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Our research focuses on functional genomics of tRNA, RNA epigenetics and RNA folding.
Our research focuses on functional genomics of tRNA, RNA epigenetics and RNA folding.


tRNA is essential for protein synthesis and life. Biological genomes contain up to several hundred tRNA genes. Translational regulation is related to the dynamic properties of each tRNA that constantly change to facilitate stress response and cellular adaptation to new environments and to control gene expression in differentiated organisms. We have developed tRNA microarrays that measure the abundance and the fraction of aminoacylation of each tRNA. Using these microarray technologies, we are exploring the effect of varying tRNA concentration and aminoacylation fraction on translation in bacteria and in cancer cells.  
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 chemical types of post-transcriptional modifications have been identified in thousands of sites in RNAs 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 are working on a general microarray method that will detect and quantify the extent of modifications in any RNA. We are applying this high throughput, microarray method to study the function of RNA modifications at the genomic level during cell growth, adaptation and development.   
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.   


The goals of RNA folding are to understand how RNA folds into defined structures and how RNA structures are stabilized. We use a wide array of biophysical, structural and biochemical methods to elucidate the principles RNA folding and stability. Folding during transcription is also studied to mimic RNA folding in the cell.
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.


<font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]
<font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]

Revision as of 13:09, 7 July 2008

Research Summary

Our research focuses on functional genomics of tRNA, RNA epigenetics and 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.

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