Epigenetic control of transgenerational genome plasticity

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 questions why mammals have either lost or never acquired such an epigenetic memory during evolution (Heard and Martienssen, 2014). Considering that epigenetic marks are also important regulators of gene activity, epigenetics plays a major role in plant adaptation to new environmental conditions or stresses, and can potentially be used as tool to improve crop production and food security. However, despite the characterization of numerous epigenetic factors, the primary determinants of an epigenetic switch (= event of stable change in the epigenetic information) are still elusive. Previously, we reported that some genetic proprieties such as DNA composition and sequence repetitiveness correlate with the stability of epigenetic switches (Catoni et al., 2017). The underlying mechanisms, however, are still unknown. The advertised PhD project carried out in my lab will thus focus on determining the genetic and epigenetic mechanisms controlling epigenetic switches. As part of the project, existing and newly generated data for the model plant Arabidopsis thaliana will be used to characterize the players involved in controlling epigenetic switches, and the final aim of the project is to transfer the new findings to crop plants to ultimately investigate their epigenetic memory patterns.
Depending by student background and individual interests, the project will focus in one of these areas:
1- Explore the links between genome stability and genome evolution, investigating how epigenetic marks affect genome plasticity, which directly control the speed of genome evolution. The candidate will learn how to efficiently handle big data sets using command line tools developed for the Linux environment and the R programming language.
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. The ideal candidate will develop a broad knowledge in all aspects of genomics studies, from library preparation to data analysis, learning how to build models based on biological experiments. This role is ideal for a candidate who wishes to bridge wet lab experiments and bioinformatic.
3- Study the consequences of Transposable element (TE) mobilization. TEs 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 (Lisch, 2013). The aim of this project is to discover, characterize and investigate the role of active TEs in plants, going beyond the concept of a single reference genome. The ideal candidate should have affinity with molecular biology and will become familiar with cutting edge technologies such as third generation sequencing (PACBio or Nanopore) and CRISP-Cas9 editing system in plants.