2025
Age-invariant genes: multi-tissue identification and characterization of murine reference genes
González J, Thrush-Evensen K, Meer M, Levine M, Higgins-Chen A. Age-invariant genes: multi-tissue identification and characterization of murine reference genes. Aging 2025, 17: 170-202. PMID: 39888841, PMCID: PMC11810059, DOI: 10.18632/aging.206195.Peer-Reviewed Original ResearchRNA-seq datasetsReference genesRNA-seqHallmarks of agingPathway enrichment analysisGenes-thoseCpG islandsShorter transcriptRT-qPCRMolecular functionsExpression studiesGene normalizationTissue-specificEnrichment analysisMouse tissuesGenesMurine tissuesAged tissuesHallmarksYoung organismsLifespanTranscriptionCpGTissuePathwayAge-invariant genes: multi-tissue identification and characterization of murine reference genes
González J, Thrush-Evensen K, Meer M, Levine M, Higgins-Chen A. Age-invariant genes: multi-tissue identification and characterization of murine reference genes. Aging 2025, 17: 170-202. PMID: 39873648, PMCID: PMC11810070, DOI: 10.18632/aging.206192.Peer-Reviewed Original ResearchConceptsRNA-seq datasetsReference genesRNA-seqHallmarks of agingPathway enrichment analysisGenes-thoseCpG islandsShorter transcriptRT-qPCRMolecular functionsExpression studiesGene normalizationTissue-specificEnrichment analysisMouse tissuesGenesMurine tissuesAged tissuesHallmarksYoung organismsLifespanTranscriptionCpGTissuePathway
2024
Field Isolation and Laboratory Vector-Host Studies of Brazoran Virus (Peribunyaviridae: Orthobunyavirus) from Florida.
Armstrong P, Anderson J, Sharma R, Misencik M, Bransfield A, Vossbrinck C, Brackney D. Field Isolation and Laboratory Vector-Host Studies of Brazoran Virus (Peribunyaviridae: Orthobunyavirus) from Florida. American Journal Of Tropical Medicine And Hygiene 2024, 110: 968-970. PMID: 38531101, PMCID: PMC11066360, DOI: 10.4269/ajtmh.23-0799.Peer-Reviewed Original ResearchConceptsCulex quinquefasciatusMultiple mouse tissuesVector competenceDisseminated infectionNucleotide identityTexas isolatesL segmentField isolatesS segmentFlorida strainBlood mealMidgut infectionDisease signsMouse tissuesLaboratory trialsCulex erraticusIntradermal inoculationAedes aegyptiQuinquefasciatusCulex mosquitoesCulexIsolatesSouthern FloridaSuckling miceVirus transmission
2022
Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock
Minteer C, Morselli M, Meer M, Cao J, Higgins‐Chen A, Lang SM, Pellegrini M, Yan Q, Levine ME. Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock. Aging Cell 2022, 21: e13553. PMID: 35104377, PMCID: PMC8844113, DOI: 10.1111/acel.13553.Peer-Reviewed Original ResearchConceptsMouse embryonic fibroblastsDNA methylationEpigenetic agingImportant chromatin regulatorsPolycomb group (PcG) factorsAnti-aging interventionsChromatin regulatorsEmbryonic fibroblastsCellular senescenceTissue agingCellular agingEpigenetic clocksMultiple tissuesMouse tissuesCaloric restrictionMechanistic insightsAging changesKidney fibroblastsReduced representationTime pointsPhysiological agingMouse culturesSuch alterationsTick-TockTissue
2021
CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini
Wang H, Huang R, Li L, Zhu J, Li Z, Peng C, Zhuang X, Lin H, Shi S, Huang P. CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini. Cell Discovery 2021, 7: 25. PMID: 33867522, PMCID: PMC8053708, DOI: 10.1038/s41421-021-00265-2.Peer-Reviewed Original ResearchSmall noncoding RNAsMethylated nucleosidesHepatic reprogrammingPolynucleotide kinaseHigh-throughput sequencingSRNA transcriptomeTissue-specific differencesSmall ncRNAsT4 polynucleotide kinaseNoncoding RNAsAdapter ligationMouse tissuesAcid pyrophosphataseReprogrammingComplex landscapeMethylationTerminusReverse transcriptionRNASequencingTranscriptome-wide quantification of double-stranded RNAs in live mouse tissues by dsRIP-Seq
Gao Y, Chen S, Halene S, Tebaldi T. Transcriptome-wide quantification of double-stranded RNAs in live mouse tissues by dsRIP-Seq. STAR Protocols 2021, 2: 100366. PMID: 33778776, PMCID: PMC7982789, DOI: 10.1016/j.xpro.2021.100366.Peer-Reviewed Original ResearchConceptsDouble-stranded RNALive mouse tissuesDeleterious innate immune responseInnate immune responseEndogenous double-stranded RNAMouse tissuesMultiple regulatory functionsRecognition of RNADownstream computational analysisImmune responseRNA editingActivate innate immune responsesRegulatory functionsComplete detailsRNAImmunoprecipitationTissue isolationComplete protocolGao etComputational analysisSequencingTissueEditing
2020
Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models
Gregory JA, Hoelzli E, Abdelaal R, Braine C, Cuevas M, Halpern M, Barretto N, Schrode N, Akbalik G, Kang K, Cheng E, Bowles K, Lotz S, Goderie S, Karch CM, Temple S, Goate A, Brennand KJ, Phatnani H. Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models. Cells 2020, 9: 1406. PMID: 32516938, PMCID: PMC7349756, DOI: 10.3390/cells9061406.Peer-Reviewed Original ResearchConceptsCell type-restricted expressionDisease-associated interactionsGene expression profilingHiPSC-derived motor neuronsHuman-induced pluripotent stem cellsPluripotent stem cellsCell-type specific perturbationsImmortalized cell linesRibosomal proteinsGenomic studiesExpression profilingMolecular mechanismsOff-target RNAMouse tissuesCell typesStem cellsPrimary mouse astrocytesExperimental replicatesCell linesMixed speciesMouse astrocytesExpressionMotor neuronsRiboTagCellsMethods Matter: Standard Production Platforms for Recombinant AAV Produce Chemically and Functionally Distinct Vectors
Rumachik NG, Malaker SA, Poweleit N, Maynard LH, Adams CM, Leib RD, Cirolia G, Thomas D, Stamnes S, Holt K, Sinn P, May AP, Paulk NK. Methods Matter: Standard Production Platforms for Recombinant AAV Produce Chemically and Functionally Distinct Vectors. Molecular Therapy — Methods & Clinical Development 2020, 18: 98-118. PMID: 32995354, PMCID: PMC7488757, DOI: 10.1016/j.omtm.2020.05.018.Peer-Reviewed Original ResearchPost-translational modificationsHost cell speciesHuman HEK293 cellsComparative production analysisEpigenomic sequencingInsect cellsHuman cytokine profilingProteomic profilingMultiple analytical approachesHEK293 cellsExpression kineticsMouse tissuesCell typesCell speciesHost cell protein impuritiesRAAV genomesDenaturation assaysGenomeProduction platformMajor discoveriesProfilingRAAV capsidsMass spectrometryReceptor bindingCells
2016
Neuronal Calcium Sensor 1 Has Two Variants with Distinct Calcium Binding Characteristics
Wang B, Boeckel GR, Huynh L, Nguyen L, Cao W, De La Cruz EM, Kaftan EJ, Ehrlich BE. Neuronal Calcium Sensor 1 Has Two Variants with Distinct Calcium Binding Characteristics. PLOS ONE 2016, 11: e0161414. PMID: 27575489, PMCID: PMC5004852, DOI: 10.1371/journal.pone.0161414.Peer-Reviewed Original ResearchConceptsNeuronal calcium sensor-1NCS-1Altered cell functionCell linesCalcium-dependent processesCalcium binding proteinNeurological diseasesFunctional changesLevel of expressionDrug potencyProtein expressionCell functionMRNA levelsHuman cell linesRelative expressionMost tissuesCell deathPrevious reportsMouse tissuesDifferent human cell linesCell growthFunctional roleBinding characteristicsFunctional differencesTissue
2015
Geometry of the Gene Expression Space of Individual Cells
Korem Y, Szekely P, Hart Y, Sheftel H, Hausser J, Mayo A, Rothenberg M, Kalisky T, Alon U. Geometry of the Gene Expression Space of Individual Cells. PLOS Computational Biology 2015, 11: e1004224. PMID: 26161936, PMCID: PMC4498931, DOI: 10.1371/journal.pcbi.1004224.Peer-Reviewed Original ResearchConceptsGene expression spaceExpression spaceCell typesConcept of cell typesGene expressionGene expression of single cellsHigh-dimensional gene expression spaceEvolutionary trade-offIntestinal progenitor cellsSingle-cell dataSingle-cell datasetsSingle-cell technologiesSingle cellsMultiple tasksExpression statesIntestinal crypt cellsPathogen sensingMouse tissuesGenesExpression profilesTask
2014
Nrf2 Amplifies Oxidative Stress via Induction of Klf9
Zucker SN, Fink EE, Bagati A, Mannava S, Bianchi-Smiraglia A, Bogner PN, Wawrzyniak JA, Foley C, Leonova KI, Grimm MJ, Moparthy K, Ionov Y, Wang J, Liu S, Sexton S, Kandel ES, Bakin AV, Zhang Y, Kaminski N, Segal BH, Nikiforov MA. Nrf2 Amplifies Oxidative Stress via Induction of Klf9. Molecular Cell 2014, 53: 916-928. PMID: 24613345, PMCID: PMC4049522, DOI: 10.1016/j.molcel.2014.01.033.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesBleomycinCell Line, TumorGene Expression RegulationGenes, ReporterHumansKruppel-Like Transcription FactorsLuciferasesLungMiceNF-E2-Related Factor 2NIH 3T3 CellsOxidative StressPromoter Regions, GeneticProtein BindingPulmonary FibrosisReactive Oxygen SpeciesSignal TransductionConceptsReactive oxygen speciesKey transcriptional regulatorMetabolism of ROSOxidative stressPathogenesis of bleomycinKruppel-like factor 9Thioredoxin reductase 2Subsequent cell deathTranscription factor 2Antioxidant gene expressionUbiquitous regulatorsTranscriptional regulatorsIntracellular reactive oxygen speciesLung injuryFeedforward regulationPulmonary fibrosisGene expressionOxidant injuryROS clearanceCell deathReductase 2Mouse tissuesCultured cellsNF-E2Factor 9
2006
p204 Is Required for the Differentiation of P19 Murine Embryonal Carcinoma Cells to Beating Cardiac Myocytes ITS EXPRESSION IS ACTIVATED BY THE CARDIAC GATA4, NKX2.5, AND TBX5 PROTEINS*
Ding B, Liu CJ, Huang Y, Hickey RP, Yu J, Kong W, Lengyel P. p204 Is Required for the Differentiation of P19 Murine Embryonal Carcinoma Cells to Beating Cardiac Myocytes ITS EXPRESSION IS ACTIVATED BY THE CARDIAC GATA4, NKX2.5, AND TBX5 PROTEINS*. Journal Of Biological Chemistry 2006, 281: 14882-14892. PMID: 16556595, DOI: 10.1074/jbc.m511747200.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceCell Line, TumorChromatinGATA4 Transcription FactorGene Expression Regulation, DevelopmentalHomeobox Protein Nkx-2.5Homeodomain ProteinsMiceMolecular Sequence DataMuscle, SkeletalMyocytes, CardiacNuclear ProteinsPhosphoproteinsT-Box Domain ProteinsTranscription FactorsConceptsNuclear export signalExport signalTranscription factorsP19 cellsC2C12 skeletal muscle myoblastsP19 murine embryonal carcinoma cellsEmbryonal carcinoma stem cellsAdult mouse tissuesMurine embryonal carcinoma cellsTBX5 transcription factorSkeletal muscle myoblastsEmbryonal carcinoma cellsCarcinoma stem cellsP204 expressionP204 proteinExpression of GATA4Regulatory regionsTBX5 proteinReporter constructsAntisense RNAMuscle myoblastsCardiac myocytesMouse tissuesStem cellsGATA4
2003
Impaired membrane resealing and autoimmune myositis in synaptotagmin VII–deficient mice
Chakrabarti S, Kobayashi KS, Flavell RA, Marks CB, Miyake K, Liston DR, Fowler KT, Gorelick FS, Andrews NW. Impaired membrane resealing and autoimmune myositis in synaptotagmin VII–deficient mice. Journal Of Cell Biology 2003, 162: 543-549. PMID: 12925704, PMCID: PMC2173791, DOI: 10.1083/jcb.200305131.Peer-Reviewed Original ResearchConceptsVII-deficient miceAntinuclear antibody responseInflammatory autoimmune diseasePolymyositis/dermatomyositisProgressive muscle weaknessCreatine kinase releaseInflammatory myopathiesAutoimmune myositisMuscle weaknessAutoimmune diseasesAutoimmune disordersExtensive fibrosisAntibody responseCollagen depositionDefective plasma membrane repairMembrane repairTrypanosoma cruzi invasionSkeletal muscleMiceExocytosis of lysosomesCruzi invasionInvasionPlasma membrane repairMouse tissuesLysosomal exocytosis
1998
An Evolutionarily Conserved Gene on Human Chromosome 5q33–q34,UBH1,Encodes a Novel Deubiquitinating Enzyme
Hansen-Hagge T, Janssen J, Hameister H, Papa F, Zechner U, Seriu T, Jauch A, Becke D, Hochstrasser M, Bartram C. An Evolutionarily Conserved Gene on Human Chromosome 5q33–q34,UBH1,Encodes a Novel Deubiquitinating Enzyme. Genomics 1998, 49: 411-418. PMID: 9615226, DOI: 10.1006/geno.1998.5275.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceCaenorhabditis elegansChromosome MappingChromosomes, Human, Pair 14Chromosomes, Human, Pair 5Conserved SequenceDNA PrimersEndopeptidasesEvolution, MolecularHumansIn Situ HybridizationLeukemiaMiceMolecular Sequence DataMultigene FamilyNervous SystemNeuronsPolymerase Chain ReactionPseudogenesSaccharomyces cerevisiaeSequence AlignmentSequence Homology, Amino AcidTranscription, GeneticTranslocation, GeneticUbiquitin ThiolesteraseConceptsGene familyDeubiquitinating enzymeNovel multigene familyGalactosidase fusion proteinSitu hybridizationNovel deubiquitinating enzymeNorthern blot analysisConserved geneCaenorhabditis elegansHypothetical proteinsMultigene familyHuman genesLow-level expressionFunctional membersHuman chromosomesProtein displayFusion proteinMouse tissuesEscherichia coliChromosome 5q33Blot analysisBreakpoint sequencesEnzyme 1GenesEnzymeMice That Lack Thrombospondin 2 Display Connective Tissue Abnormalities That Are Associated with Disordered Collagen Fibrillogenesis, an Increased Vascular Density, and a Bleeding Diathesis
Kyriakides T, Zhu Y, Smith L, Bain S, Yang Z, Lin M, Danielson K, Iozzo R, LaMarca M, McKinney C, Ginns E, Bornstein P. Mice That Lack Thrombospondin 2 Display Connective Tissue Abnormalities That Are Associated with Disordered Collagen Fibrillogenesis, an Increased Vascular Density, and a Bleeding Diathesis. Journal Of Cell Biology 1998, 140: 419-430. PMID: 9442117, PMCID: PMC2132586, DOI: 10.1083/jcb.140.2.419.Peer-Reviewed Original ResearchConceptsTSP2-null miceEmbryonic stem cellsCollagen fibrillogenesisGenetic disorder resultsCell surface propertiesHomologous recombinationExtracellular proteinsMutant animalsBlastocyst injectionAppropriate breedingStructural roleMendelian frequencyMouse tissuesMesenchymal cellsStem cellsUnusual phenotypeCell functionMutant miceThrombospondin-2TSP2Von Willebrand factorSkin fibroblastsConnective tissue abnormalitiesLarge fibrilsWillebrand factor
1997
Molecular Cloning, cDNA Sequence Analysis, and Chromosomal Localization of MousePkd2
Wu G, Mochizuki T, Le T, Cai Y, Hayashi T, Reynolds D, Somlo S. Molecular Cloning, cDNA Sequence Analysis, and Chromosomal Localization of MousePkd2. Genomics 1997, 45: 220-223. PMID: 9339380, DOI: 10.1006/geno.1997.4920.Peer-Reviewed Original ResearchConceptsCDNA sequenceIntegral membrane proteinsMembrane-spanning domainsCDNA sequence analysisAmino acid levelsGenomic localizationPKD2 mRNAChromosomal localizationMembrane proteinsMolecular cloningMouse mutationMurine homologueExpression analysisCandidate genesChromosome 5Sequence analysisMouse tissuesKidney phenotypePKD2CloningPolycystic kidney phenotypeGenesAutosomal dominant polycystic kidney diseaseDominant polycystic kidney diseasePolycystic kidney diseaseThe E6–AP Ubiquitin–Protein Ligase (UBE3A) Gene Is Localized within a Narrowed Angelman Syndrome Critical Region
Sutcliffe J, Jiang Y, Galjaard R, Matsuura T, Fang P, Kubota T, Christian S, Bressler J, Cattanach B, Ledbetter D, Beaudet A. The E6–AP Ubiquitin–Protein Ligase (UBE3A) Gene Is Localized within a Narrowed Angelman Syndrome Critical Region. Genome Research 1997, 7: 368-377. PMID: 9110176, PMCID: PMC139148, DOI: 10.1101/gr.7.4.368.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAngelman SyndromeAnimalsBlotting, NorthernBlotting, SouthernChromosome AberrationsChromosome MappingChromosomes, Artificial, YeastChromosomes, Human, Pair 15Cloning, MolecularCosmidsElectrophoresis, Gel, Pulsed-FieldFemaleGene DeletionGene DosageGene Expression Regulation, DevelopmentalGenetic MarkersGenomic ImprintingHumansIn Situ HybridizationLigasesMaleMiceMice, Mutant StrainsMolecular Sequence DataPaternityPrader-Willi SyndromeSequence Homology, Amino AcidSequence Homology, Nucleic AcidTissue DistributionTranscription, GeneticTranslocation, GeneticUbiquitin-Protein LigasesConceptsLigase geneUbiquitin protein ligase geneAngelman syndromeEntire transcriptional unitCandidate regionsMaternal-specific expressionE6-AP ubiquitinTranscriptional unitsPaternal deficiencyRT-PCR analysisMouse homologPrader-Willi syndromePaternal uniparental disomyPhysical mapDe novo truncating mutationsNovo truncating mutationsRecent identificationUBE3A locusMouse tissuesGenesUbe3a expressionLociUniparental disomyProtein levelsAS region
1995
Mek MAPK/Erk kinase (vertebrates) (MAP kinase kinase, MAPKK)
Erikson R, Alessandrini A, Crews C. Mek MAPK/Erk kinase (vertebrates) (MAP kinase kinase, MAPKK). 1995, 275-277. DOI: 10.1016/b978-012324719-3/50085-6.Peer-Reviewed Original ResearchMAPK/ERK kinaseMAP kinaseERK kinaseReversible protein phosphorylationAmino acid sequenceRelated gene productsMEK1/MEK2Microtubule-associated proteinsOutside vertebratesPhosphorylation eventsERK2 geneProtein phosphorylationKinase domainRaf-1MEK kinaseGene productsAcid sequenceTyrosine residuesFusion proteinKinaseMouse tissuesExogenous substratesByr1MEKProtein
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