Our research focuses on (i) functional genomics and biology of tRNA including microbiomes and (ii) epitranscriptomics including microbiome-host interactions.
tRNA biology: Translational regulation relies on the dynamic properties of tRNA that constantly change to facilitate response and adaptation to new environments and to control gene expression. We developed high throughput sequencing technologies that measure tRNA abundance, charging and modifications in one single sequencing library. We are investigating the roles of tRNA in translational control and extra-translational functions in mammalian cells.
Microbiome: We also developed tRNA-seq 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. We also show that tRNA modification dynamics in the microbiome correlates with tuning the expression of specific microbial proteins, indicating that tRNA-seq can provide new insights in microbiome biology. We are further developing this approach to explore the potentials of tRNA-seq to study microbiomes from humans and from the oceans.
Epitranscriptomics: Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites in the transcriptome. 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, resulting in 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.
Microbiome-host interactions through epitranscriptomics: We are working on elucidating the function of mammalian host mRNA and tRNA modifications in response to the gut microbiome. We found that microbiome reprograms the host m6A modifications transcriptome-wide in a tissue-dependent manner, suggesting that this dynamic epitranscriptomic mark is used in yet unknown ways in microbiome response. We also found that a microbiome dependent, host tRNA modification alters the cellular small RNA pool, suggesting yet another pathway of microbiome response through RNA modifications.
University of Colorado at Boulder
Boulder, CO
postdoctoral - Biochemistry
1993
Yale University
New Haven, CT
Ph.D. - Biophysics/Biochemistry
1990
University des Saarlands
Germany
BS/MS - Chemistry
1986
Prokaryotic RNA N1-Methyladenosine Erasers Maintain tRNA m1A Modification Levels in Streptomyces venezuelae.
Prokaryotic RNA N1-Methyladenosine Erasers Maintain tRNA m1A Modification Levels in Streptomyces venezuelae. ACS Chem Biol. 2024 Jul 19; 19(7):1616-1625.
PMID: 38912606
Internal mRNA 2'-O-methyl mapping by nanopore sequencing and consequence on mRNA stability and role in cancer.
Internal mRNA 2'-O-methyl mapping by nanopore sequencing and consequence on mRNA stability and role in cancer. Mol Cell. 2024 Jun 20; 84(12):2215-2217.
PMID: 38906112
Modifications in the T arm of tRNA globally determine tRNA maturation, function, and cellular fitness.
Modifications in the T arm of tRNA globally determine tRNA maturation, function, and cellular fitness. Proc Natl Acad Sci U S A. 2024 Jun 25; 121(26):e2401154121.
PMID: 38889150
Designing 3D SnS@Cu-Ni Nanoporous Column Array Electrode for High-Capacity and High-Rate Lithium-Ion Batteries.
Designing 3D SnS@Cu-Ni Nanoporous Column Array Electrode for High-Capacity and High-Rate Lithium-Ion Batteries. Small Methods. 2024 Jun 08; e2400411.
PMID: 38850177
Quantification of tRNA m1A modification by templated-ligation qPCR.
Quantification of tRNA m1A modification by templated-ligation qPCR. RNA. 2024 May 16; 30(6):739-747.
PMID: 38471794
Hearing loss prevalence and burden of disease in China: Findings from provincial-level analysis.
Hearing loss prevalence and burden of disease in China: Findings from provincial-level analysis. Chin Med J (Engl). 2024 May 09.
PMID: 38725346
Antibiotic-Induced Gut Microbiota Dysbiosis Modulates Host Transcriptome and m6A Epitranscriptome via Bile Acid Metabolism.
Antibiotic-Induced Gut Microbiota Dysbiosis Modulates Host Transcriptome and m6A Epitranscriptome via Bile Acid Metabolism. Adv Sci (Weinh). 2024 May 07; e2307981.
PMID: 38713722
Vis-NIR spectroscopic discriminant analysis of aflatoxin B1 excessive standard in peanut meal as feedstuff materials.
Vis-NIR spectroscopic discriminant analysis of aflatoxin B1 excessive standard in peanut meal as feedstuff materials. Spectrochim Acta A Mol Biomol Spectrosc. 2024 Sep 05; 317:124394.
PMID: 38723467
mRNA epitranscriptomics.
mRNA epitranscriptomics. RNA. 2024 Apr 16; 30(5):465-467.
PMID: 38531649
Impaired sensitivity to thyroid hormones is associated with albuminuria in the euthyroid population: results from NHANES.
Impaired sensitivity to thyroid hormones is associated with albuminuria in the euthyroid population: results from NHANES. Hormones (Athens). 2024 Jun; 23(2):245-255.
PMID: 38340288
American Association for the Advancement of Science (AAAS) Fellow
2015
NIH Director’s Pioneer award
2011 - 2016
NIH EUREKA award
2009 - 2013
American Cancer Society, Junior Faculty Research Award
1995 - 1997
Cancer Research Foundation, Raymond F. Zelko Young Investigator
1994
Damon Runyon-Walter Winchell Cancer Research Fund
1991 - 1993