives. Nat Commun 5:4268. doi: 10.1038/ncomms5268 (pubmed)

Bonhomme S, Nogué F, Rameau C, Schaefer DG (2013) Usefulness of Physcomitrella patens for studying plant organogenesis. Methods Mol Biol 959:21–43. doi: 10.1007/978-1-62703-221-6_2 (pubmed)

Podevin N, Davies H V, Hartung F, et al (2013) Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding. Trends Biotechnol 31:375–83. doi: 10.1016/j.tibtech.2013.03.004 (pubmed)

Kamisugi Y, Schaefer DG, Kozak J, et al (2012) MRE11 and RAD50, but not NBS1, are essential for gene targeting in the moss Physcomitrella patens. Nucleic Acids Res 40:3496–510. doi: 10.1093/nar/gkr1272 (pubmed)

Thévenin, J., Dubos, C, Xu, W, Le Gourrierec, J, Kelemen, Z, Charlot, F, Nogue, F, Lepiniec, L and Dubreucq, B (2012) A new system for fast and quantitative analysis of heterologous gene expression in plants. New Phytol, 193, 504-512 (pubmed)

Vivancos, J., Spinner, L., Mazubert, C., Charlot, F., Paquet, N., Thareau, V., Dron, M., Nogue, F. and Charon, C. (2012) The function of the RNA-binding protein TEL1 in moss reveals ancient regulatory mechanisms of shoot development. Plant Mol Biol 78:323–36. doi: 10.1007/s11103-011-9867-9 (pubmed)

Kamisugi, Y., Schaefer, D.G., Kozak, J., Charlot, F., Vrielynck, N., Hola, M., Angelis, K.J., Cuming, A.C. and Nogue, F. (2011) MRE11 and RAD50, but not NBS1, are essential for gene targeting in the moss Physcomitrella patens. Nucleic Acids Res. 40(8):3496-510. doi: 10.1093/nar/gkr1272 (pubmed)

Proust H, Hoffmann B, Xie X, Yoneyama K, Schaefer DG, Yoneyama K, Nogué F, Rameau C. (2011) Strigolactones regulate protonema branching and act as a quorum sensing-like signal in the moss Physcomitrella patens. Development. 138(8):1531-9. doi: 10.1242/dev.058495 (pubmed)

Marimuthu MP, Jolivet S, Ravi M, Pereira L, Davda JN, Cromer L, Wang L, Nogué F, Chan SW, Siddiqi I, Mercier R. (2011) Synthetic clonal reproduction through seeds. Science. 18;331(6019):876 (pubmed)

Schaefer DG, Delacote F, Charlot F, Vrielynck N, Guyon-Debast A, Le Guin S, Neuhaus JM, Doutriaux MP, Nogué F. (2010) RAD51 loss of function abolishes gene targeting and de-represses illegitimate integration in the moss Physcomitrella patens. DNA Repair (Amst). 9(5):526-33 (pubmed)

De Muyt A, Pereira L, Vezon D, Chelysheva L, Gendrot G, Chambon A, Lainé S, Pelletier G, Mercier R, Nogué F, Grelon M (2009). A High Throughput Genetic Screen Identifies New Early Meiotic Recombination Functions in Arabidopsis thaliana. PLoS Genetics PLoS Genet. 5(9):e1000654 (online)

Liénard D, Nogué F (2009). Physcomitrella patens: a non-vascular plant for recombinant protein production. Methods Mol Biol. 483, 135-44. (pubmed)

Mercier R, Jolivet S, Vignard J, Durand S, Drouaud J, Pelletier G, Nogué F (2008). Outcrossing as an explanation of the apparent unconventional genetic behavior of Arabidopsis thaliana hth mutants. Genetics. 180, 2295-2297 (online)

Liénard D, Durambur G, Kiefer-Meyer MC, Nogué F, Menu-Bouaouiche L, Charlot F, Gomord V, Lassalles JP (2008). Water transport by aquaporins in the extant plant Physcomitrella patens. Plant Physiol. 146, 1207-1218. doi: 10.1534/genetics.108.095208

Alboresi A, Caffarri S, Nogué F, Bassi R, Morosinotto T (2008). In silico and biochemical analysis of Physcomitrella patens photosynthetic antenna: identification of subunits which evolved upon land adaptation. PLoS One. 3, e2033. (online)

Trouiller B, Charlot F, Choinard S, Schaefer DG, Nogué F (2007). Comparison of gene targeting efficiencies in two mosses suggests that it is a conserved feature of Bryophyte transformation. Biotechnol Lett. 29, 1591-1598 (pubmed)

Trouiller B, Schaefer DG, Charlot F, Nogué F (2006). MSH2 is essential for the preservation of genome integrity and prevents homeologous recombination in the moss Physcomitrella patens. Nucleic Acids Res 34, 232-242. doi: 10.1007/s10529-007-9423-5 (pdf)

Guermonprez H, Nogué F, Bonhomme S (2006) Screening and Analysis of Pollen Tube Mutations. In: Malhó R (ed) Plant Cell Monographs, Vol. 3. Springer-Verlag, Berlin/Heidelberg, pp 243–263

Kopecný D, Tarkowski P, Majira A, Bouchez-Mahiout I, Nogué F, Laurière M, Sandberg G, Laloue M, Houba-Herin N (2006). Probing cytokinin homeostasis in Arabidopsis thaliana by constitutively overexpressing two forms of the maize cytokinin oxidase/dehydrogenase 1 gene. Plant Science 171, 114-122.

Trouiller B, Schaefer DG, Charlot F, Nogué F (2006) MSH2 is essential for the preservation of genome integrity and prevents homeologous recombination in the moss Physcomitrella patens. Nucleic Acids Res 34:232–42. doi: 10.1093/nar/gkj423

Mercier R, Jolivet S, Vezon D, et al (2005) Two meiotic crossover classes cohabit in Arabidopsis: one is dependent on MER3,whereas the other one is not. Curr Biol 15:692–701. doi: 10.1016/j.cub.2005.02.056 (online)

Vincent P, Chua M, Nogue F, et al (2005) A Sec14p-nodulin domain phosphatidylinositol transfer protein polarizes membrane growth of Arabidopsis thaliana root hairs. J Cell Biol 168:801–12. doi: 10.1083/jcb.200412074 (online)

Böhme K, Li Y, Charlot F, et al (2004) The Arabidopsis COW1 gene encodes a phosphatidylinositol transfer protein essential for root hair tip growth. Plant J 40:686–98. doi: 10.1111/j.1365-313X.2004.02245.x (online)

Brun F, Gonneau M, Laloue M, Nogué F (2003) Identification of Physcomitrella patens genes specific of bud and gametophore formation. Plant Sci 165:1267–1274. doi: 10.1016/S0168-9452(03)00335-2 (online)

Nogué F, Gonneau M, Faure J denis (2003) Cytokinins. In: Henry H, Norman A (eds) Encyclopedia of hormones. Academic Press, San Diego (Etats-Unis) 0-12-341103-3, San Diego, pp 371–378

Hamant O, Nogué F, Belles-Boix E, et al (2002) The KNAT2 homeodomain protein interacts with ethylene and cytokinin signaling. Plant Physiol 130:657–65. doi: 10.1104/pp.004564 (online)

Brun F, Gonneau M, Doutriaux MP, et al (2001) Cloning of the PpMSH-2 cDNA of Physcomitrella patens, a moss in which gene targeting by homologous recombination occurs at high frequency. Biochimie 83:1003–8 (online)

Nogué F, Grandjean O, Craig S, et al (2000) Higher levels of cell proliferation rate and cyclin CycD3 expression in the Arabidopsis amp1 mutant. Plant Growth Regul 32:275–283. doi: 10.1023/A:1010716203798

Nogué N, Hocart H, Letham DS, et al (2000) Cytokinin synthesis is higher in the Arabidopsis amp1 mutant. Plant Growth Regul 32:267–273. doi: 10.1023/A:1010720420637 (pdf)

Clemenceau D, Cousseau J, Martin V, et al (1996) Synthesis and Cytokinin Activity of Two Fluoro Derivatives of N 6 -Isopentenyladenine. J Agric Food Chem 44:320–323. doi: 10.1021/jf9501148 (online)

Nogué F, Mornet R, Laloue M (1996) Specific photoaffinity labelling of a thylakoid membrane protein with an azido-cytokinin agonist. Plant Growth Regul 18:51–58. doi: 10.1007/BF00028488 (pdf)

Nogué F, Jullien M, Mornet R, Laloue M (1995) The response of a cytokinin resistant mutant is highly specific and permits a new cytokinin bioassay. Plant Growth Regul 17:87–94. doi: 10.1007/BF00024166 (pdf)


Further Readings: Page Meiosis and recombination





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