The interface between RNA-binding proteins and their effectors
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. We are broadly interested in the modes of communication between RBPs and their effectors, particularly in the converging RBP–effector interactions and their roles in reducing the complexity of RNA networks. Functional analyses of RBP–effector interactions along with the RNA-binding information allow our lab to better understand RBP activities, their regulation of biological processes, and their contribution to human diseases, including cancer and neurological disorders.
An example of converging RBP–effectors interactions. Several RBPs (blue ovals) can bind the CCR4-NOT effector complex (gray shapes). Purple dashed and W indicate parts of the intrinsically disordered regions and tryptophan residues in contact with the effector. RBP-bound RNA is omitted for clarity.
Functional repertoires of ancient RNA-based enzymes in modern-day cells
In the course of evolution, an impressive array of multiprotein RNA processing complexes has replaced all but a few RNA-based enzymes (i.e. ribozymes) that persist in extant cells. What attributes might be rendering these ancient catalysts superior to proteins in cells of higher organisms is an enduring puzzle. Taking deep conservation as an indicator of an important function, we are addressing these questions by employing bottom-up and top-down approaches to decipher the compositional variability, RNA targeting specificity, and regulatory scope enabled by these seemingly gratuitously complex enzymes in eukaryotes. We are currently exploring unannotated roles of two such relics, ribonuclease (RNase) P and RNase MRP, in mammalian cells.
Schematic of mammalian RNase P (based on Wu et al, 2018)
RNase P
Cleavage of tRNA and tRNA-like precursors by RNase P
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 and what function it may serve remain largely unsolved problems. Our current studies are aimed at understanding how 'writers' of RNA modifications can act in a tissue-specific manner, and how they may play particularly critical roles in development, functioning, and disease of the nervous system.
m  A
m  A
m  C
hm  C
Structures of some of the base-modified nucleosides
Method development
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 an idea that could one day help other laboratories with their research.