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
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
Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution.
Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution. Sci Adv. 2023 02 22; 9(8):eabq4632.
PMID: 36812328
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
Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation.
Hernandez-Alias X, Katanski CD, Zhang W, Assari M, Watkins CP, Schaefer MH, Serrano L, Pan T. Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation. Nucleic Acids Res. 2022 Dec 20.
PMID: 36537222
Validation of the Chinese Translation of the "Meaning of Life" in Patients with Hearing Loss or Tinnitus.
Validation of the Chinese Translation of the "Meaning of Life" in Patients with Hearing Loss or Tinnitus. J Am Acad Audiol. 2022 Dec 10.
PMID: 36495866
Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications.
Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res. 2022 12 02; 9(1):68.
PMID: 36461064
Clinical impact of Fn-induced high expression of KIR2DL1 in CD8 T lymphocytes in oesophageal squamous cell carcinoma.
Clinical impact of Fn-induced high expression of KIR2DL1 in CD8 T lymphocytes in oesophageal squamous cell carcinoma. Ann Med. 2022 Dec; 54(1):51-62.
PMID: 34935568
DKK1 as a robust predictor for adjuvant platinum chemotherapy benefit in resectable pStage II-III gastric cancer.
DKK1 as a robust predictor for adjuvant platinum chemotherapy benefit in resectable pStage II-III gastric cancer. Transl Oncol. 2022 Nov 01; 27:101577.
PMID: 36332599
tRNA abundance, modification and fragmentation in nasopharyngeal swabs as biomarkers for COVID-19 severity.
tRNA abundance, modification and fragmentation in nasopharyngeal swabs as biomarkers for COVID-19 severity. Front Cell Dev Biol. 2022; 10:999351.
PMID: 36393870
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