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Our main research interests

DNA stores heritable information in the form of a four letter code; A, C, G and T. Textbook genetics tells us that the code can be mutated (e.g. letter A turns into letter G), and that such mutations alter the functions of genes. In plants, it is becoming increasingly clear that heritable alterations in gene function can also be caused by meiotically stable epimutations, which arise independently of DNA changes. A well-known example of an epimutation is the accidental gain or loss of DNA methylation, the chemical modification of a cytosine (the letter C in the DNA code) into 5-methylcytosine.

We have previously shown that experimentally-induced as well as spontaneously occurring epimutations can be remarkably stable across generations, and can in some cases even contribute to the heritability of important plant traits. Because of these observations, epigenetic modifications - such as DNA methylation - have emerged as potentially important factors in plant evolution, and as possible molecular targets for the improvement of commercial crops.

Our group aims to explore the agricultural and evolutionary implications of heritable epimutations in plants. One major aspect of this work is the development of computational methods for the analysis of population-level epigenomic sequencing data. The goal is to find efficient ways to detect ‘epimutatable’ regions in plant genomes, and to characterize these regions in terms of epigenomic patterns of variation both within and across plant species. A second aspect of our work is to infer the sources, stability and phenotypic impact of heritable epimutations either by direct observation of multi-generational data, or indirectly by using inference methods from evolutionary genetics.

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Key reviews and perspectives

Vidali A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F*. (2016)
Genome Biology 17:264.

Taudt A, Colomé-Tatché M, Johannes F*. (2016)

van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ, Colomé-Tatché M, Johannes F*. (2015).
Rate, spectrum and evolutionary dynamics of spontaneous epimutations.
Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1424254112.

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 RC, Colot V*, Johannes F* (2014).

Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F* (2012).
Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation.
Proc. Natl. Acad. Sci. USA doi:10.1073/pnas.1212955109.

Johannes F* and Colomé-Tatché M (2011).
Quantitative epigenetics through epigenomic perturbation of isogenic lines.
Genetics 188:1015–1017.

Johannes F, Porcher E, Teixeira F, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Bouchez D, Dillmann C, Guerche P, Hospital F, Colot V (2009).
Assessing the impact of transgenerational epigenetic variation on complex traits.
PLoS Genetics 5: e1000530.

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Key computational methods

Taudt A, Nguyen MA, Heinig M, Johannes F, Colomé-Tatché M (preprint).
chromstaR: Tracking combinatorial chromatin state dynamics in space and time.
BioRxiv

Heinig M, Colomé-Tatché M, Taudt A, Rintisch C, Schafer S, Pravenec M, Hubner N, Vingron M, Johannes F (2015).
histoneHMM: Differential analysis of histone modifications with broad genomic footprints.
BMC Bioinformatics 16:60.

Cortijo S, Wardenaar R, M. Colomé-Tatché M, Johannes F*, Colot V* (2014).
Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip.
Methods in Molecular Biology 1112:125-49.

Seifert M, Cortijo S, Colomé-Tatché M, Johannes F, Roudier R, Colot V (2012).
MeDIP-HMM: Genome-wide identification of distinct DNA methylation states from high-density tiling arrays.
Bioinformatics doi:10.1093/bioinformatics/bts562.