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