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Pan, Tao

One or more keywords matched the following properties of Pan, Tao

Property	Value
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.

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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

Item Type	Name
Concept	Amino Acids
Concept	Amino Acid Sequence
Concept	Amino Acyl-tRNA Synthetases
Concept	Boronic Acids
Concept	gamma-Aminobutyric Acid
Concept	Digestive System Neoplasms
Concept	Edetic Acid
Concept	Nucleic Acid Hybridization
Concept	RNA, Transfer, Amino Acyl
Concept	Nucleic Acid Conformation
Concept	Plasmodium yoelii
Concept	Nucleic Acid Renaturation
Concept	Sequence Homology, Nucleic Acid
Concept	Regulatory Sequences, Nucleic Acid
Concept	Yeasts
Concept	Protein Transport
Concept	Nucleic Acid Denaturation
Concept	Nucleic Acid Heteroduplexes
Concept	Chromosomes, Artificial, Yeast
Concept	Amino Acid Substitution
Concept	Aminoacylation
Concept	Amino Acid Motifs
Concept	Amino Acid Transport Systems
Concept	RNA, Transfer, Amino Acid-Specific
Concept	Transfer RNA Aminoacylation
Concept	RNA Transport
Concept	Periodic Acid
Concept	Digestive System Surgical Procedures
Concept	Membrane Transport Proteins
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	Multiple substrate binding sites in the ribozyme from Bacillus subtilis RNase P.
Academic Article	Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding.
Academic Article	Recognition of the T stem-loop of a pre-tRNA substrate by the ribozyme from Bacillus subtilis ribonuclease P.
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 folding of a large ribozyme without kinetic traps.
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	Pathway modulation, circular permutation and rapid RNA folding under kinetic control.
Academic Article	Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P.
Academic Article	Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites.
Academic Article	A thermodynamic framework and cooperativity in the tertiary folding of a Mg2+-dependent ribozyme.
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	Exploring the regulation of tRNA distribution on the genomic scale.
Academic Article	Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization.
Academic Article	Crystal structure of the specificity domain of ribonuclease P.
Academic Article	Mechanistic insights on the folding of a large ribozyme during transcription.
Academic Article	Crystal structure of the RNA component of bacterial ribonuclease P.
Academic Article	RNA folding: models and perspectives.
Academic Article	Structure of ribonuclease P--a universal ribozyme.
Academic Article	RNA folding during transcription.
Academic Article	Basis for structural diversity in homologous RNAs.
Academic Article	A systematic, ligation-based approach to study RNA modifications.
Academic Article	A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics.
Academic Article	Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine.
Academic Article	Reduced contact order and RNA folding rates.
Academic Article	Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA.
Academic Article	High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma.
Academic Article	tRNA over-expression in breast cancer and functional consequences.
Academic Article	Innate immune and chemically triggered oxidative stress modifies translational fidelity.
Academic Article	Profiling non-lysyl tRNAs in HIV-1.
Academic Article	Functional analysis of human tRNA isodecoders.
Academic Article	Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion.
Academic Article	Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures.
Academic Article	Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.
Academic Article	Selective charging of tRNA isoacceptors induced by amino-acid starvation.
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	Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding.
Academic Article	Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium.
Academic Article	Selection of circularly permuted ribozymes from Bacillus subtilis RNAse P by substrate binding.
Academic Article	Probing RNA structure by lead cleavage.
Academic Article	Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P.
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	Genome-wide analysis of aminoacylation (charging) levels of tRNA using microarrays.
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	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	Stepwise conversion of a mesophilic to a thermophilic ribozyme.
Academic Article	Diversity of tRNA genes in eukaryotes.
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	Adaptive translation as a mechanism of stress response and adaptation.
Academic Article	Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA.
Academic Article	Diversity of human tRNA genes from the 1000-genomes project.
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	N6-methyladenosine–encoded epitranscriptomics.
Academic Article	Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis.
Academic Article	Determining the fidelity of tRNA aminoacylation via microarrays.
Academic Article	Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair.
Academic Article	Codon optimality controls differential mRNA translation during amino acid starvation.
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	Determination of tRNA aminoacylation levels by high-throughput sequencing.
Award or Honor Receipt	Cancer Research Foundation, Raymond F. Zelko Young Investigator
Academic Article	RNA modification landscape of the human mitochondrial tRNALys regulates protein synthesis.
Academic Article	A study of the lengthening and contractility of the surgical margins in digestive tract cancer.
Academic Article	[The extensibility and retractility of surgical margins in digestive tract cancer].
Academic Article	Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG.
Academic Article	CMT disease severity correlates with mutation-induced open conformation of histidyl-tRNA synthetase, not aminoacylation loss, in patient cells.
Academic Article	HIV protease cleaves the antiviral m6A reader protein YTHDF3 in the viral particle.
Academic Article	Detection and quantification of glycosylated queuosine modified tRNAs by acid denaturing and APB gels.
Academic Article	Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation.
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	[Clinical analysis of 21 cases of cholesteatoma recidivism after canal-wall-up mastoidectomy with tympanoplasty].
Academic Article	[Electrophysiological characteristics of EABR and its value assessment of cochlear implant].
Academic Article	[Effects of neoadjuvant chemotherapy on the prognostic mortality risk of invasive transitional bladder cancer: a meta-analysis].
Academic Article	ImmReg: the regulon atlas of immune-related pathways across cancer types.
Academic Article	[Postoperative hearing in tympanoplasty preserving the manubrium of malleus and tensor tympani muscle tendon].
Academic Article	Pan-cancer assessment of mutational landscape in intrinsically disordered hotspots reveals potential driver genes.
Academic Article	Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing.
Academic Article	Epitranscriptome profiling of spleen mRNA m6A methylation reveals pathways of host responses to malaria parasite infection.
Academic Article	Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation.
Academic Article	[Surgical issues and managements in cochlear reimplantation in 32 children].
Grant	Discovering the epigenetics of RNA modifications
Grant	Studies of RNA modifications on the genomic scale
Grant	Kinetic/Thermodynamic/Structural Studies of RNA Folding
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
Academic Article	Efficacy and Safety of Direct Oral Anticoagulants Compared With Heparin for Preventing Thromboembolism in Hospitalized Patients With COVID-19: A Systematic Review and Meta-Analysis.
Academic Article	Probiotics improve symptoms of patients with COVID-19 through gut-lung axis: a systematic review and meta-analysis.
Academic Article	Design, construction, and functional characterization of a tRNA neochromosome in yeast.
Academic Article	Engineered mischarged transfer RNAs for correcting pathogenic missense mutations.
Academic Article	Lumen-apposing metal stents versus traditional self-expanding metal stents for endoscopic ultrasound-guided drainage of pancreatic fluid collections: a systematic review and meta-analysis.

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