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Appointments:
Associate Professor
Department of Biochemistry and
Molecular Biology
Committee on Microbiology
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Education:
Ph.D., Yale University, 1990
Diplom, University des Saarlandes, 1986
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Contact:
Phone: (773) 702-4179
Lab:
(773) 702-4680
Fax:
(773)
792-0439
E-Mail:
taopan@uchicago.edu
Address:
The University of Chicago
GCIS W134
929 East 57th Street
Chicago, Illinois 60637
Lab: GCIS W125
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Related Research Interests:
Gene
Regulation/Expression
Systems Biology
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Tao Pan, Ph.D.
Functional Genomics of tRNA, RNA Epigenetics, RNA
Folding
Research Summary
tRNA is essential for protein synthesis and life. Biological genomes
contain hundreds of tRNA genes. Translational regulation is related to
the dynamic properties of tRNA that constantly change to facilitate
stress response and cellular adaptation to new environments and to
control gene expression in differentiated organisms. We developed
microarray methods that measure tRNA abundance and its fraction of
aminoacylation at the genomic scale. We are exploring roles of tRNA in
translational control in bacteria and in mammalian cells including
cancer.
Over 100 types of post-transcriptional modifications have been
identified in thousands of RNA sites from bacteria to man. They include
methylation of bases and the ribose backbone, rotation and reduction of
uridine, base deamination, elaborate addition of ring structures and
carbohydrate moieties, and so on. RNA modification enzymes represent
1-2% of all genes in bacteria. Hundreds of guide RNAs and dozens of
proteins are used to direct modifications in eukaryotic rRNAs. RNA
modifications are involved in stress response, environmental
adaptation, antibiotic resistance and human neurology. We developed a
microarray method that detects and quantifies changes in modification
fraction at the genomic scale. We are applying this high throughput
method to study the function of RNA modifications at the genomic level
during cell growth, adaptation and development.
Non-coding RNAs perform biological function without being translated
into proteins. Recent estimates suggest that in human, the number of
non-coding RNAs may be comparable to the number of coding RNAs. We are
working on high throughput methods for folding studies of non-coding
RNAs, and for structural determination using cryo-Electron Microscopy.
Folding during transcription is also studied to understand non-coding
RNA folding in the cell.
Selected Papers
Fang X-W, Thiyagarajan P, Sosnick TR and Pan T. (2002).
The
rate-limiting step in the folding of a large ribozyme without kinetic
traps. Proc. Natl. Acad. Sci. USA 99, 8518-8523.
Krasilnikov A, Yang X-J, Pan T and Mondragon A. (2003).
Crystal
structure of the specificity domain of ribonuclease P. Nature 421,
760-764.
Fang X-W, Srividya N, Sosnick TR and Pan T. (2003).
Stepwise
conversion of a mesophilic to a thermophilic ribozyme. J. Mol. Biol.
330, 177-183.
Xie Z, Srividya N, Sosnick TR, Pan T and Scherer N.
(2004).
Single molecule studies highlight conformational heterogeneity in the
early folding steps of a large ribozyme. Proc. Natl. Acad. Sci. USA
101, 534-539.
Barrera A and Pan T. (2004). Interaction of the Bacillus
subtilis RNase P with the 30S ribosomal subunit. RNA, in press.
Dittmar KA, Mobley EM, Radek A and Pan T. (2004).
Exploring the
regulation of tRNA distribution on the genomic scale. J. Mol. Biol.
337, 31-47.
Torres A,Swinger K, Krasilnikov A, Pan T and Mondragon
A. (2005). Crystal structure of the RNA component of bacterial
Ribonuclease P, Nature 437, 584-587.
Baird N, Westhof E, Qin H, Pan T and Sosnick TR. (2005).
The structure of a folding
intermediate reveals interplay between core and peripheral elements in
RNA folding, J. Mol. Biol. 362, 712-722.
Le T, Harlepp S, Guet CC, Dittmar K., Emonet T, Pan T
and Cluzel P. (2005).
Real-time profiling of a specific RNA within a single bacterium. Proc.
Natl. Acad. Sci. USA 102, 9160-9164.
Dittmar KA, Sorensen M, Elf J, Ehrenberg M and Pan T.
(2005). Selective charging of
tRNA isoacceptors induced by amino acid starvation. EMBO Reports 6,
151-157.
Dittmar KA, Goodenbour JM and Pan T.
(2006). Tissue specific
differences in human transfer RNA expression. PLoS Genetics, in press.
Saikia M, Dai Q, Decatur WA, Fournier MJ, Piccirilli JA
and PanT. (2006). A systematic, ligation based approach to
study RNA modifications, RNA 12, 2025-2033.
Goodenbour JM and T. Pan. (2006). Diversity of tRNA
genes in eukaryotes. Nucl. Acids Res. 34, 6137-46.
Dittmar KA, Goodenbour JM & Tao Pan. 2006). Tissue
specific differences in human transfer RNA expression. PLoS Genetics 2,
2107-2115 (e221).
Saikia M, Dai Q, Decatur WA, Fournier MJ, Piccirilli JA
& Tao Pan. (2006). A systematic, ligation based approach to study
RNA modifications, RNA 12, 2025-2033.
Dai Q, Fong R, Saikia M, Stephenson D, Yu Y-T, Tao Pan
& Piccirilli JA. (2007). Identification of Recognition Residues for
Ligation-Based Detection and Quantitation of Pseudouridine and
N6-Methyladeonsine, Nucl. Acids Res., in press.
Wong T, Sosnick TR & Tao Pan. (2007). Folding of
non-coding RNAs during transcription facilitated by pausing-induced
non-native structures, Proc. Natl. Acad. Sci. USA, in press.
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Faculty and Research
Programs
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