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Vincent Colot

Arabidopsis Epigenomics and Epigenetics (A2E)

Goal
To unravel chromatin-based epigenetic processes and chromatin dynamics in the flowering plant Arabidopsis using genomic and genetic approaches.

Background


Chromatin is the natural substrate on which DNA transactions take place within the nucleus of eukaryotic cells. Long considered as mainly a DNA packaging device, chromatin is now viewed as a highly dynamic structure which impacts on all aspects of genome activity, namely transcription, replication, repair, recombination and transposition, as well as chromosome segregation. How distinct chromatin states are established, maintained and erased, and how they modulate the accessibility of DNA are key questions that remain largely unanswered.

Research highlights


The flowering plant Arabidopsis is an excellent model for the study of chromatin organization and dynamics, thanks to its fully sequenced genome and extensive collections of mutants in chromatin remodeling, histone and DNA modifications. Our approaches are based in part on the use of epigenomic techniques to obtain detailed maps of specific chromatin modifications and chromatin-associated proteins along the genome. These so-called epigenomic maps are being established in different genetic or developmental contexts in order to characterize the factors involved in chromatin organization as well as the extent of chromatin changes that occur across the genome during cell differentiation and plant organogenesis.
Our other main interest is to determine the contribution of heritable variations in chromatin states, so-called epigenetic variants, to heritable phenotypic variation, especially in the context of complex traits. To this end, we have created a large population of “epigenetic” recombinant inbred lines (epiRILs), starting from two parents with virtually identical genomes but contrasted profiles of DNA methylation, a classic epigenetic mark. Analysis of the epiRILs revealed a remarkably high degree of heritability for several complex traits, as well as stable segregation of multiple parental DNA methylation variants for at least eight generations. These findings highlight the potential relevance of epigenetic variation to population and evolutionary genetics.

Cortijo,S, Wardenaar, R, Colomé-Tatché, M., Gilly, A., Etcheverry, M, et al. (2014) Mapping the epigenetic basis of complex traits. Science. 2014 Feb 6. [Epub ahead of print]

Silveira, AB, Trontin, C, Cortijo, S, Barau, J, Vieira Del Bem, LE, Loudet, O, Colot, V and Vincentz, M. (2013) Extensive natural epigenetic variation at a de novo originated gene. PLoS Genet 9, e1003437

Colome-Tatché,M, Cortijo, S, Wardenaar, R, Morgado, L, Lahouze, B, et al. (2012) Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc Nat Acad Sci USA 109, 16240-16245

Roudier F, Ahmed I, Berard C, Sarazin A, Mary-Huard T, et al. (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30, 1928-1938

Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, et al. (2009) Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 5 (6): e1000530.

Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, et al. (2009) A Role for RNAi in the selective correction of DNA methylation defects. Science 323: 1600-1604.