Epigenetics, Chromatin and Development


Bouyer D., Heese M., Chen P., Harashima H., Roudier F., Grüttner C, and Schnittger A. "Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators.". PLoS Genet 14:e1007797; DOI:10.1371/journal.pgen.1007797 (2018)

Morao A. K., Caillieux E., Vincent Colot V. and Roudier F. "Cell type-specific profiling of chromatin modifications and associated proteins". Methods Mol Biol. 1675 111-130 Springer NY, Edited by Marian Bemer and Célia Baroux (2018)

"Cortijo S., Charoensawan V., Roudier F. and...". (2018)
Cortijo S., Charoensawan V., Roudier F. and Wigge P.A. (2018). Chromatin Immunoprecipitation Sequencing (ChIP-Seq) for Transcription Factors and Chromatin Factors in Arabidopsis thaliana Roots: From Material Collection to Data Analysis. Methods Mol Biol., In book: "Root Development: Methods and Protocols" Clifton NJ, Edited by Daniela Ristova and Elke Barbez, 1761:231-248. PMID:29525962

"Bellegarde F., Herbert L., Séré D., Caillieux...". (2018)
Bellegarde F., Herbert L., Séré D., Caillieux E., Boucherez J., Fizames C., Roudier F., Gojon A. and Martin A. (2018). Polycomb Repressive Complex 2 attenuates the very high expression of the Arabidopsis gene NRT2.1. Scientific Reports, 8:7905; DOI:10.1038/s41598-018-26349-w. PMID:29784958


"Birnbaum, K. D. and Roudier, F. (2017)....". (2017)
Birnbaum, K. D. and Roudier, F. (2017). Epigenetic memory and cell fate reprogramming in plants. Regeneration 4:15–20.PMID:28316791

"Rosspopoff O., Chelysheva L., Saffar J.,...". (2017)
Rosspopoff O., Chelysheva L., Saffar J., Lecorgne L., Gey D., Caillieux C, Vincent Colot, Roudier F., Hilson P., Berthome R., Da Costa M. and Rech P. (2017). Direct conversion of root primordium into shoot meristem relies on timing of stem cell niche development. Development 144:1187-1200. PMID:28174250

"Bouyer D., Kramdi A., Kassam M., Heese M.,...". (2017)
Bouyer D., Kramdi A., Kassam M., Heese M., Schnittger A., Roudier F. and Colot V. (2017). DNA methylation dynamics during early plant life. Genome Biol. 18:179. PMID:28942733

"Tran D., Galletti R., Neumann E.D., Dubois...". (2017)
Tran D., Galletti R., Neumann E.D., Dubois A., Sharif-Naeini R., Geitmann A., Frachisse J-M., Hamant O., Ingram G.C. (2017). A mechanosensitive Ca(2+) channel activity is dependent on the developmental regulator DEK1. Nat Commun. 18:1009. PMID:29044106

"Chica C., Louis A., Roest Crollius H., Colot...". (2017)
Chica C., Louis A., Roest Crollius H., Colot V.# and Roudier F.# (2017). Comparative epigenomics in the Brassicaceae reveals two evolutionarily conserved modes of PRC2-mediated gene regulation. Genome Biol. 18:207. #Co-corresponding authors. PMID:29084582


"Marquès-Bueno M.M., Morao A.K., Cayrel A.,...". (2016)
Marquès-Bueno M.M., Morao A.K., Cayrel A., Platre M., Barberon M., Caillieux E., Colot V., Jaillais Y.#, Roudier F.# and Vert G.# (2016). A versatile Multisite Gateway-compatible promoter and transgenic line collection for cell-type specific functional genomics in Arabidopsis. Plant J. 85:320-333. # Co-corresponding authors. PMID:26662936

"Morao A. K., Bouyer D.# and Roudier F.#...". (2016)
Morao A. K., Bouyer D.# and Roudier F.# (2016). Emerging concepts in chromatin-level regulation of plant cell differentiation: timing, counting, sensing and maintaining. Curr. Opin. Plant Biol. 11:27-34. #Co-corresponding authors. PMID:27522467

"de Lucas M., Pu L., Turco G. M., Gaudinier...". (2016)
de Lucas M., Pu L., Turco G. M., Gaudinier A., Morao A. K., Harashima H., Kim D., Ron M., Sugimoto K., Roudier F. and Brady S.M. (2016). Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell Type Proliferation and Differentiation. Plant Cell 10:2616-2631. PMID:27650334


"Magnard JL, Roccia A, Caissard JC, Vergne P,...". (2015)
Magnard JL, Roccia A, Caissard JC, Vergne P, Sun P, Hecquet R, Dubois A, Hibrand-Saint Oyant L, Jullien F, Nicolè F, Raymond O, Huguet S, Baltenweck R, Meyer S, Claudel P, Jeauffre J, Rohmer M, Foucher F, Hugueney P, Bendahmane M and Baudino S. (2015). PLANT VOLATILES. Biosynthesis of monoterpene scent compounds in roses. Science 349:81-3. PMID:26138978. Perspective in Science.

"Willing E-M., Rawat V., Mandáková T., Maumus...". (2015)
Willing E-M., Rawat V., Mandáková T., Maumus F., James G.V., Nordström K.J.V., Becker C., Warthmann N., Chica C., Szarzynska B., Zytnicki M., Albani M. C., Kiefer C., Bergonzi S., Castaings L., Mateos J.L., Berns M. C., Bujdoso N., Piofczyk T., de Lorenzo L., Barrero-Sicilia C., Mateos I., Piednoël M., Hagmann J., Chen-Min-Tao R., Iglesias-Fernández R., Schuster S.C., Alonso-Blanco C., Roudier F., Carbonero P., Paz-Ares J., Davis S.J., Pecinka A., Quesneville H., Colot V., Lysak M.A., Weigel D., Coupland G. and Schneeberger K.(2015). Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants 1:14023. PMID:27246759

"Ikeuchi M., Iwase A., Rymen B., Harashima H.,...". (2015)
Ikeuchi M., Iwase A., Rymen B., Harashima H., Shibata M., Ohnuma M., Breuer C., Morao A.K., de Lucas M., De Veylder L., Justin Goodrich J., Brady S. M., Roudier F. and Sugimoto K. (2015). PRC2 represses dedifferentiation of mature somatic cells in Arabidopsis. Nature Plants 1:15089. PMID:27250255. N&V in Nature Plants.


"Chardin C., Girin T., Roudier F., Meyer C....". (2014)
Chardin C., Girin T., Roudier F., Meyer C. and Krapp A. (2014). The plant RWP-RK transcription factors: key regulators of nitrogen responses and of gametophyte development. J. Exp. Bot. 65:5577-87.PMID:24987011

"Cortijo S., Wardenaar R., Colomé-Tatché M.,...". (2014)
Cortijo S., Wardenaar R., Colomé-Tatché M., Gilly A., Etcheverry M., Labadie K., Caillieux E., Hospital F., Aury J-M, Wincker P., Roudier F., Jansen R.C., Colot V. and Johannes F. (2014). Mapping the epigenetic basis of complex traits. Science 343:1145-8. PMID:24505129. Perspective in Science, Highlight in NRG, F1000 [4]


"Bendahmane M, Dubois A, Raymond O and Bris...". (2013)
Bendahmane M, Dubois A, Raymond O and Bris ML. (2013). Genetics and genomics of flower initiation and development in roses. J. Exp. Bot. 64:847-57. PMID:23364936

"Marchive C., Roudier F., Castaings L., Bréhaut...". (2013)
Marchive C., Roudier F., Castaings L., Bréhaut V., Blondet E., Colot V., Meyer C. and Krapp A. (2013). Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants. Nature Comm. 4:1713.PMID:2359188. F1000 [4].

"Grimanelli D.# and Roudier F.# (2013)....". (2013)
Grimanelli D.# and Roudier F.# (2013). Epigenetics and development in plants: green light to convergent innovations. Curr. Top. Dev. Biol. 104:189-222. #Co-corresponding authors. PMID:23587242

"Chica C., Szarzynska B., Chen-Min-Tao R.,...". (2013)
Chica C., Szarzynska B., Chen-Min-Tao R., Duvernois-Berthet E., Kassam M., Colot V# and Roudier F.# (2013). Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation. Frontiers in Life Sciences 7, 80-87. # Co-corresponding authors.


"Dubois A., Carrere S., Raymond O., Pouvreau...". (2012)
Dubois A., Carrere S., Raymond O., Pouvreau B., Cottret L., Roccia A., Onesto J-P., Sakr S., Atanassova R., Baudino S., Foucher F., Le Bris M., Gouzy J. and Bendahmane M. (2012). Transcriptome database resource and gene expression atlas for the rose. BMC Genomics 20;13:638. PMID:23164410

"Bourbousse C., Ahmed I., Roudier F., Zabulon...". (2012)
Bourbousse C., Ahmed I., Roudier F., Zabulon G., Blondet E., Balzergue S., Colot V., Bowler C. and Barneche F. (2012). Histone H2B Monoubiquitination Facilitates the Rapid Modulation of Gene Expression during Arabidopsis Photomorphogenesis. PLoS Genet 8: e1002825. PMID:22829781

"Pontier D., Picart C., Roudier F., Garcia D.,...". (2012)
Pontier D., Picart C., Roudier F., Garcia D., Lahmy S., Azevedo J., Alart E., Laudié M., Karlowski W. M., Cooke R., Colot V., Voinnet O. and Lagrange T. (2012). NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Mol. Cell 48: 121-132. PMID:22940247. F1000 [4].

"Seifert M., Cortijo S., Colome-Tatche M.,...". (2012)
Seifert M., Cortijo S., Colome-Tatche M., Johannes F., Roudier F. and Colot V. (2012). MeDIP-HMM: Genome-wide identification of distinct DNA methylation states from high-density tiling arrays. Bioinformatics 28:2930-9. PMID:22989518


"Dubois A., Remay A., Raymond O., Balzergue...". (2011)
Dubois A., Remay A., Raymond O., Balzergue S., Chauvet A., Maene M., Pécrix Y., Yang S.H., Jeauffre J., Thouroude T., Boltz V., Martin-Magniette M-L., Janczarski S., Legeai F., Renou J-P., Vergne P., Le Bris M., Foucher F. and Bendahmane M. (2011). Genomic approach to study floral development genes in Rosa sp. PLoS One 6:e28455. PMID:22194838

"Banaei A.M., Roudier F., Seifert M., Berard...". (2011)
Banaei A.M., Roudier F., Seifert M., Berard C., Magniette M.L., Ashtiyani R.K., Houben A., Colot V. and Mette M.F. (2011). Additive inheritance of histone modifications in Arabidopsis thaliana intra-specific hybrids. Plant J. 67, 691-700. PMID:21554454

"Bouyer D., Roudier F., Heese M., Ellen D....". (2011)
Bouyer D., Roudier F., Heese M., Ellen D. Andersen E. D., Gey D., Nowack M. K., Goodrich J., Renou J-P., Grini P. E., Colot V. and Schnittger A. (2011). Polycomb Repressive Complex 2 controls the embryo to seedling phase transition. PLoS Genet. 7: e1002014.PMID:21423668. F1000 [1].

"Berger N., Dubreucq B., Roudier F., Dubos C....". (2011)
Berger N., Dubreucq B., Roudier F., Dubos C. and Lepiniec L. (2011). Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27. Plant Cell 23: 4065-4078. PMID:22080598

"Roudier F.#, Ahmed I., Bérard C., Sarazin A.,...". (2011)
Roudier F.#, Ahmed I., Bérard C., Sarazin A., Mary-Huard T., Cortijo S., Bouyer D., Caillieux E., Duvernois-Berthet E., Al-Shikhley L., Giraut L., Despres B, Drevensek S., Barneche F., Dérozier S., Brunaud V., Aubourg S., Schnittger A., Bowler C., Martin-Magniette M-L., Robin S., Caboche M. and Colot V.# (2011). Integrative epigenomic mapping defines four major chromatin signatures in Arabidopsis. EMBO J. 30: 1928−1938. # co-corresponding authors.PMID:21487388. F1000 [1].


"Dubois A., Raymond O., Maene M., Baudino S.,...". (2010)
Dubois A., Raymond O., Maene M., Baudino S., Langlade N.B., Boltz V., Vergne P. and Bendahmane M. (2010). Tinkering with the C-function: a molecular frame for the selection of double flowers in cultivated roses. PLoS One 18:e9288. PMID:20174587

"Roudier F., Gissot L., Beaudoin F., Haslam...". (2010)
Roudier F., Gissot L., Beaudoin F., Haslam R., Michaelson L., Marion J., Molino D., Lima A., Bach L., Morin H., Tellier F., Palauqui J-C., Bellec Y., Renne C., Miquel M., Dacosta M., Vignard J., Rochat C., Markham J.E., Moreau P., Napier J. and Faure J-D. (2010). Very-long-chain fatty acids are involved in polar auxin transport and developmental patterning in Arabidopsis. Plant Cell 22:364-75.PMID:20145257. F1000 [2].


"Teixeira F.K., Heredia F., Sarazin A.,...". (2009)
Teixeira F.K., Heredia F., Sarazin A., Roudier F., Boccara M., Ciaudo C., Cruaud C., Poulain J., Berdasco M., Fraga M.F., Voinnet O., Wincker P., Esteller M. and Colot V. (2009). A role for RNAi in the selective correction of DNA methylation defects.Science 323, 1600-1604. PMID:19179494. Perspective in Science.

"Bérard C., Martin-Magniette M.-L., To A.,...". (2009)
Bérard C., Martin-Magniette M.-L., To A., Roudier F., Colot V. and Robin S. (2009). Mélanges gaussiens bidimensionnels pour la comparaison de deux échantillons de chromatine immunoprécipitée. La revue Modulad 40, 53-68.

"Roudier F.#, Teixeira F.K.# and Colot V....". (2009)
Roudier F.#, Teixeira F.K.# and Colot V. (2009). Chromatin indexing in Arabidopsis: an epigenomic tale of tails and more. Trends Genet. 25:511-7. # Equal contribution. PMID:19850370


"Turck F. #, Roudier F.#, Farrona S., Martin-Magnie". (2007)
Turck F. #, Roudier F.#, Farrona S., Martin-Magniette M-L., Guillaume E., Buisine N., Gagnot S., Martienssen R., Coupland G. and Colot V. (2007). Arabidopsis TFL2/LHP1 Specifically Associates with Genes through Recognition of the Chromatin Mark H3K27me3. PLoS Genet. 3, e86. # Co-first authors. PMID:17542647. F1000 [2].


"Wellmer F., Alves-Ferreira M., Dubois A.,...". (2006)
Wellmer F., Alves-Ferreira M., Dubois A., Riechmann J.L. and Meyerowitz E.M. (2006). Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genet. 2:e117. PMID:16789830

"Smyczynski C., Roudier F., Gissot L.,...". (2006)
Smyczynski C., Roudier F., Gissot L., Vaillant E., Grandjean O., Morin H., Masson T., Bellec Y., Geelen D. and Faure J-D. (2006). The C-terminus of the immunophilin PASTICCINO1 is required for plant development and for interaction with a NAC-like transcription factor. J. Biol. Chem. 281:25475-84. PMID:16803883


"Roudier F., Fernandez A.G., Fujita M.,...". (2005)
Roudier F., Fernandez A.G., Fujita M., Schindelman G., Borner G.H., Himmelspach R., Song, S., Dupree P., Baskin T.I., Wasteneys G.O. and Benfey P.N. (2005). COBRA, an Arabidopsis extracellular Glycosyl-Phosphatidyl-Inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation. Plant Cell 17, 1749-63. PMID:15849274. F1000 [1].


"Roudier F., Fedorova E., Lebris M., Lecomte...". (2003)
Roudier F., Fedorova E., Lebris M., Lecomte P., Györgyey J., Vaubert D., Abad P., Kondorosi A. and Kondorosi E. (2003). The Medicago A2-type cyclin is auxin regulated and involved in meristem formation but dispensable for endoreduplication-associated developmental programs. Plant Phys. 131, 1-13. PMID:12644661

"Vinardell, J.M., Fedorova, E., Cebolla A,...". (2003)
Vinardell, J.M., Fedorova, E., Cebolla A, Kevei, Z., Horvath, G., Kelemen Z., Tarayre S., Roudier F., Mergaert, P., Kondorosi, A. and Kondorosi, E. (2003). Endoreduplication mediated by the anaphase-promoting complex activator CCS52A is required for symbiotic cell differentiation in Medicago truncatula nodules. Plant Cell 15, 2093-2105. PMID:12953113. F1000 [1].


"Roudier F., Schindelman G, DeSalle R. and...". (2002)
Roudier F., Schindelman G, DeSalle R. and Benfey P. N. (2002). The COBRA family of putative GPI-anchored proteins in Arabidopsis : a new fellowship in expansion. Plant Phys. 130: 538-48. PMID:12376623


"Kondorosi E., Roudier F. and Gendreau E....". (2000)
Kondorosi E., Roudier F. and Gendreau E. (2000). Plant cell-size control: growing by ploidy? Curr. Opin. Plant Biol. 6, 488-492. PMID:11074380

"Roudier F., Fedorova E., Györgyey J., Feher...". (2000)
Roudier F., Fedorova E., Györgyey J., Feher A., Brown S., Kondorosi A. and Kondorosi E. (2000). Cell cycle function of a Medicago A2-type cyclin and its interaction with the A-type cyclin-dependent kinase and the Rb protein. Plant J. 23, 73-83. PMID:10929103


"Cebolla A., Vinardell J.M., Kiss E., Olah B.,...". (1999)
Cebolla A., Vinardell J.M., Kiss E., Olah B., Roudier F., Kondorosi A. and Kondorosi E. (1999). The mitotic inhibitor ccs52 is required for endoreduplication and ploidy-dependent cell enlargement in plants. EMBO J. 18, 4476-4484. PMID:10449413