2023
Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch
Sadeeshkumar H, Balaji A, Sutherland A, Mootien S, Anthony K, Breaker R. Screening for small molecule inhibitors of SAH nucleosidase using an SAH riboswitch. Analytical Biochemistry 2023, 666: 115047. PMID: 36682579, PMCID: PMC11149561, DOI: 10.1016/j.ab.2023.115047.Peer-Reviewed Original ResearchConceptsHigh-throughput screenAutoinducer-2Reporter geneBacterial processesEssential bacterial processesGram-negative bacterial cellsQuorum sensing signalsΒ-galactosidase reporter geneSmall molecule inhibitorsAntibiotic drug discoveryNatural riboswitchesAntimicrobial drug developmentRNA elementsPhysiological signalingRiboswitchBacterial cellsMolecule inhibitorsS-adenosylmethionineEscherichia coliCritical functionsNew targetsGenesDrug discoverySmall moleculesPromising target
2021
Modulation of Phosphoprotein Activity by Phosphorylation Targeting Chimeras (PhosTACs)
Chen PH, Hu Z, An E, Okeke I, Zheng S, Luo X, Gong A, Jaime-Figueroa S, Crews CM. Modulation of Phosphoprotein Activity by Phosphorylation Targeting Chimeras (PhosTACs). ACS Chemical Biology 2021, 16: 2808-2815. PMID: 34780684, PMCID: PMC10437008, DOI: 10.1021/acschembio.1c00693.Peer-Reviewed Original ResearchConceptsSer/Thr phosphataseChemical biology approachPP2A holoenzymeProtein dephosphorylationBiology approachProtein substratesTranscriptional activationProtein phosphorylationCatalytic subunitCell biologyReporter geneProtein activityRetinoblastoma proteinOff-target effectsCritical proteinsDephosphorylationTernary complexPhosphorylationKinase inhibitorsFOXO3aPROTACsProteinChimerasPhosphataseDrug resistanceOlfactory receptor coding sequences cause silencing of episomal constructs in multiple cell lines
Abbas G, Tang S, Noble J, Lane R. Olfactory receptor coding sequences cause silencing of episomal constructs in multiple cell lines. Molecular And Cellular Neuroscience 2021, 117: 103681. PMID: 34742908, PMCID: PMC8669572, DOI: 10.1016/j.mcn.2021.103681.Peer-Reviewed Original Research In PressConceptsSensory neuronsOR expressionCell linesCoding sequenceOdorant receptorsOlfactory sensory neuronsReceptor coding sequenceMultiple cell linesMultiple odorant receptorsMammalian olfactory systemEpisomal constructsLevel of expressionTrans factorsComplex multi-step processOR genesBicistronic mRNAEpisomal expressionCMV promoterGFP geneReporter geneFibroblast cell lineOlfactory systemStable expressionGenesNeuronsGenome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression
Singh N, De Kumar B, Paulson A, Parrish M, Scott C, Zhang Y, Florens L, Krumlauf R. Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression. Journal Of Developmental Biology 2021, 9: 6. PMID: 33546292, PMCID: PMC7931043, DOI: 10.3390/jdb9010006.Peer-Reviewed Original ResearchHistone marksGenome-wide binding analysisRepressive histone marksActive histone marksTranscriptional repressor RESTExpression of Hoxb1Specific regulatory functionsEmbryonic stem cellsAnimal developmentGene repressionHoxb1 functionGene regulationNeural fateRepressor RESTRepressive roleTranscription factorsHoxb1Diverse DNATarget genesReporter geneGene expressionRegulatory functionsStem cellsMotifBinding analysis
2019
GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner
Lou S, Cotter KA, Li T, Liang J, Mohsen H, Liu J, Zhang J, Cohen S, Xu J, Yu H, Rubin MA, Gerstein M. GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner. PLOS Genetics 2019, 15: e1007860. PMID: 31469829, PMCID: PMC6742416, DOI: 10.1371/journal.pgen.1007860.Peer-Reviewed Original ResearchConceptsNon-coding variantsTranscription factorsLarge linkage disequilibrium blocksCell type-specific mannerPhenotype of interestMolecular effectsFine-mapping causal variantsCell-specific mannerParticular cell typeLinkage disequilibrium blockEvolutionary conservationTF bindingChIP-seqRegulatory networksPerformance of GRAMCausal variantsReporter geneGene expressionExpression profilesGenomic variantsAssociated geneLuciferase assayCell typesK562 cell lineSpecific mannerBayesian estimation of genetic regulatory effects in high-throughput reporter assays
Majoros WH, Kim YS, Barrera A, Li F, Wang X, Cunningham SJ, Johnson GD, Guo C, Lowe WL, Scholtens DM, Hayes MG, Reddy TE, Allen AS. Bayesian estimation of genetic regulatory effects in high-throughput reporter assays. Bioinformatics 2019, 36: 331-338. PMID: 31368479, PMCID: PMC7999138, DOI: 10.1093/bioinformatics/btz545.Peer-Reviewed Original ResearchConceptsHigh-throughput reporterBiological replicatesGenetic regulatory effectsAdditional biological replicatesGenetic association testsAllelic effectsReporter geneGene expressionSequencing coverageDisease mutationsDisease-causing variantsRegulatory differencesLinkage disequilibriumGenetic variantsExperimental replicatesRegulatory effectsPoisson binomial distributionAllele frequenciesPatient's DNASupplementary dataBayesian hierarchical modelBayesian estimationRare variantsReporterDNA
2017
Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress
LeBlanc C, Zhang F, Mendez J, Lozano Y, Chatpar K, Irish V, Jacob Y. Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress. The Plant Journal 2017, 93: 377-386. PMID: 29161464, DOI: 10.1111/tpj.13782.Peer-Reviewed Original ResearchConceptsCRISPR/Green fluorescent protein (GFP) reporter geneCRISPR/Cas9 systemFluorescent protein reporter geneCRISPR/Cas9Off-target mutationsArabidopsis plantsEukaryotic genomesDifferent organismsSomatic tissuesCitrus plantsCas9 systemDNA breaksReporter geneTarget mutagenesisTargeted mutationsMutation rateMutagenesisImportance of temperatureArabidopsisHeat stressPlantsMutationsQuantitative assayEukaryotesChapter 15 Mouse Models of Epigenetic Inheritance: Classification, Mechanisms, and Experimental Strategies
Mao S, Li Y, Liu B, Chi T. Chapter 15 Mouse Models of Epigenetic Inheritance: Classification, Mechanisms, and Experimental Strategies. 2017, 231-243. DOI: 10.1016/b978-0-12-805388-1.00015-8.Peer-Reviewed Original ResearchEpigenetic inheritanceChromatin modificationsHeritable chromatin modificationsHeritable epigenetic statesSimple reporter geneEpigenetic stateExperimental strategiesEpigenetic mechanismsMolecular basisReporter geneMouse modelInheritanceInheritance modelEnvironmental factorsCompelling evidenceMechanistic studiesEmbryogenesisExtensive contributionsGenesTraitsMechanismMechanistic problemsModificationInducerOffspring
2016
Mitosis-associated repression in development
Esposito E, Lim B, Guessous G, Falahati H, Levine M. Mitosis-associated repression in development. Genes & Development 2016, 30: 1503-1508. PMID: 27401553, PMCID: PMC4949323, DOI: 10.1101/gad.281188.116.Peer-Reviewed Original ResearchConceptsSequence-specific repressorsEarly Drosophila embryoLive-imaging methodsMitotic silencingSnail repressionAnimal developmentSnail repressorDrosophila embryosNascent transcriptsNeurogenic ectodermTranscriptional repressionTarget enhancersPresumptive mesodermReporter geneRepressionRepressorMesodermTranscriptionMitosisEmbryosBroad patternsPervasive featureSilencingEctodermGenesPharmacodynamics of anti-HIV gene therapy using viral vectors and targeted endonucleases
Roychoudhury P, De Silva Feelixge H, Pietz H, Stone D, Jerome K, Schiffer J. Pharmacodynamics of anti-HIV gene therapy using viral vectors and targeted endonucleases. Journal Of Antimicrobial Chemotherapy 2016, 71: 2089-2099. PMID: 27090632, PMCID: PMC4954920, DOI: 10.1093/jac/dkw104.Peer-Reviewed Original ResearchConceptsVector serotypeViral vectorsDose selectionAnti-HIV gene therapyHIV-infected cellsEngineered viral vectorsGene therapy applicationsDose-response relationshipFunctional cureGene expressionGene therapyReporter geneSigmoid dose-response relationshipTransduction efficiencyCurative approachViral uptakeTherapeutic outcomesTarget cellsIndividual target cellsDoseExpress transgenesVirus replicationTherapy applicationsLatent genomesActivation of endonucleasesAn Engineered Rare Codon Device for Optimization of Metabolic Pathways
Wang Y, Li C, Khan M, Wang Y, Ruan Y, Zhao B, Zhang B, Ma X, Zhang K, Zhao X, Ye G, Guo X, Feng G, He L, Ma G. An Engineered Rare Codon Device for Optimization of Metabolic Pathways. Scientific Reports 2016, 6: 20608. PMID: 26852704, PMCID: PMC4745014, DOI: 10.1038/srep20608.Peer-Reviewed Original ResearchConceptsRare codonsCognate tRNAMetabolic pathwaysExpression levelsProtein expressionTarget protein expressionAspartyl-tRNA synthetaseCodons AGGReporter geneRelevant enzymesCopy numberEscherichia coliCodonFatty acid yieldGenesSteady-state kineticsE. coliTRNAPathwayExpressionColiIntermediate levelsTwo-fold increaseSynthetaseAcid yieldImaging Functional Nucleic Acid Delivery to Skin
Kaspar RL, Hickerson RP, González-González E, Flores MA, Speaker TP, Rogers FA, Milstone LM, Contag CH. Imaging Functional Nucleic Acid Delivery to Skin. Methods In Molecular Biology 2016, 1372: 1-24. PMID: 26530911, DOI: 10.1007/978-1-4939-3148-4_1.Peer-Reviewed Original ResearchConceptsNucleic acid deliveryNucleic acid-based therapiesAcid deliveryAcid-based therapiesFunctional deliveryFunctional nucleic acid deliveryTherapeutic nucleic acidsNucleic acidsOptical imaging technologiesReal-time monitoringTriplex nucleic acidsInteraction of lightMonogenic skin diseasesLight-tissue interactionsGene editingGene silencingOptical imagingNoninvasive imaging technologyTopical deliveryTime monitoringImaging technologyReporter geneLayered structureGeneral strategyEnzymatic reactions
2015
Improvement of HIV-1 and Human T Cell Lymphotropic Virus Type 1 Replication-Dependent Vectors via Optimization of Reporter Gene Reconstitution and Modification with Intronic Short Hairpin RNA
Shunaeva A, Potashnikova D, Pichugin A, Mishina A, Filatov A, Nikolaitchik O, Hu W, Mazurov D. Improvement of HIV-1 and Human T Cell Lymphotropic Virus Type 1 Replication-Dependent Vectors via Optimization of Reporter Gene Reconstitution and Modification with Intronic Short Hairpin RNA. Journal Of Virology 2015, 89: 10591-10601. PMID: 26269177, PMCID: PMC4580202, DOI: 10.1128/jvi.01940-15.Peer-Reviewed Original ResearchMeSH KeywordsBiological AssayCD4-Positive T-LymphocytesCell Linegamma-GlobinsGenes, ReporterGenetic EngineeringGenetic VectorsGreen Fluorescent ProteinsHEK293 CellsHIV-1Human T-lymphotropic virus 1HumansIntronsLuciferasesLuminescent ProteinsMicroRNAsRNA SplicingRNA, Small InterferingTransfectionVirionVirus ReplicationConceptsCell-to-cell transmissionCell-mediated infectionVirus type 1HIV-1Gamma-globinTarget cellsHTLV-1Infected cellsHIV-1-infected cellsHuman immunodeficiency virus type 1Human T-cell lymphotropic virus type 1Immunodeficiency virus type 1Type 1Human gamma-globin geneHIV-1 EnvCell-free infectionVirus-producing cellsGamma-globin genesInfected target cellsStudy HIV-1Reporter vectorReporter geneRetrovirus HTLV-1Level of reporter gene expressionShort hairpin RNAIsocost Lines Describe the Cellular Economy of Genetic Circuits
Gyorgy A, Jiménez J, Yazbek J, Huang H, Chung H, Weiss R, Del Vecchio D. Isocost Lines Describe the Cellular Economy of Genetic Circuits. Biophysical Journal 2015, 109: 639-646. PMID: 26244745, PMCID: PMC4572570, DOI: 10.1016/j.bpj.2015.06.034.Peer-Reviewed Original ResearchConceptsGenetic circuitsRibosome binding site strengthsBinding site strengthsPlasmid copy numberProduction of proteinsInduced genesCellular economyCopy numberReporter genePlasmidLiving cellsGenesRegulatory pathProteinTranslation resourcesSite strengthProtein concentrationRibosomeLinesEffects of such couplingCells
2014
Development of a novel method to create double-strand break repair fingerprints using next-generation sequencing
Soong CP, Breuer GA, Hannon RA, Kim SD, Salem AF, Wang G, Yu R, Carriero NJ, Bjornson R, Sundaram RK, Bindra RS. Development of a novel method to create double-strand break repair fingerprints using next-generation sequencing. DNA Repair 2014, 26: 44-53. PMID: 25547252, DOI: 10.1016/j.dnarep.2014.12.002.Peer-Reviewed Original ResearchConceptsHomologous recombinationNHEJ repairChromosomal lociDSB repair pathway choiceDNA double-strand break repairEndogenous chromosomal locusEfficient DNA double-strand break repairDouble-strand break repairDSB repair proteinsRepair pathway choiceDNA damaging agentsSequencing-based approachesDSB repair activityNext-generation sequencing-based approachChromatin interactionsGenomic integrityDSB repairMammalian cellsNext-generation sequencingBreak repairPathway choiceRepair proteinsReporter geneDamaging agentsRepair assaysA dexamethasone-inducible gene expression system is active in Citrus plants
Rossignol P, Orbović V, Irish V. A dexamethasone-inducible gene expression system is active in Citrus plants. Scientia Horticulturae 2014, 172: 47-53. DOI: 10.1016/j.scienta.2014.02.041.Peer-Reviewed Original ResearchGene expression systemExpression systemΒ-glucuronidase (GUS) reporter geneInducible gene expression systemSynthetic transcription factorsGene of interestPromoter driving expressionCrop plantsGene functionTransgenic approachesTranscription factorsCitrus plantsNew traitsReporter geneCitrus cultivarsPlantsTransgene activityGenesSynthetic glucocorticoid dexamethasoneTiming of activityGlucocorticoid receptorSuch manipulationsGlucocorticoid dexamethasoneLhGRTraitsImproved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases
Rogers FA, Lloyd JA, Tiwari MK. Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases. Artificial DNA PNA & XNA 2014, 5: e27792. PMID: 25483840, PMCID: PMC4014521, DOI: 10.4161/adna.27792.Peer-Reviewed Original ResearchConceptsMobility gel shift assaysDNA double-strand breaksTarget sequenceGel shift assaysDouble-strand breaksGene-targeted mutagenesisActivation of apoptosisG-quadruplex formationGenomic modificationsDNA repairShift assaysReporter geneMolecular mechanismsPolypurine sequenceStrand breaksTriplex technologyTarget siteMutagenesisTriplex structureGenesGuanine baseTriplex formationGuanine basesSequenceAG30Chapter 8 Towards the Molecular Mechanisms of Transgenerational Epigenetic Inheritance Insights from Transgenic Mice
Kaundal R, Yang Y, Nottoli T, Chi T. Chapter 8 Towards the Molecular Mechanisms of Transgenerational Epigenetic Inheritance Insights from Transgenic Mice. 2014, 75-85. DOI: 10.1016/b978-0-12-405944-3.00008-8.Peer-Reviewed Original ResearchTransgenerational epigenetic inheritanceChromatin marksChromatin modificationsEpigenetic inheritanceGlobal epigenetic reprogrammingTraditional transgenic miceCopy numberGene-targeting methodsSite-specific integrationMitotic inheritanceHeritable perturbationsEpigenetic reprogrammingTransgenerational inheritanceTractable systemEpigenetic modificationsUnderlying genesEpigenetic perturbationsCpG methylationTransgenic miceGenetic strategiesReporter geneCOL1A1 locusMolecular mechanismsSubsequent embryogenesisGermline transmission
2013
Identification of Biologically Relevant Enhancers in Human Erythroid Cells*
Su MY, Steiner LA, Bogardus H, Mishra T, Schulz VP, Hardison RC, Gallagher PG. Identification of Biologically Relevant Enhancers in Human Erythroid Cells*. Journal Of Biological Chemistry 2013, 288: 8433-8444. PMID: 23341446, PMCID: PMC3605659, DOI: 10.1074/jbc.m112.413260.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBasic Helix-Loop-Helix Transcription FactorsCells, CulturedChromatinChromatin ImmunoprecipitationConserved SequenceE1A-Associated p300 ProteinEnhancer Elements, GeneticErythroid CellsGATA1 Transcription FactorGene Expression RegulationGenes, ReporterHigh-Throughput Nucleotide SequencingHumansKruppel-Like Transcription FactorsLuciferases, FireflyMolecular Sequence AnnotationNF-E2 Transcription Factor, p45 SubunitOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotidePromoter Regions, GeneticProtein BindingProto-Oncogene ProteinsRNA, MessengerSequence Analysis, DNAT-Cell Acute Lymphocytic Leukemia Protein 1TranscriptomeConceptsHuman erythroid cellsCandidate enhancersTranscriptional start siteErythroid cellsTranscription factorsGenome-wide association study catalogCell type-specific enhancersPrimary human erythroid cellsRegulation of programsGenome-wide mapsErythroid transcription factorsErythroid cell developmentSpecialized cell typesIdentification of enhancersGene expression analysisErythroid traitsMinimal conservationChromatin immunoprecipitationModerate conservationStart siteRelevant enhancersCellular developmentGenetic lociExpression analysisReporter gene
2012
Highly Attenuated Recombinant Vesicular Stomatitis Virus VSV-12′GFP Displays Immunogenic and Oncolytic Activity
van den Pol A, Davis J. Highly Attenuated Recombinant Vesicular Stomatitis Virus VSV-12′GFP Displays Immunogenic and Oncolytic Activity. Journal Of Virology 2012, 87: 1019-1034. PMID: 23135719, PMCID: PMC3554062, DOI: 10.1128/jvi.01106-12.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsGene Expression ProfilingGenes, ReporterGliomaGreen Fluorescent ProteinsHumansMiceMice, SCIDMolecular Sequence DataOncolytic VirusesRNA, ViralSequence Analysis, DNASurvival AnalysisTreatment OutcomeVaccines, AttenuatedVaccines, SyntheticVesiculovirusViral Plaque AssayViral VaccinesConceptsVesicular stomatitis virusGreen fluorescent proteinReporter geneOne-step growth curveVesicular stomatitis virus genomeAttenuated vesicular stomatitis virusCancer cellsHigh-titer antibody responsesInjection of tumorHuman cancer cellsSuppressed tumor growthRNA transcriptsOncolytic virusesIntratumoral injectionSCID micePostnatal daySafety profileFluorescent proteinTumor growthVSV-G/GFPGenesRecombinant virusesStomatitis virusImmune responseAntibody response
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