An exploration of plant epigenetics
Angiosperm genomes are characterized by being rich in both tandem and dispersed repeats, especially retrotransposable elements, which contribute to the dynamic nature of their genomes over evolutionary time. Despite this dynamism, repeat mobility and amplification are considered to be constrained via heterochromatinization. The mechanism driving this process involves cytosine methylation and the activity of RNA-dependent RNA polymerase (RdRP) and a specific class of the endonuclease family Dicer called Dicer-Like 3 (DCL3), which together generate a diverse array of 24 nucleotide (nt) RNA fragments. These small interfering RNAs (siRNAs) are targeted back to the DNA where they facilitate siRNA-directed DNA methylation (RdDM) and histone modifications. However, epigenetic mechanisms involved in constraining repeat amplification and mobility may not be the same across all land plants, in particular they may be different in gymnosperms and this might contribute to their more stable genomes over time (Leitch AR, Leitch IJ. 2012. Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytologist 194(3): 629-646). We have three central questions, if you are interested in research into these areas, then please contact me.
 How does polyploidy perturb epigenetics processes?  Is gymnosperm epigenetics different, and if so in what way and what are the consequences?  How does RdDM impact genome evolution, in particular the evolution of giant genomes?