A handful of large molecular assemblies have evolved to serve as core engines at specific stages of mRNA processing. There also exists a much larger number of diverse RBPs that participates in mRNA processing by instructing these core assemblies when, where, and, sometimes, how to act. In doing so, RBPs control much of the gene expression output and thus significantly contribute to phenotypes of individual cells. This is illustrated by our studies of the neuronal RBP Unkempt, which confers the early bipolar morphology to immature neurons, or by frequent mutations of RBPs in human disease, including neurological disorders and cancer. We are broadly interested in the mechanisms by which RBPs regulate the core RNA-processing assemblies, as well as in their impact on cell homeostasis and their misregulation in human disease.
Cell polarization induced by Unkempt (Genes & Dev, 2015)
Mechanistic model of translational repression by Unkempt
Processing of non-coding RNAs by RNases P and MRP
Ribonucleases (RNases) P and MRP are deeply conserved and essential ribozymes that play key roles in biogenesis of tRNAs and rRNAs from their precursor transcripts, respectively. During the evolution, the nuclear RNase P gradually transformed from a small, RNA-dominated ribozyme into a half-megadalton protein-rich ribonucleoprotein complex, while maintaining a catalytic RNA core. The reasons for the increased complexity of RNase P, preservation of the catalytic RNA, and the emergence of RNase MRP in higher organisms remain poorly understood. We are addressing these questions by employing bottom-up and top-down approaches to decipher the compositional variability, targeting specificity, and regulatory scope enabled by the seemingly gratuitous complexity of these ribozymes in eukaryotes.
Cleavage of tRNA and tRNA-like precursors by RNase P
Schematic of mammalian RNase P (based on Wu et al, 2018)
Tissue-specific regulation of the epitranscriptome
More that 100 distinct biochemical modifications of RNA have been discovered within a cell. Several of these RNA modifications appear to affect RNA structure, some have been shown to regulate RNA processing, and a handful are known to have important roles in maintenance of cell homeostasis. In analogy to the epigenome, the ensemble of functionally relevant RNA modifications has become known as the 'epitranscriptome'. However, how deposition of RNA modifications is regulated, how the modifications are interpreted, and what their function really is remain largely unsolved problems. Our current studies are aimed at understanding how 'writers' of RNA modifications are able to deposit different modification patterns in different tissues, with a particular focus on the brain.
Structures of some of the base-modified nucleosides
We are constantly on the lookout for ways to improve and broaden our ability to study RNA. We thus devise novel methods that help our own research of RNA, or methods that are not directly linked to our main projects but are sparked by a great idea that could one day help other RNA laboratories with their research. Our current efforts in this area include development of a novel method for purification of circular RNAs, a novel method to study in vivo interactions of RBPs with nascent RNA, and a novel global approach to study localized translation in cells,