- Professor, Department of Biochemistry and Molecular Biology, Committee on Microbiology
Ph.D., Yale University, 1990
Diplom, University des Saarlandes, 1986
The University of Chicago
929 East 57th Street
Chicago, Illinois 60637
Lab: GCIS W125
Phone: (773) 702-4179
Lab: (773) 702-4680
Our research focuses on functional genomics and biology of tRNA including microbiomes and epitranscriptomics (RNA modifications).
tRNA biology: Translational regulation is linked to the dynamic properties of tRNA that constantly change to facilitate stress response and adaptation to new environments and to control gene expression. We developed high throughput sequencing technologies that measure tRNA abundance, charging and modifications. We are investigating the roles of tRNA in translational control and extra-translational functions in mammalian cells.
Microbiome: We are also applying our tRNA-seq technology as another approach for microbiome characterization. Standard microbiome characterizations include 16S-seq or shotgun metagenomics. Although powerful, these DNA-based methods do not directly report the microbiome activity such as dynamic gene expression which requires the studies of RNA in the microbiome. Our microbiome tRNA-seq results show extensive variations of tRNA abundance and modification patterns in microbiomes from different sources, indicating that tRNA-seq can provide new insights in microbiome dynamics. We are further developing this approach to explore the potentials of tRNA-seq to study microbiome activities.
Epitranscriptomics: Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites in all cells. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, addition of ring structures and carbohydrate moieties, and so on. mRNA modifications are involved in cell differentiation, proliferation, and many other cellular functions and human diseases. Some mRNA modifications can also be removed by cellular enzymes, leading to the dynamic regulation of their functions. We are investigating the function and mechanisms of mRNA modifications such as N6-methyladenosine (m6A) in the regulation of gene expression. For example, we discovered that m6A modification can alter the local mRNA structure to regulate binding of mRNA binding proteins transcriptome-wide (m6A switch), resulting in changes in mRNA abundance and alternative splicing. We are also developing sequencing methods that can identify mRNA modifications at single base resolution, quantify their fractions, and with the goal of achieving single-cell sequencing of the epitranscriptome.