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Pan, Tao

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

Property	Value
keywords	RNA modification
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.

Property

Value

keywords

RNA modification

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	Alanine-tRNA Ligase
Concept	Aspartate-tRNA Ligase
Concept	Histidine-tRNA Ligase
Concept	RNA Ligase (ATP)
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	Methionine-tRNA Ligase
Concept	DNA Ligases
Concept	RNA-Directed DNA Polymerase
Concept	RNA, Bacterial
Concept	RNA, Transfer, Asp
Concept	RNA, Transfer, Lys
Concept	RNA, Viral
Concept	RNA Probes
Concept	RNA Nucleotidyltransferases
Concept	RNA Polymerase I
Concept	RNA Splicing
Concept	RNA, Transfer, Glu
Concept	RNA, Transfer, Ser
Concept	RNA
Concept	RNA Polymerase II
Concept	DNA-Directed RNA Polymerases
Concept	RNA Processing, Post-Transcriptional
Concept	RNA, Transfer
Concept	RNA, Transfer, Ile
Concept	Tyrosine-tRNA Ligase
Concept	RNA Splice Sites
Concept	RNA, Catalytic
Concept	RNA Interference
Concept	RNA-Binding Proteins
Concept	RNA Editing
Concept	RNA Cleavage
Concept	RNA, Small Nucleolar
Concept	RNA, Small Cytoplasmic
Concept	RNA, Transfer, Amino Acid-Specific
Concept	RNA, Transfer, Arg
Concept	RNA, Messenger
Concept	RNA, Transfer, Asn
Concept	Transfer RNA Aminoacylation
Concept	RNA, Untranslated
Concept	RNA 3' End Processing
Concept	RNA Folding
Concept	RNA Transport
Concept	RNA, Small Interfering
Concept	RNA, Ribosomal
Concept	RNA, Small Nuclear
Concept	RNA, Protozoan
Concept	Sequence Analysis, RNA
Concept	RNA Stability
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	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 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	Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity.
Academic Article	Recognition of the 5' leader and the acceptor stem of a pre-tRNA substrate by the ribozyme from Bacillus subtilis RNase P.
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	Folding of a large ribozyme during transcription and the effect of the elongation factor NusA.
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	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	Interaction of the Bacillus subtilis RNase P with the 30S ribosomal subunit.
Academic Article	Exploring the regulation of tRNA distribution on the genomic scale.
Academic Article	Getting hotter with RNA.
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	Real-time RNA profiling within a single bacterium.
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	Folding of a universal ribozyme: the ribonuclease P RNA.
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	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	Tissue-specific differences in human transfer RNA expression.
Academic Article	Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA.
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	tRNA: Vast reservoir of RNA molecules with unexpected regulatory function.
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	Cellular dynamics of RNA modification.
Academic Article	Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding.
Academic Article	An evolutionarily conserved mechanism for controlling the efficiency of protein translation.
Academic Article	Structural basis for altering the stability of homologous RNAs from a mesophilic and a thermophilic bacterium.
Academic Article	Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I.
Academic Article	Selection of circularly permuted ribozymes from Bacillus subtilis RNAse P by substrate binding.
Academic Article	Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11.
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	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	A role for tRNA modifications in genome structure and codon usage.
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	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	Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription.
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	My adventure in tRNA biology, so far.
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	Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress.
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	Probing RNA Modification Status at Single-Nucleotide Resolution in Total RNA.
Academic Article	Efficient and quantitative high-throughput tRNA sequencing.
Academic Article	Probing N6-methyladenosine (m6A) RNA Modification in Total RNA with SCARLET.
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	The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA.
Academic Article	RNA modifications: what have we learned and where are we headed?
Academic Article	N6-methyladenosine–encoded epitranscriptomics.
Academic Article	Interaction of tRNA with MEK2 in pancreatic cancer cells.
Academic Article	Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis.
Academic Article	Structures of the m(6)A Methyltransferase Complex: Two Subunits with Distinct but Coordinated Roles.
Academic Article	Determining the fidelity of tRNA aminoacylation via microarrays.
Academic Article	ALKBH1-Mediated tRNA Demethylation Regulates Translation.
Academic Article	Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair.
Academic Article	tRNA base methylation identification and quantification via high-throughput sequencing.
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	tRNA Misacylation with Methionine in the Mouse Gut Microbiome in Situ.
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	Selective Enzymatic Demethylation of N2 ,N2 -Dimethylguanosine in RNA and Its Application in High-Throughput tRNA Sequencing.
Academic Article	Determination of tRNA aminoacylation levels by high-throughput sequencing.
Academic Article	Dynamic RNA Modifications in Gene Expression Regulation.
Academic Article	Identification of N6-methyladenosine reader proteins.
Academic Article	RNA modification landscape of the human mitochondrial tRNALys regulates protein synthesis.
Academic Article	An additional class of m6A readers.
Academic Article	Modifications and functional genomics of human transfer RNA.
Academic Article	Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing.
Academic Article	Queuosine modification protects cognate tRNAs against ribonuclease cleavage.
Academic Article	N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation.
Academic Article	Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis.
Academic Article	Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome.
Academic Article	Sensitive and quantitative probing of pseudouridine modification in mRNA and long noncoding RNA.
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	CMT disease severity correlates with mutation-induced open conformation of histidyl-tRNA synthetase, not aminoacylation loss, in patient cells.
Academic Article	A dual function PUS enzyme.
Academic Article	HIV protease cleaves the antiviral m6A reader protein YTHDF3 in the viral particle.
Academic Article	5-Methylcytosine RNA Modifications Promote Retrovirus Replication in an ALYREF Reader Protein-Dependent Manner.
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	Tissue-specific reprogramming of host tRNA transcriptome by the microbiome.
Academic Article	Pseudouridine RNA modification detection and quantification by RT-PCR.
Academic Article	ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing.
Academic Article	Mitochondrial genome of Protobothrops dabieshanensis (Squamata: Viperidae: Crotalinae).
Academic Article	Long noncoding RNA LINC00511 promotes cell growth and invasion in triple-negative breast cancer by interacting with Snail.
Academic Article	Quantitative probing of glycosylated queuosine modifications in tRNA.
Academic Article	ImmReg: the regulon atlas of immune-related pathways across cancer types.
Academic Article	Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling.
Academic Article	tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes.
Academic Article	Long non-coding RNA ZNF674-AS1 regulates miR-23a/E-cadherin axis to suppress the migration and invasion of non-small cell lung cancer cells.
Academic Article	Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations.
Academic Article	A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation.
Academic Article	Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing.
Academic Article	Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
Academic Article	Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications.
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.
Concept	RNA, Long Noncoding
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	Recognition and mechanism of N6-methyl adenosine modifications
Grant	FOLDING AND CATALYSIS OF THE RIBOZYME FROM RNASE P
Grant	Defining the role of pseudouridine modifications in HIV biology
Grant	N6-methyladenosine and the biology of HIV
Grant	Kinetic/Thermodynamic/Structural studies of RNA folding
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	Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination.
Academic Article	Quantification of tRNA m1A modification by templated-ligation qPCR.
Academic Article	mRNA epitranscriptomics.
Grant	Nasal RNA response to respiratory viral infections
Grant	Transfer RNA sequencing and application to cancer research and clinics
Academic Article	Prokaryotic RNA N1-Methyladenosine Erasers Maintain tRNA m1A Modification Levels in Streptomyces venezuelae.
Academic Article	Modifications in the T arm of tRNA globally determine tRNA maturation, function, and cellular fitness.
Academic Article	Internal mRNA 2'-O-methyl mapping by nanopore sequencing and consequence on mRNA stability and role in cancer.
Academic Article	Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing.
Academic Article	snoRNA-facilitated protein secretion revealed by transcriptome-wide snoRNA target identification.
Academic Article	Bioinformatics of simultaneous, quantitative measurements of full-length tRNA and tRNA fragments by MSR sequencing.

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