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.