Pan:What we do

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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.
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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.  
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Translational regulation is related to the dynamic properties of tRNA that constantly change to facilitate stress response and adaptation to new environments and to control gene expression. We developed microarray methods that measure tRNA abundance, fraction of aminoacylation and misacylation at the genomic scale. We are exploring roles of tRNA in translational control in mammalian cells.
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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.
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A central tenet of biology is the accurate flow of information from nucleic acids to proteins through the genetic code. It is commonly believed that translation deviating from the genetic code is avoided at all times. We discovered that mammalian cells can deliberately reprogram the genetic code through tRNA misacylation upon innate immune activation and chemically triggered oxidative stress. The reprogramming is regulated by fluctuating levels of reactive oxygen species (ROS) in the cell. We are investigating how regulated mis-translation is used as a mechanism for stress response.
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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.
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Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites from bacteria to humans. 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. RNA modifications are involved in stress response, environmental adaptation, and antibiotic resistance. Some modifications can be removed by cellular enzymes, leading to dynamic regulation of their function. We are investigating the function of RNA modifications in cell growth, adaptation and development.
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<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]]
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We are also investigating how RNA folds during transcription to understand RNA folding and structural rearrangement in the cell.
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<font color=#000000 size=2> [[Pan Lab |Main]] | [[Pan:What we do|What we do]] | [[Pan:Who we are|Who we are]] | [[Pan:Research positions|Research positions]] | [[Pan:Press|Press]] |  [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]

Revision as of 15:23, 20 July 2012

Research Summary

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

Translational regulation is related to the dynamic properties of tRNA that constantly change to facilitate stress response and adaptation to new environments and to control gene expression. We developed microarray methods that measure tRNA abundance, fraction of aminoacylation and misacylation at the genomic scale. We are exploring roles of tRNA in translational control in mammalian cells.

A central tenet of biology is the accurate flow of information from nucleic acids to proteins through the genetic code. It is commonly believed that translation deviating from the genetic code is avoided at all times. We discovered that mammalian cells can deliberately reprogram the genetic code through tRNA misacylation upon innate immune activation and chemically triggered oxidative stress. The reprogramming is regulated by fluctuating levels of reactive oxygen species (ROS) in the cell. We are investigating how regulated mis-translation is used as a mechanism for stress response.

Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites from bacteria to humans. 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. RNA modifications are involved in stress response, environmental adaptation, and antibiotic resistance. Some modifications can be removed by cellular enzymes, leading to dynamic regulation of their function. We are investigating the function of RNA modifications in cell growth, adaptation and development.

We are also investigating how RNA folds during transcription to understand RNA folding and structural rearrangement in the cell.

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