Epigenetics contribution to plant genome evolution

Epigenetics is the major discipline studying heritable changes of gene activity that do not involve changes in the underlying DNA sequence. Plants are an excellent model for epigenetic studies because in these organisms epigenetic modifications can be stably transmitted across generations, constituting the molecular bases of an “epigenetic memory”. In contrast to mammals where an efficient reset of the epigenetic information occurs during fertilization and embryo development, plants are a unique model system to investigate how epigenetic information can be transmitted through several generations. The nature of this difference is yet unclear, however, the ability to memorize such epigenetic information is well characterised in plants and raises the question of why mammals have either lost or never acquired such an epigenetic memory during evolution (Heard and Martienssen, 2014). In addition, epigenetic marks are also important regulators of Transposable element (TE), which are parasitic DNA elements able to move from their original position in the host genome to a new chromosomal location and multiplying their copies, similarly to viruses. Plant genomes are rich in TEs, which account for the most variable portion of the genome and their mobilization has a strong implication in their genome plasticity and evolution (Lisch, 2013).

The advertised PhD project carried out in my lab will thus focus on determining the genetic and epigenetic mechanisms controlling epigenetic switches, and on the understanding of their effects on plant plasticity and evolution. As part of the project, existing and newly generated genomics and data will be used to characterize the players involved in controlling epigenetics, and the final aim of the project is to transfer the new findings into crop plants to exploit their use in agriculture.

The proposed project can focus in one of these areas:
1- Explore the links between genome stability and evolution, investigating how epigenetics affect genome plasticity, which directly controls the speed of genome evolution.
2- Investigate the bases of epigenetic variation, studying how epialleles (= genes with identical DNA sequence but different epigenetic marks) are generated, and which factors control their stability.
3- Study the consequences of Transposable element (TE) mobilization.

The aim of this approach is to discover, characterize and investigate the role of active TEs in plants, going beyond the concept of a single reference genome.