MicroRNAs (miRNAs) are critical in many facets of plant biology, where they mediate gene silencing processes by acting as sequence-specific guides of silencing complexes. Core to understanding how they perform their function is determining the factors that control miRNA target recognition, however this remains elusive. It is now clear that although high complementarity of a miRNA-target pair is a prerequisite for strong target recognition, factors beyond complementarity exist that strongly modulate this interaction.
One likely factor is the RNA secondary structure of the mRNA targets, where this secondary structure may facilitate or prevent accessibility of the miRNA to its binding site. Firstly, we aim to identify conserved RNA secondary structures in plant miRNA target genes, determine their predicted impact on target accessibility and then functionally test their importance of these structures through mutagenesis. Furthermore, we will determine whether these secondary structures can alter in planta, acting as “riboswitches”, facilitating or preventing miRNA target recognition depending on their conformation. We envision this project will elucidate the higher ordered molecular architecture of miRNA binding sites, gaining insights into the complexity of miRNA-mediated regulation in plants, and how miRNA may be interacting with other factors the fulfill their function.