Tao Pan, PhD

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

Circadian regulation of apolipoprotein gene expression affects testosterone production in mouse testis.
Yang L, Ma T, Zhao L, Jiang H, Zhang J, Liu D, Zhang L, Wang X, Pan T, Zhang H, Wang A, Chao HW, Jin Y, Chen H. Circadian regulation of apolipoprotein gene expression affects testosterone production in mouse testis. Theriogenology. 2021 Oct 15; 174:9-19.
PMID: 34416563

Quantitative probing of glycosylated queuosine modifications in tRNA.
Zhang W, Pan T. Quantitative probing of glycosylated queuosine modifications in tRNA. Methods Enzymol. 2021; 658:73-82.
PMID: 34517960

ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing.
Zhang LS, Xiong QP, Peña Perez S, Liu C, Wei J, Le C, Zhang L, Harada BT, Dai Q, Feng X, Hao Z, Wang Y, Dong X, Hu L, Wang ED, Pan T, Klungland A, Liu RJ, He C. ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing. Nat Cell Biol. 2021 07; 23(7):684-691.
PMID: 34253897

Discovery of 2,4-pyrimidinediamine derivatives as potent dual inhibitors of ALK and HDAC.
Pan T, Dan Y, Guo D, Jiang J, Ran D, Zhang L, Tian B, Yuan J, Yu Y, Gan Z. Discovery of 2,4-pyrimidinediamine derivatives as potent dual inhibitors of ALK and HDAC. Eur J Med Chem. 2021 Nov 15; 224:113672.
PMID: 34237620

Pseudouridine RNA modification detection and quantification by RT-PCR.
Zhang W, Pan T. Pseudouridine RNA modification detection and quantification by RT-PCR. Methods. 2021 May 18.
PMID: 34020036

Tissue-specific reprogramming of host tRNA transcriptome by the microbiome.
Huang J, Chen W, Zhou F, Pang Z, Wang L, Pan T, Wang X. Tissue-specific reprogramming of host tRNA transcriptome by the microbiome. Genome Res. 2021 Jun; 31(6):947-957.
PMID: 33858843

CMT2N-causing aminoacylation domain mutants enable Nrp1 interaction with AlaRS.
Sun L, Wei N, Kuhle B, Blocquel D, Novick S, Matuszek Z, Zhou H, He W, Zhang J, Weber T, Horvath R, Latour P, Pan T, Schimmel P, Griffin PR, Yang XL. CMT2N-causing aminoacylation domain mutants enable Nrp1 interaction with AlaRS. Proc Natl Acad Sci U S A. 2021 03 30; 118(13).
PMID: 33753480

A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities.
Wang Y, Katanski CD, Watkins C, Pan JN, Dai Q, Jiang Z, Pan T. A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities. Nucleic Acids Res. 2021 03 18; 49(5):e30.
PMID: 33337498

Management of magnetic foreign body ingestion in children.
Zhang S, Zhang L, Chen Q, Zhang Y, Cai D, Luo W, Chen K, Pan T, Gao Z. Management of magnetic foreign body ingestion in children. Medicine (Baltimore). 2021 Jan 15; 100(2):e24055.
PMID: 33466161

[Clinical analysis of 21 cases of cholesteatoma recidivism after canal-wall-up mastoidectomy with tympanoplasty].
Huang Y, Pan T, Lu Z, Wang Y, Ma F. [Clinical analysis of 21 cases of cholesteatoma recidivism after canal-wall-up mastoidectomy with tympanoplasty]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi. 2021 01 05; 35(1):66-69.
PMID: 33540978

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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