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overview Our research focuses on (i) functional genomics and biology of tRNA including microbiomes and (ii) epitranscriptomics including microbiome-host interactions. tRNA biology: Translational regulation relies on the dynamic properties of tRNA that constantly change to facilitate response and adaptation to new environments and to control gene expression. We developed high throughput sequencing technologies that measure tRNA abundance, charging and modifications in one single sequencing library. We are investigating the roles of tRNA in translational control and extra-translational functions in mammalian cells. Microbiome: We also developed tRNA-seq as another approach for microbiome characterization. Standard microbiome characterizations include 16S-seq or shotgun metagenomics. Although powerful, these DNA-based methods do not directly report the microbiome activity such as dynamic gene expression which requires the studies of RNA in the microbiome. Our microbiome tRNA-seq results show extensive variations of tRNA abundance and modification patterns in microbiomes from different sources. We also show that tRNA modification dynamics in the microbiome correlates with tuning the expression of specific microbial proteins, indicating that tRNA-seq can provide new insights in microbiome biology. We are further developing this approach to explore the potentials of tRNA-seq to study microbiomes from humans and from the oceans. Epitranscriptomics: Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites in the transcriptome. 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 and human diseases. Some mRNA modifications can also be removed by cellular enzymes, resulting in the dynamic regulation of their functions. We are investigating the function and mechanisms of mRNA modifications such as N6-methyladenosine (m6A) in the regulation of gene expression. For example, we discovered that m6A modification can alter the local mRNA structure to regulate binding of mRNA binding proteins transcriptome-wide (m6A switch), resulting in changes in mRNA abundance and alternative splicing. Microbiome-host interactions through epitranscriptomics: We are working on elucidating the function of mammalian host mRNA and tRNA modifications in response to the gut microbiome. We found that microbiome reprograms the host m6A modifications transcriptome-wide in a tissue-dependent manner, suggesting that this dynamic epitranscriptomic mark is used in yet unknown ways in microbiome response. We also found that a microbiome dependent, host tRNA modification alters the cellular small RNA pool, suggesting yet another pathway of microbiome response through RNA modifications.
One or more keywords matched the following items that are connected to Pan, Tao
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Concept Adenine
Concept Alanine-tRNA Ligase
Concept Adenosine
Concept Anticodon
Concept Apolipoproteins
Concept Avidin
Concept Adenosine Monophosphate
Concept Alanine
Concept Amino Acids
Concept Amino Acyl-tRNA Synthetases
Concept Antineoplastic Agents
Concept Anticoagulants
Concept Antiviral Agents
Concept Antibodies, Monoclonal
Concept CME-Carbodiimide
Concept Aspartate-tRNA Ligase
Concept Arginine
Concept Base Sequence
Concept Cations, Divalent
Concept Biotin
Concept Bacterial Outer Membrane Proteins
Concept Bacterial Proteins
Concept Binding Sites
Concept Butadienes
Concept Bromates
Concept Endoribonucleases
Concept Ceftriaxone
Concept Boronic Acids
Concept Carbon Radioisotopes
Concept Codon
Concept Fungal Proteins
Concept gamma-Aminobutyric Acid
Concept Cisplatin
Concept Cobamides
Concept Cross-Linking Reagents
Concept Citrate (si)-Synthase
Concept DNA-Binding Proteins
Concept DNA, Mitochondrial
Concept Cycloheximide
Concept Iron
Concept Cytidine
Concept Diethyl Pyrocarbonate
Concept DNA, Bacterial
Concept Cations, Monovalent
Concept Edetic Acid
Concept Heparin, Low-Molecular-Weight
Concept Environmental Pollutants
Concept Hydro-Lyases
Concept Enzyme Inhibitors
Concept Exons
Concept Erythropoietin
Concept Exonucleases
Concept Diamines
Concept DNA
Concept Ferrous Compounds
Concept Interferons
Concept Methyltransferases
Concept Models, Chemical
Concept Nitrogen
Concept Ribonuclease T1
Concept Histidine-tRNA Ligase
Concept Hydrogen Peroxide
Concept Hydroxides
Concept Hypertonic Solutions
Concept Peroxides
Concept Gels
Concept Leucine
Concept Magnesium
Concept Lead
Concept RNA Ligase (ATP)
Concept Potassium Chloride
Concept Esters
Concept Prions
Concept Protein Denaturation
Concept Nucleoside Q
Concept Glutamate-tRNA Ligase
Concept RNA Precursors
Concept RNA, Fungal
Concept RNA, Ribosomal, 28S
Concept RNA, Transfer, Amino Acyl
Concept RNA, Transfer, Leu
Concept RNA, Transfer, Met
Concept RNA, Transfer, Phe
Concept Nitriles
Concept Nucleotides
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Concept Organophosphorus Compounds
Concept Peptide Elongation Factors
Concept Methionine-tRNA Ligase
Concept Plasmids
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Concept Protein Processing, Post-Translational
Concept Protease Inhibitors
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Concept Proteins
Concept Pyrazines
Concept Histone Deacetylases
Concept Mixed Function Oxygenases
Concept Transcription Factors
Concept Guanosine
Concept RNA-Directed DNA Polymerase
Concept Ribonucleotides
Concept RNA, Bacterial
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Concept Pseudouridine
Concept Siloxanes
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Concept RNA, Transfer, Glu
Concept RNA, Transfer, Ser
Concept Sodium
Concept Ribonuclease, Pancreatic
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Concept RNA, Transfer, Ile
Concept Technetium Tc 99m Sulfur Colloid
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Concept Styrenes
Concept Protein Biosynthesis
Concept Thiourea
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Concept Tritium
Concept Tryptophan
Concept Tyrosine-tRNA Ligase
Concept Arsenites
Concept Histocompatibility Antigens Class I
Concept Codon, Terminator
Concept Gene Library
Concept PrPSc Proteins
Concept Radiopharmaceuticals
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Concept Protein Subunits
Concept RNA Splice Sites
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Concept Eukaryotic Initiation Factor-2
Concept HIV Protease
Concept Indole Alkaloids
Concept DNA Probes
Concept Alternative Splicing
Concept Protein Structure, Tertiary
Concept Methionine
Concept Neuropilin-1
Concept Oligodeoxyribonucleotides
Concept RNA-Binding Proteins
Concept MAP Kinase Kinase 2
Concept DNA, Complementary
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Concept DNA-Activated Protein Kinase
Concept Aptamers, Nucleotide
Concept Caspase 3
Concept eIF-2 Kinase
Concept Protein Transport
Concept Endogenous Retroviruses
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Concept Reactive Oxygen Species
Concept Protein Folding
Concept GC Rich Sequence
Concept Mitochondrial Proteins
Concept Riboswitch
Concept DNA Repair Enzymes
Concept Transcriptional Elongation Factors
Concept Green Fluorescent Proteins
Concept Endopeptidase K
Concept Codon, Initiator
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Concept 5' Untranslated Regions
Concept 3' Untranslated Regions
Concept Stem Cell Factor
Concept Amino Acid Transport Systems
Concept Base Pairing
Concept Evodia
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Concept Plant Extracts
Concept Polybrominated Biphenyls
Concept Saccharomyces cerevisiae Proteins
Concept Powders
Concept Databases, Protein
Concept Promoter Regions, Genetic
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Concept Ribonucleases
Concept RNA, Transfer, Amino Acid-Specific
Concept RNA, Transfer, Arg
Concept tRNA Methyltransferases
Concept Rosaniline Dyes
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Concept Sodium Chloride
Concept Calcium-Calmodulin-Dependent Protein Kinase Type 2
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Concept Testosterone
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Concept Inverted Repeat Sequences
Concept Polyphenols
Concept TOR Serine-Threonine Kinases
Concept Urea
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Concept Minor Histocompatibility Antigens
Concept Argonaute Proteins
Concept Codon, Nonsense
Concept Proto-Oncogene Proteins p21(ras)
Concept NADPH Oxidases
Concept Apoptosomes
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Concept Histone Deacetylase Inhibitors
Concept Phosphatidylinositol 3-Kinases
Concept Molecular Motor Proteins
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Concept Activating Transcription Factor 4
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Concept CLOCK Proteins
Concept Heterogeneous-Nuclear Ribonucleoproteins
Concept Heterogeneous-Nuclear Ribonucleoprotein Group C
Concept RNA, Small Interfering
Concept Ribosomal Protein S6 Kinases, 70-kDa
Concept Protein Interaction Maps
Concept Cytochromes c
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Concept Toll-Like Receptors
Concept Phospholipase C gamma
Concept Protein Phosphatase 2
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Concept Metals
Concept Nuclear Proteins
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Academic Article Probing of tertiary interactions in RNA: 2'-hydroxyl-base contacts between the RNase P RNA and pre-tRNA.
Academic Article Domain structure of the ribozyme from eubacterial ribonuclease P.
Academic Article The cleavage step of ribonuclease P catalysis is determined by ribozyme-substrate interactions both distal and proximal to the cleavage site.
Academic Article Altering the intermediate in the equilibrium folding of unmodified yeast tRNAPhe with monovalent and divalent cations.
Academic Article Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein.
Academic Article Recognition of a pre-tRNA substrate by the Bacillus subtilis RNase P holoenzyme.
Academic Article Probing RNA structure and function, by circular permutation.
Academic Article Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering.
Academic Article Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity.
Academic Article Folding of a large ribozyme during transcription and the effect of the elongation factor NusA.
Academic Article A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme.
Academic Article The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits.
Academic Article Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA.
Academic Article Dimeric and monomeric Bacillus subtilis RNase P holoenzyme in the absence and presence of pre-tRNA substrates.
Academic Article Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme.
Academic Article The thermodynamic origin of the stability of a thermophilic ribozyme.
Academic Article Mechanistic insights on the folding of a large ribozyme during transcription.
Academic Article Real-time RNA profiling within a single bacterium.
Academic Article Structure of ribonuclease P--a universal ribozyme.
Academic Article RNA folding during transcription.
Academic Article Folding of a universal ribozyme: the ribonuclease P RNA.
Academic Article High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma.
Academic Article Efficient chemical synthesis of AppDNA by adenylation of immobilized DNA-5'-monophosphate.
Academic Article Innate immune and chemically triggered oxidative stress modifies translational fidelity.
Academic Article Functional analysis of human tRNA isodecoders.
Academic Article Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs.
Academic Article Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion.
Academic Article The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA.
Academic Article tRNA: Vast reservoir of RNA molecules with unexpected regulatory function.
Academic Article Distinct functions of erythropoietin and stem cell factor are linked to activation of mTOR kinase signaling pathway in human erythroid progenitors.
Academic Article Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch.
Academic Article Misacylation of tRNA with methionine in Saccharomyces cerevisiae.
Academic Article An evolutionarily conserved mechanism for controlling the efficiency of protein translation.
Academic Article Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I.
Academic Article Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11.
Academic Article Probing RNA structure by lead cleavage.
Academic Article Genome-wide analysis of tRNA charging and activation of the eIF2 kinase Gcn2p.
Academic Article Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast.
Academic Article Selective control of amino acid metabolism by the GCN2 eIF2 kinase pathway in Saccharomyces cerevisiae.
Academic Article RNA folding during transcription: protocols and studies.
Academic Article Misacylation of specific nonmethionyl tRNAs by a bacterial methionyl-tRNA synthetase.
Academic Article N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.
Academic Article Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons.
Academic Article Anti-tumor effects of an engineered "killer" transfer RNA.
Academic Article Novel RNA substrates for the ribozyme from Bacillus subtilis ribonuclease P identified by in vitro selection.
Academic Article The 3' substrate determinants for the catalytic efficiency of the Bacillus subtilis RNase P holoenzyme suggest autolytic processing of the RNase P RNA in vivo.
Academic Article The rate-limiting step in the folding of a large ribozyme without kinetic traps.
Academic Article Vaccinia and influenza A viruses select rather than adjust tRNAs to optimize translation.
Academic Article Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria.
Academic Article A self-defeating anabolic program leads to ß-cell apoptosis in endoplasmic reticulum stress-induced diabetes via regulation of amino acid flux.
Academic Article N6-methyl-adenosine modification in messenger and long non-coding RNA.
Academic Article Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress.
Academic Article Overexpression of initiator methionine tRNA leads to global reprogramming of tRNA expression and increased proliferation in human epithelial cells.
Academic Article Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface.
Academic Article N6-methyladenosine-dependent regulation of messenger RNA stability.
Academic Article Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress.
Academic Article N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions.
Academic Article High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing.
Academic Article Adaptive translation as a mechanism of stress response and adaptation.
Academic Article RNA epigenetics.
Academic Article A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus.
Academic Article Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress.
Academic Article Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities.
Academic Article Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures.
Academic Article N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding.
Academic Article A dual fluorescent reporter for the investigation of methionine mistranslation in live cells.
Academic Article Correction: Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities.
Academic Article N6-methyladenosine–encoded epitranscriptomics.
Academic Article Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis.
Academic Article ALKBH1-Mediated tRNA Demethylation Regulates Translation.
Academic Article Codon optimality controls differential mRNA translation during amino acid starvation.
Academic Article Function and origin of mistranslation in distinct cellular contexts.
Academic Article RNA modifications and structures cooperate to guide RNA-protein interactions.
Academic Article Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli.
Academic Article N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein.
Academic Article Hili Inhibits HIV Replication in Activated T Cells.
Academic Article Identification of N6-methyladenosine reader proteins.
Academic Article RNA modification landscape of the human mitochondrial tRNALys regulates protein synthesis.
Academic Article N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation.
Academic Article Methods for Identification of Protein-RNA Interaction.
Academic Article Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG.
Academic Article HIV protease cleaves the antiviral m6A reader protein YTHDF3 in the viral particle.
Academic Article An aggregation-specific enzyme-linked immunosorbent assay: detection of conformational differences between recombinant PrP protein dimers and PrP(Sc) aggregates.
Academic Article Biochemical fingerprints of prion infection: accumulations of aberrant full-length and N-terminally truncated PrP species are common features in mouse prion disease.
Academic Article 5-Methylcytosine RNA Modifications Promote Retrovirus Replication in an ALYREF Reader Protein-Dependent Manner.
Academic Article A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities.
Academic Article CMT2N-causing aminoacylation domain mutants enable Nrp1 interaction with AlaRS.
Academic Article ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing.
Academic Article Discovery of 2,4-pyrimidinediamine derivatives as potent dual inhibitors of ALK and HDAC.
Academic Article A novel peroxymonosulfate (PMS)-enhanced iron coagulation process for simultaneous removal of trace organic pollutants in water.
Academic Article Natural polyphenols enhanced the Cu(II)/peroxymonosulfate (PMS) oxidation: The contribution of Cu(III) and HO•.
Academic Article Circadian regulation of apolipoprotein gene expression affects testosterone production in mouse testis.
Academic Article Inhibition of DNA-PK by gefitinib causes synergism between gefitinib and cisplatin in NSCLC.
Academic Article Pan-cancer assessment of mutational landscape in intrinsically disordered hotspots reveals potential driver genes.
Academic Article Age-related endoplasmic reticulum stress represses testosterone synthesis via attenuation of the circadian clock in Leydig cells.
Academic Article Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution.
Concept Protein Domains
Concept Proteasome Inhibitors
Concept RNA, Long Noncoding
Concept Intrinsically Disordered Proteins
Concept ErbB Receptors
Concept Protein Aggregates
Grant Discovering the epigenetics of RNA modifications
Grant Kinetic/Thermodynamic/Structural Studies of RNA Folding
Grant Recognition and mechanism of N6-methyl adenosine modifications
Grant FOLDING AND CATALYSIS OF THE RIBOZYME FROM RNASE P
Grant Mis-translation as a new mechanism of stress response in biology
Grant Defining the role of pseudouridine modifications in HIV biology
Grant Kinetic/Thermodynamic/Structural studies of RNA folding
Grant Mis-translation as a new mechanism of stress response in biology
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