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
Design, construction, and functional characterization of a tRNA neochromosome in yeast.
Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell. 2023 Nov 05.
PMID: 37944512
BPTF Drives Gastric Cancer Resistance to EGFR Inhibitor by Epigenetically Regulating the C-MYC/PLCG1/Perk Axis.
BPTF Drives Gastric Cancer Resistance to EGFR Inhibitor by Epigenetically Regulating the C-MYC/PLCG1/Perk Axis. Adv Sci (Weinh). 2023 Oct 20; e2303091.
PMID: 37863665
Major Indole Alkaloids in Evodia Rutaecarpa: The Latest Insights and Review of Their Impact on Gastrointestinal Diseases.
Major Indole Alkaloids in Evodia Rutaecarpa: The Latest Insights and Review of Their Impact on Gastrointestinal Diseases. Biomed Pharmacother. 2023 Nov; 167:115495.
PMID: 37741256
Spectral separation degree method for Vis-NIR spectroscopic discriminant analysis of milk powder adulteration.
Spectral separation degree method for Vis-NIR spectroscopic discriminant analysis of milk powder adulteration. Spectrochim Acta A Mol Biomol Spectrosc. 2023 Nov 15; 301:122975.
PMID: 37301030
Probiotics improve symptoms of patients with COVID-19 through gut-lung axis: a systematic review and meta-analysis.
Probiotics improve symptoms of patients with COVID-19 through gut-lung axis: a systematic review and meta-analysis. Front Nutr. 2023; 10:1179432.
PMID: 37284648
Microbial community structure dynamics of invasive bullfrog with meningitis-like infectious disease.
Microbial community structure dynamics of invasive bullfrog with meningitis-like infectious disease. Front Microbiol. 2023; 14:1126195.
PMID: 36992930
Characteristics of the Northern Hemisphere cold regions changes from 1901 to 2019.
Characteristics of the Northern Hemisphere cold regions changes from 1901 to 2019. Sci Rep. 2023 Mar 08; 13(1):3879.
PMID: 36890155
[Surgical issues and managements in cochlear reimplantation in 32 children].
[Surgical issues and managements in cochlear reimplantation in 32 children]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi. 2023 Mar; 37(3):218-221.
PMID: 36843522
[Surgical issues and managements in cochlear reimplantation in 32 children].
[Surgical issues and managements in cochlear reimplantation in 32 children]. Lin Chuang Er Bi Yan Hou Tou Jing Wai Ke Za Zhi. 2023 Mar; 37(3):218-221.
PMID: 36843522
Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation.
Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation. Nucleic Acids Res. 2023 02 22; 51(3):e17.
PMID: 36537222
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