The role of a mysterious epigenetic RNA modification in adapting the eukaryotic epitranscriptome to environmental change

How organisms respond and adapt to ever-changing environments remains a most critically important question in ecology and evolution. Climate change and human activity are causing unprecedented pressures onto organisms to cope with stresses. Individual organisms must rapidly adjust their physiology by modulating gene expression and protein repertoires, which provide raw material for natural selection to confer long-term adaptation on a population and species level. Epigenetics is a crucial mechanism through which organisms may respond rapidly to environmental change. DNA methylation is one such process that affects gene expression and provides molecular diversity for natural selection to act on. However, epigenetic modification of mRNA instead of DNA may be an even more important process that could generate molecular diversity more rapidly and flexibly than DNA methylation. Therefore, identifying the causes and consequences of such "epitranscriptomic" RNA modifications is critically important for understanding and predicting molecular evolution. A particularly intriguing RNA modification is spliced leader trans-splicing (SLTS). This process adds a short nucleotide motif to the 5'-end of some eukaryotic mRNAs. This motif is not translated but its presence may have effects on mRNA processing that may ultimately affect the physiological and ecological phenotype of the organism. SLTS is poorly understood and only patchily characterised in a limited number of organisms. Therefore, we know very little about the evolutionary history of SLTS and its role in allowing organisms to respond to environmental factors.

In this project, the student will first capitalise on computational pipelines that our lab developed and publicly available sequencing data to address exciting questions such as: How common is SLTS throughout the eukaryotic tree of life? How does SLTS frequency vary among lineages? Did SLTS evolve in parallel in phylogenetically independent lineages? The student will then carry out stress experiments on invertebrates established in our labs (for example, marine crustaceans, algae or nematodes), collect samples from field populations, and use state-of-the-art RNA and DNA sequencing technologies (Oxford NanoPore MinION) to identify: Effects of experimental treatments on genome-wide SLTS patterns. Spatial structure of SLTS patterns in field samples. Relationships between patterns of SLTS and genetic/epigenetic diversity. Modern biology is increasingly interdisciplinary, relying on computational data analysis and traditional fieldwork and lab-based skills. This project will provide training in all these aspects, a combination that is highly sought after in both academic and industrial career tracks.