Research in our group focuses on understanding the structures and functions of RNA molecules involved in fundamental biological processes and exploring the opportunities for developing RNA-targeted therapeutics to treat both genetic and infectious diseases. Our laboratory interconnects biochemistry, biophysics, and biology, providing the members of our laboratory an excellent opportunity to learn a wide array of biochemical and biophysical techniques while pursuing cutting-edge research in the field of RNA structural biology. The followings are the current research directions in our laboratory.

RNA structures associated with cap-independent viral translation

In contrast to the 5ꞌ-cap-based canonical translation in most eukaryotes, many viral genomes and a subset of cellular mRNAs are translated via cap-independent mechanisms that involve structured RNA elements such as internal ribosome entry sites (IRESs) and 3ꞌ cap-independent translation elements (3ꞌ-CITEs). However, our understanding of how these RNA structures are organized and how they recognize translation initiation factors or the ribosome remains largely elusive. Our laboratory is focused on determining the 3-dimensional structures of RNA elements associated with the viral cap-independent translation and understanding how these structures hijack the canonical, cap-dependent translation machinery from the host cell to mediate and regulate the non-canonical, cap-independent viral translation.

RNA structures associated with human repeat expansion disorders

Besides the mechanisms that involve mutant proteins expressed from the mRNAs with expanded nucleotide repeats, pathogenic pathways in human disorders such as Huntington’s disease, myotonic dystrophy fragile-X syndrome, and amyotrophic lateral sclerosis also involve RNA-related toxicity induced by the RNA structures of the corresponding mRNAs. However, our understanding of the structures formed by these mRNAs and their specific roles in pathogenesis remains elusive. Our laboratory is focused on developing the strategies to study the structural elements in both protein-coding and non-coding regions of these mRNAs and their contributions to disease pathogenesis. We use synthetic antibodies that specifically bind the RNA structures formed by the expanded mRNAs to investigate their structures, cellular locations, and life cycles.

RNA crystallization and structure determination strategies

Among several biophysical methods, X-ray crystallography has been the most developed and most widely used method for determining the high-resolution structures of biomacromolecules, including RNA molecules. However, RNA structures represent only a tiny fraction of all deposited high-resolution structures in the protein data bank (PDB), underscoring the difficulties associated with RNA crystallography. We have been developing RNA binding proteins, specifically synthetic antibodies (Fab fragments), as chaperones for RNA crystallization and structure determination. In addition to selecting RNA target-specific Fabs using phage display selection, we are interested in developing a suite of portable protein-RNA modules using in vitro selection that can be easily engineered into an RNA of interest as affinity tags, which would have applications in RNA crystallography as well as in RNA imaging and immunoprecipitation.

Approaches for developing RNA crystallization chaperone modules

Outcomes of our research will provide insights into the mechanisms of fundamental biological processes and unlock ample opportunities for developing targeted therapeutics to treat both genetic and infectious diseases. Moreover, a structural understanding of the landscape of RNA structures combined with mechanistic insights into how particular structural features enable the biological function will be tremendously valuable for developing algorithms to predict new RNA structures using bioinformatics and computational tools.