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'''Research Summary'''
'''Research Summary'''


Our research focuses on functional genomics of tRNA, RNA epigenetics and RNA folding.
Our research focuses on functional genomics and the biology of tRNA and epitranscriptomics (aka RNA epigenetics).


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.
'''tRNA biology:''' 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 high throughput sequencing methods (DM-tRNA-seq) that measure tRNA abundance, charging fraction and quantify modification fractions. We are investigating the roles of tRNA in translational control and extra-translational functions in mammalian cells.
A central tenet of biology is the accurate flow of information from nucleic acids to proteins through the genetic code. In contrast to common beliefs, we discovered that cells in all three domains of life (mammals, bacteria, hyperthermophilic archaea) can deliberately reprogram the genetic code through tRNA misacylation under selective conditions. We are investigating how regulated mis-translation (aka adaptive mistranslation) is used as a mechanism for stress response.


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 developing genome-wide methods and applying these to study the function of RNA modifications in cell growth, adaptation and development.
'''Epitranscriptomics:''' Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites in all cells. 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. tRNA and rRNA modifications are involved in stress response, environmental adaptation, and antibiotic resistance. Certain mRNA and tRNA modifications can be removed by cellular enzymes, leading to dynamic regulation of their functions. We are investigating the function of RNA modifications in cell growth, adaptation and development.
 
For N6-methyladenosine (m6A) modifications in mRNAs, we discovered that m6A modification can alter the local mRNA secondary structure to regulate binding of mRNA binding proteins transcriptome-wide (m6A switch). The m6A switch mechanism significantly affects mRNA abundance and alternative splicing. We are also developing sequencing methods that can identify mRNA modifications at single base resolution, quantify their modification fractions, and require only minute amount of input material.
Non-coding RNAs perform biological function without being translated into proteins. Some estimates suggest that in human, the number of non-coding RNAs may be comparable to the number of coding RNAs. We are investigating how RNA folds during transcription to understand 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:Research positions|Research positions]] | [[Pan:Press|Press]] |  [[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:Research positions|Research positions]] | [[Pan:Press|Press]] |  [[Pan:Publications|Publications]] | [[Pan:Protocols|Protocols]] | [[Pan:Links|Links]] | [[Pan:Contact us|Contact us]]

Revision as of 07:44, 6 March 2017

Research Summary

Our research focuses on functional genomics and the biology of tRNA and epitranscriptomics (aka RNA epigenetics).

tRNA biology: 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 high throughput sequencing methods (DM-tRNA-seq) that measure tRNA abundance, charging fraction and quantify modification fractions. We are investigating the roles of tRNA in translational control and extra-translational functions in mammalian cells. A central tenet of biology is the accurate flow of information from nucleic acids to proteins through the genetic code. In contrast to common beliefs, we discovered that cells in all three domains of life (mammals, bacteria, hyperthermophilic archaea) can deliberately reprogram the genetic code through tRNA misacylation under selective conditions. We are investigating how regulated mis-translation (aka adaptive mistranslation) is used as a mechanism for stress response.


Epitranscriptomics: Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites in all cells. 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. tRNA and rRNA modifications are involved in stress response, environmental adaptation, and antibiotic resistance. Certain mRNA and tRNA modifications can be removed by cellular enzymes, leading to dynamic regulation of their functions. We are investigating the function of RNA modifications in cell growth, adaptation and development. For N6-methyladenosine (m6A) modifications in mRNAs, we discovered that m6A modification can alter the local mRNA secondary structure to regulate binding of mRNA binding proteins transcriptome-wide (m6A switch). The m6A switch mechanism significantly affects mRNA abundance and alternative splicing. We are also developing sequencing methods that can identify mRNA modifications at single base resolution, quantify their modification fractions, and require only minute amount of input material.

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