Tao Pan

Research topics: Functional genomics of tRNA, RNA epigenetics, RNA folding.

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.

Research topics: Functional genomics of tRNA, RNA epigenetics, RNA folding.

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....

Qu, X-H., G. J. Smith, K.T. Lee, T. R. Sosnick, Tao Pan & N. F. Scherer: Single-Molecule Non-equilibrium Periodic Mg2+-concentration Jump Experiments Reveal Details of the Early Folding Pathways of a Large RNA, Proc. Natl. Acad. Sci. USA 105, 6602-6607 (2008). 

Smith, G.J., K.T. Lee, X-H. Qu, Z. Xie, J. Pesic, T.R. Sosnick, Tao Pan & N.F. Scherer: Discrete single molecule dynamics suggest relatively simple but rugged structure for a large collapsed-state RNA, J. Mol. Biol. 378, 941-951 (2008). 

Dai, Q., R. Fong, M. Saikia, D. Stephenson, Y.-T. Yu, Tao Pan & J.A. Piccirill: Identification of Recognition Residues for Ligation-Based Detection and Quantitation of Pseudouridine and N6-Methyladeonsine, Nucl. Acids Res. 35, 6322-6329 (2007). 

Wong, T., T.R. Sosnick & Tao Pan: Folding of non-coding RNAs during transcription facilitated by pausing-induced non-native structures, Proc. Natl. Acad. Sci. USA 104, 17995-18000 (2007). 

Dittmar, K.A., J.M. Goodenbour & Tao Pan: Tissue specific differences in human transfer RNA expression. PLoS Genetics 2, 2107-2115 (e221, 2006). 

Saikia, M., Q. Dai, W.A. Decatur, M.J. Fournier, J.A. Piccirilli & Tao Pan: A systematic, ligation based approach to study RNA modifications, RNA 12, 2025-2033 (2006). 

Goodenbour, J.M. & Tao Pan: Diversity of tRNA genes in eukaryotes. Nucl. Acids Res. 34, 6137-46 (2006). 

Baird, N.J., N. Srividya, A. Krasilnikov, A. Mondragón, T. R. Sosnick & Tao Pan: Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium, RNA 12, 598-606 (2006). 

Torres, A., K. Swinger, A. Krasilnikov, A., Tao Pan & A. Mondragon: Crystal structure of the RNA component of bacterial Ribonuclease P, Nature 437, 584-587 (2005). 

Baird, N., E. Westhof, H. Qin, Tao Pan & T.R. Sosnick: The structure of a folding intermediate reveals interplay between core and peripheral elements in RNA folding, J. Mol. Biol. 362, 712-722 (2005). 

Le, T., S. Harlepp, C.C. Guet, K. Dittmar, T. Emonet, Tao Pan & P. Cluzel: Real-time profiling of a specific RNA within a single bacterium. Proc. Natl. Acad. Sci. USA 102, 9160-9164 (2005). 

Dittmar, K.A., M. Sorensen, J. Elf, M. Ehrenberg & Tao Pan: Selective charging of tRNA isoacceptors induced by amino acid starvation. EMBO Reports 6, 151-157 (2005). 

Qu, X-H., G. J. Smith, K.T. Lee, T. R. Sosnick, Tao Pan & N. F. Scherer: Single-Molecule Non-equilibrium Periodic Mg2+-concentration Jump Experiments Reveal Details of the Early Folding Pathways of a Large RNA, Proc. Natl. Acad. Sci. USA 105, 6602-6607 (2008). 

Smith, G.J., K.T. Lee, X-H. Qu, Z. Xie, J. Pesic, T.R. Sosnick, Tao Pan & N.F. Scherer: Discrete single molecule dynamics suggest relatively simple but rugged structure for a large collapsed-state RNA, J. Mol. Biol. 378, 941-951 (2008). 

Dai, Q., R. Fong, M. Saikia, D. Stephenson, Y.-T. Yu, Tao Pan & J.A. Piccirill: Identification of Recognition Residues for Ligation-Based Detection and Quantitation of Pseudouridine and N6-Methyladeonsine, Nucl. Acids Res. 35, 6322-6329 (2007). 

Wong, T., T.R. Sosnick & Tao Pan: Folding of non-coding RNAs during transcription facilitated by pausing-induced non-native structures, Proc. Natl. Acad. Sci. USA 104, 17995-18000 (2007). 

Dittmar, K.A., J.M. Goodenbour & Tao Pan: Tissue specific differences in human transfer RNA expression. PLoS Genetics 2, 2107-2115 (e221, 2006).