2023
KidneyNetwork: using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease
Boulogne F, Claus L, Wiersma H, Oelen R, Schukking F, de Klein N, Li S, Westra H, van der Zwaag B, van Reekum F, Sierks D, Schönauer R, Li Z, Bijlsma E, Bos W, Halbritter J, Knoers N, Besse W, Deelen P, Franke L, van Eerde A. KidneyNetwork: using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease. European Journal Of Human Genetics 2023, 31: 1300-1308. PMID: 36807342, PMCID: PMC10620423, DOI: 10.1038/s41431-023-01296-x.Peer-Reviewed Original ResearchConceptsCo-expression networkTissue-specific expressionCandidate genesGene functionPhenotypic consequences of genetic variationPathogenic variantsConsequences of genetic variationInterpretation of genetic variantsGenetic causeRare variantsGene-phenotype associationsHereditary kidney diseaseExome sequencing dataDisease-associated genesGene expression dataPlausible candidate genesCandidate gene prioritizationKidney disease phenotypesUnbiased mannerCystic kidneysNovel genesGenetic variationPhenotypic consequencesGene prioritizationSequence data
2020
Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines
Cao X, Khitun A, Na Z, Dumitrescu DG, Kubica M, Olatunji E, Slavoff SA. Comparative Proteomic Profiling of Unannotated Microproteins and Alternative Proteins in Human Cell Lines. Journal Of Proteome Research 2020, 19: 3418-3426. PMID: 32449352, PMCID: PMC7429271, DOI: 10.1021/acs.jproteome.0c00254.Peer-Reviewed Original ResearchConceptsRibosome profilingHuman cell linesQuantitative mass spectrometry-based proteomicsCell linesMass spectrometry-based proteomicsLabel-free quantitative proteomicsComplex human proteomeLabel-free comparative proteomicsAlternative open reading framesStress-dependent expressionSpectrometry-based proteomicsTissue-specific expressionOpen reading frameComparative proteomic profilingUnannotated ORFsComparative proteomicsUnannotated proteinsMammalian cellsHuman proteomeQuantitative proteomicsDifferential translationReading frameProteomic profilingHuman leukemia cell linesRegulated expression
2019
Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility
Robson A, Makova SZ, Barish S, Zaidi S, Mehta S, Drozd J, Jin SC, Gelb BD, Seidman CE, Chung WK, Lifton RP, Khokha MK, Brueckner M. Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 14049-14054. PMID: 31235600, PMCID: PMC6628794, DOI: 10.1073/pnas.1808341116.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell MovementCell ProliferationChromatin Assembly and DisassemblyCiliaDisease Models, AnimalEpigenesis, GeneticGene Expression Regulation, NeoplasticHeartHeart Defects, CongenitalHistonesHumansLoss of Function MutationMiceRegulatory Factor X Transcription FactorsSignal TransductionUbiquitin-Conjugating EnzymesUbiquitin-Protein LigasesUbiquitinationXenopusConceptsHistone H2B monoubiquitinationCilia genesH2B monoubiquitinationCilia motilityFunctional gene ontologyHuman congenital heart diseaseUpstream transcriptional regulatorsTissue-specific expressionChromatin remodeling genesChromatin remodelingEpigenetic controlH2Bub1 levelsTranscriptional regulatorsChIP-seqDepletion phenotypeGene OntologyGenomic analysisTranscription factorsKnockdown resultsLeft-right asymmetryCilia functionHeart developmentH2Bub1RNF20Complex consisting
2015
Identification of Multiple Structurally Distinct, Nonpeptidic Small Molecule Inhibitors of Protein Arginine Deiminase 3 Using a Substrate-Based Fragment Method
Jamali H, Khan HA, Stringer JR, Chowdhury S, Ellman JA. Identification of Multiple Structurally Distinct, Nonpeptidic Small Molecule Inhibitors of Protein Arginine Deiminase 3 Using a Substrate-Based Fragment Method. Journal Of The American Chemical Society 2015, 137: 3616-3621. PMID: 25742366, PMCID: PMC4447334, DOI: 10.1021/jacs.5b00095.Peer-Reviewed Original ResearchConceptsProtein arginine deiminasesExhibit tissue-specific expressionTissue-specific expressionNonpeptidic small-molecule inhibitorsFamily of enzymesSmall molecule inhibitorsDistinct inhibitorsArginine residuesMolecule inhibitorsPAD inhibitorsArginine deiminasesLow molecular weightPAD3Selective inhibitorPotent inhibitorReliable discoveryInhibitorsMolecular weightFragment method
2013
Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics*
Fagerberg L, Hallström B, Oksvold P, Kampf C, Djureinovic D, Odeberg J, Habuka M, Tahmasebpoor S, Danielsson A, Edlund K, Asplund A, Sjöstedt E, Lundberg E, Szigyarto C, Skogs M, Takanen J, Berling H, Tegel H, Mulder J, Nilsson P, Schwenk J, Lindskog C, Danielsson F, Mardinoglu A, Sivertsson Å, von Feilitzen K, Forsberg M, Zwahlen M, Olsson I, Navani S, Huss M, Nielsen J, Ponten F, Uhlén M. Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics*. Molecular & Cellular Proteomics 2013, 13: 397-406. PMID: 24309898, PMCID: PMC3916642, DOI: 10.1074/mcp.m113.035600.Peer-Reviewed Original ResearchConceptsHuman protein-coding genesProtein-coding genesSpatial expression patternsTissue-specific expressionExpression patternsGenome-wide integrationIndividual gene levelAntibody-based profilingQuantitative transcriptomic analysisProtein expression dataHuman Protein AtlasMajor human organsTranscriptomic analysisHuman proteinsExpression mapProtein AtlasGene levelExpression dataHuman biologyProtein analysisGenesMolecular constituentsSame tissueRNAExpression
2011
Highly Tissue Specific Expression of Sphinx Supports Its Male Courtship Related Role in Drosophila melanogaster
Chen Y, Dai H, Chen S, Zhang L, Long M. Highly Tissue Specific Expression of Sphinx Supports Its Male Courtship Related Role in Drosophila melanogaster. PLOS ONE 2011, 6: e18853. PMID: 21541324, PMCID: PMC3082539, DOI: 10.1371/journal.pone.0018853.Peer-Reviewed Original ResearchMeSH KeywordsAnimal StructuresAnimalsBase PairingBase SequenceBrainConserved SequenceCourtshipDrosophila melanogasterFemaleGene Expression ProfilingGene Expression RegulationGenome, InsectGreen Fluorescent ProteinsMaleMolecular Sequence DataMutationOrgan SpecificityPeripheral Nervous SystemPromoter Regions, GeneticRNA, UntranslatedSexual Behavior, AnimalTransformation, GeneticConceptsDrosophila melanogasterBp regionCourtship behaviorNon-coding RNA genesWhole genome expression profilingBp upstream regionTissue-specific expressionGenome expression profilingMale courtship behaviorMale accessory glandsMelanogaster subgroupDrosophila speciesD. virilisRNA genesGene categoriesProtein functionKnockout mutationsWing hairsMale courtshipTarget genesExpression profilingGFP signalNegative regulatorEnhancer elementsExpression signals
2010
Molecular cloning and temporal–spatial expression of I element in gregarious and solitary locusts
Guo W, Wang XH, Zhao DJ, Yang PC, Kang L. Molecular cloning and temporal–spatial expression of I element in gregarious and solitary locusts. Journal Of Insect Physiology 2010, 56: 943-948. PMID: 20470781, DOI: 10.1016/j.jinsphys.2010.05.007.Peer-Reviewed Original ResearchConceptsSolitary locustsTransposable elementsAbundant transcriptsI elementsDensity-dependent polyphenismTissue-specific expressionDifferential expression patternsHigh expression levelsTranscriptome databaseTranscriptional regulationSmall RNAsMolecular cloningGenetic variationGene transcriptionTemporal-spatial expressionExpression patternsRegulatory mechanismsMigratory locustDevelopmental stagesEnvironmental changesLabial palpsElement expressionExpression levelsLocustTranscriptsMolecular characterization of two novel milk proteins in the tsetse fly (Glossina morsitans morsitans)
Yang G, Attardo GM, Lohs C, Aksoy S. Molecular characterization of two novel milk proteins in the tsetse fly (Glossina morsitans morsitans). Insect Molecular Biology 2010, 19: 253-262. PMID: 20136662, PMCID: PMC2862765, DOI: 10.1111/j.1365-2583.2009.00987.x.Peer-Reviewed Original ResearchConceptsViviparous reproductionKnockdown fliesRNA interferenceMilk protein genesTranscriptional regulation mechanismPotential phosphorylation sitesIntrauterine larval developmentRNA interference treatmentSpecific gene expressionTissue-specific expressionNovel milk proteinsSpecific expression profilesTsetse fliesHydrophobic amino acidsMajor milk proteinsNorthern blot analysisIntrauterine larvaeNovel genesPhosphorylation sitesProtein functionRT-PCR analysisTranscript abundanceProtein geneCDNA libraryGland proteins
2008
Insulator Elements in Erythrocyte Membrane Genes
Steiner L, Maksimova Y, Lin J, Owen A, Schulz V, Bodine D, Gallagher P. Insulator Elements in Erythrocyte Membrane Genes. Blood 2008, 112: 3584. DOI: 10.1182/blood.v112.11.3584.3584.Peer-Reviewed Original ResearchErythrocyte membrane protein genesPosition-effect variegationMembrane protein geneProtein geneChromatin domainsAnkyrin promoterDNA sequencesErythroid cellsInsulator elementsMapping protein-DNA interactionsHeterochromatin-mediated geneGenome-wide scaleGenomic DNA microarrayBinding of CTCFStage-specific transcriptsEnhancer-blocking functionProtein-DNA interactionsCopy number-dependent expressionTissue-specific expressionProtein gene expressionCTCF occupancyRepetitive DNAInsulator functionSeparate enhancersErythroid promoterAn insulator with barrier-element activity promotes α-spectrin gene expression in erythroid cells
Gallagher PG, Nilson DG, Steiner LA, Maksimova YD, Lin JY, Bodine DM. An insulator with barrier-element activity promotes α-spectrin gene expression in erythroid cells. Blood 2008, 113: 1547-1554. PMID: 19008453, PMCID: PMC2644083, DOI: 10.1182/blood-2008-06-164954.Peer-Reviewed Original ResearchConceptsIntron 1Erythroid cellsErythrocyte membrane protein genesExon 1Chicken HS4 insulatorGamma-globin proteinChromatin immunoprecipitation assaysEarly erythroid developmentMembrane protein geneAlpha-spectrin geneTissue-specific expressionMembrane biogenesisErythroid developmentGlobin genesHS4 insulatorImmunoprecipitation assaysProtein geneReporter geneGene expressionDevelopmental stagesGenesPromoterAdult erythrocytesExpressionSpectrin
2007
Alternate Promoters Direct Tissue-Specific Expression of Erythrocyte Ankyrin Transcripts with Novel NH2-Termini.
Steiner L, Lin J, Owens A, Sangerman J, Bodine D, Gallagher P. Alternate Promoters Direct Tissue-Specific Expression of Erythrocyte Ankyrin Transcripts with Novel NH2-Termini. Blood 2007, 110: 1710. DOI: 10.1182/blood.v110.11.1710.1710.Peer-Reviewed Original ResearchExon 1AExon 1bInitiator methionineFirst exonKb downstreamErythroid cellsNH2 terminusDNase I hypersensitive site mappingDirect tissue-specific expressionAmino acidsHypersensitive site mappingTissue-restricted patternTissue-specific expressionExon 1Alternate first exonsQuantitative RT-PCR analysisGATA-1 sitesTissue-specific promotersGene expression studiesLuciferase expressionExon 2 sequencesSkeletal muscleIsoform diversityAnkyrin repeatsAnkyrin-1 mutationsTransgenic LacZ under control of Hec-6st regulatory sequences recapitulates endogenous gene expression on high endothelial venules
Liao S, Bentley K, Lebrun M, Lesslauer W, Ruddle FH, Ruddle NH. Transgenic LacZ under control of Hec-6st regulatory sequences recapitulates endogenous gene expression on high endothelial venules. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 4577-4582. PMID: 17360566, PMCID: PMC1838643, DOI: 10.1073/pnas.0700334104.Peer-Reviewed Original ResearchConceptsDNA fragmentsTertiary lymphoid organsExpression of reporterEndogenous gene expressionBAC DNA fragmentsTissue-specific expressionBeta-galactosidase reporter geneHomologous recombination techniquesLymphoid organsLymphoid tissueEffector genesBAC clonesEndogenous genesRegulatory sequencesNasal-associated lymphoid tissueReporter geneGene expressionLacZ constructLTbetaR-Ig treatmentExon IIHEV-like vesselsGenesHigh endothelial venulesMolecular natureRecombination techniques
2003
Characterization of the Human Lung CYP2F1 Gene and Identification of a Novel Lung-specific Binding Motif*
Carr B, Wan J, Hines R, Yost G. Characterization of the Human Lung CYP2F1 Gene and Identification of a Novel Lung-specific Binding Motif*. Journal Of Biological Chemistry 2003, 278: 15473-15483. PMID: 12598524, DOI: 10.1074/jbc.m300319200.Peer-Reviewed Original ResearchConceptsCYP2F1 geneCompetitive electrophoretic mobility shift assaysBacterial artificial chromosome (BAC) clonesElectrophoretic mobility shift assaysDNA-protein complexesE-box motifArtificial chromosome clonesPrimer extension analysisTranscription start siteTissue-specific expressionDNA consensus siteMobility shift assaysTissue-specific regulationUntranslated exon 1Transient transfection studiesLuciferase reporter constructsBox motifChromosome clonesConsensus sitesE-boxNuclear proteinsStart siteExtension analysisCDNA endsUpstream sequences
1999
Cell Type‐Specific Expression of the Kv3.1 Gene Is Mediated by a Negative Element in the 5′ Untranslated Region of the Kv3.1 Promoter
Gan L, Hahn S, Kaczmarek L. Cell Type‐Specific Expression of the Kv3.1 Gene Is Mediated by a Negative Element in the 5′ Untranslated Region of the Kv3.1 Promoter. Journal Of Neurochemistry 1999, 73: 1350-1362. PMID: 10501178, DOI: 10.1046/j.1471-4159.1999.0731350.x.Peer-Reviewed Original ResearchMeSH Keywords3T3 Cells5' Untranslated RegionsAnimalsBase Sequencebeta-GalactosidaseBrainCell LineCHO CellsCloning, MolecularCricetinaeGene Expression RegulationGliomaHumansMiceMice, TransgenicMolecular Sequence DataNeuropeptidesOrgan SpecificityPC12 CellsPotassium ChannelsPotassium Channels, Voltage-GatedPromoter Regions, GeneticRatsRecombinant Fusion ProteinsRegulatory Sequences, Nucleic AcidRNA, MessengerShaw Potassium ChannelsTranscription, GeneticTransfectionConceptsType-specific expressionUntranslated regionCell type-specific enhancersCell type-specific expressionCell linesTissue-specific expressionThymidine kinase promoterCell-type specificityTransient transfection assaysKv3.1 potassium channel genePotassium channel genesKv3.1 geneDifferent tissue originsRegulatory fragmentDeletion analysisRegulatory regionsTranscriptional mechanismsTransgenic miceTransfection assaysKinase promoterFunctional analysisChannel genesType specificityPromoterGenesKsp-cadherin gene promoter. II. Kidney-specific activity in transgenic mice
Igarashi P, Shashikant C, Thomson R, Whyte D, Liu-Chen S, Ruddle F, Aronson P. Ksp-cadherin gene promoter. II. Kidney-specific activity in transgenic mice. American Journal Of Physiology 1999, 277: f599-f610. PMID: 10516285, DOI: 10.1152/ajprenal.1999.277.4.f599.Peer-Reviewed Original ResearchConceptsKsp-cadherinEscherichia coli lacZ reporter geneTissue-specific memberKsp-cadherin gene promoterRepeat-induced geneTranscriptional start siteTissue-specific expressionDifferentiation-specific expressionBeta-galactosidase enzyme activityTransgene integration sitesKidney-specific expressionLacZ reporter geneTransgenic miceEpithelial cellsKidney-specific activityStart siteRegulatory elementsGene promoterReporter genePronuclear microinjectionKb upstreamUreteric budTubular epithelial cellsDevelopmental expressionIntegration sitesA Human β-Spectrin Gene Promoter Directs High Level Expression in Erythroid but Not Muscle or Neural Cells*
Gallagher P, Sabatino D, Romana M, Cline A, Garrett L, Bodine D, Forget B. A Human β-Spectrin Gene Promoter Directs High Level Expression in Erythroid but Not Muscle or Neural Cells*. Journal Of Biological Chemistry 1999, 274: 6062-6073. PMID: 10037687, DOI: 10.1074/jbc.274.10.6062.Peer-Reviewed Original ResearchConceptsBeta-spectrin geneGene promoterHigh-level expressionGATA-1Regulatory elementsReporter geneErythroid tissuesPromoter/reporter plasmidsGel mobility shift assaysLevel expressionGATA-1 motifsFull promoter activityTissue-specific expressionMobility shift assaysAdditional regulatory elementsErythrocyte membrane proteinsHuman tissue culture cell linesTissue culture cell linesErythroid promoterMembrane proteinsShift assaysBeta spectrinHeterologous cellsCell shapeDNase I
1998
Transposon sequences drive tissue‐specific expression of the maize regulatory gene R‐s
May B, Dellaporta S. Transposon sequences drive tissue‐specific expression of the maize regulatory gene R‐s. The Plant Journal 1998, 13: 241-247. DOI: 10.1046/j.1365-313x.1998.00010.x.Peer-Reviewed Original ResearchSubterminal repeatsCACTA transposon familyEncode transcription factorsEnhancer of transcriptionTissue-specific expressionRearrangement of genesIdentical coding regionsS subcomplexGene RNew splicingR locusMicroprojectile bombardmentMinimal promoterSplicing patternsTranscription factorsAleurone cellsTransposon sequencesTransposon familyCoding regionsExpression patternsS promoterUnusual promoterAnthocyanin synthesisInitiation siteR complexes
1995
cDNA Structure, Tissue-Specific Expression, and Chromosomal Localization of the Murine Band 7.2b Gene
Gallagher P, Romana M, Lieman J, Ward D. cDNA Structure, Tissue-Specific Expression, and Chromosomal Localization of the Murine Band 7.2b Gene. Blood 1995, 86: 359-365. PMID: 7540886, DOI: 10.1182/blood.v86.1.359.bloodjournal861359.Peer-Reviewed Original ResearchConceptsTissue-specific expressionSingle membrane-spanning domainMembrane-spanning domainsBp of cDNAOpen reading frameChromosomal localizationSignificant homologyReading frameCDNA structureHuman homologueAlpha-helixProtein structureBeta sheetAmino acidsErythrocyte membranesGenesProximal regionDatabase searchingProteinSitu hybridizationCDNADistal regionWider patternsSkeletal muscleExpression
1994
Tissue-specific regulation of mouse hepatocyte nuclear factor 4 expression.
Zhong W, Mirkovitch J, Darnell J. Tissue-specific regulation of mouse hepatocyte nuclear factor 4 expression. Molecular And Cellular Biology 1994, 14: 7276-7284. PMID: 7523862, PMCID: PMC359262, DOI: 10.1128/mcb.14.11.7276.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBasic Helix-Loop-Helix Leucine Zipper Transcription FactorsBinding SitesDeoxyribonuclease IDNA ProbesDNA-Binding ProteinsGene Expression RegulationHepatocyte Nuclear Factor 4KidneyLiverLiver Neoplasms, ExperimentalMiceMice, TransgenicMolecular Sequence DataPhosphoproteinsPromoter Regions, GeneticRNATissue DistributionTranscription FactorsTransfectionTumor Cells, CulturedConceptsTransient transfection assaysLiver-enriched transcription factorsHNF-4HNF-4 geneLiver-specific expressionTranscription factorsPresence of DNase I-hypersensitive sitesHNF-1 binding siteDNase I hypersensitive sitesHepatocyte nuclear factor 4Distal enhancer elementsDNase hypersensitive sitesHepatoma-specific expressionSteroid hormone receptor superfamilyHNF-4 expressionTissue-specific expressionHNF-1 alphaHormone receptor superfamilyExpression of HNF-4RNA startDNA elementsEnhancer elementsHNF-1Promoter regionReporter constructsTissue-Specific Regulation of Mouse Hepatocyte Nuclear Factor 4 Expression
Zhong W, Mirkovitch J, Darnell J. Tissue-Specific Regulation of Mouse Hepatocyte Nuclear Factor 4 Expression. Molecular And Cellular Biology 1994, 14: 7276-7284. DOI: 10.1128/mcb.14.11.7276-7284.1994.Peer-Reviewed Original ResearchTransient transfection assaysLiver-enriched transcription factorsHNF-4HNF-4 geneLiver-specific expressionTranscription factorsPresence of DNase I-hypersensitive sitesHNF-1 binding siteDNase I hypersensitive sitesHepatocyte nuclear factor 4RNA start siteDistal enhancer elementsDNase hypersensitive sitesHepatoma-specific expressionSteroid hormone receptor superfamilyHNF-4 expressionTissue-specific expressionHormone receptor superfamilyExpression of HNF-4DNA elementsStart siteEnhancer elementsHNF-1Promoter regionHNF-1A
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