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Vincent Colot

Genome dynamics and epigenetic variation (GDEV)

Goal
To unravel chromatin-based epigenetic processes, especially in relation to the control of transposable element (TE) activity and the generation of heritable phenotypic variation.

Background

Chromatin is the natural substrate on which all DNA transactions take place. As such, it is a highly dynamic structure with the ability to modulate genomic functions and the creation of phenotypic variation. Therefore, how distinct chromatin states are established, maintained -sometimes across multiple generations-, and erased remains a fundamental question in biology.

Research areas

Our group studies the contribution of chromatin-based epigenetic processes to heritable phenotypic variation. Given the involvement of TEs in the creation of so-called epimutable alleles in plants and mammals, most our work is focused on the study of TE sequences, their distribution within genomes, the factors that control their activity, and their impact on adjacent genes. We use Arabidopsis and more recently tomato also as primary models. Our main findings concern the dynamics of DNA methylation over TE sequences during the reproductive cycle, the inheritance patterns and phenotypic impact of TE-mediated DNA methylation variants, and the control, extent, as well as (epi)mutational impact of TE mobilization.

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.

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.

Quadrana, L., and Colot, V. (2016). Plant Transgenerational Epigenetics. Annu Rev Genet 50, 467-491.

Quadrana, L., Bortolini Silveira, A., Mayhew, G.F., LeBlanc, C., Martienssen, R.A., Jeddeloh, J.A., and Colot, V. (2016). The Arabidopsis thaliana mobilome and its impact at the species level. Elife 5.

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

Cortijo, S., R. Wardenaar, M. Colome-Tatche, A. Gilly, M. Etcheverry, K. Labadie, E. Caillieux, F. Hospital, J. M. Aury, P. Wincker, F. Roudier, R. C. Jansen, V. Colot & F. Johannes (2014) Mapping the epigenetic basis of complex traits. Science, 343, 1145-8.