2025
Aberrant splicing exonizes C9orf72 repeat expansion in ALS/FTD
Yang S, Wijegunawardana D, Sheth U, Veire A, Salgado J, Arab T, Agrawal M, Zhou J, Pereira J, Gendron T, Guo J. Aberrant splicing exonizes C9orf72 repeat expansion in ALS/FTD. Nature Neuroscience 2025, 1-10. PMID: 40790269, DOI: 10.1038/s41593-025-02039-5.Peer-Reviewed Original ResearchSerine/arginine-rich splicing factor 1Nucleotide repeat expansionsSpliced isoformsDipeptide repeat (DPR) proteinsRepeat expansionAlternative 5' splice sitesCytoplasmic translation machineryAberrant splicing isoformsPatient-derived fibroblastsSplicing factor 1Amyotrophic lateral sclerosisFrontotemporal dementiaC9orf72 repeat expansionPathogen transcriptsRNA segmentsTranslation machinerySplice siteC9-ALS/FTDAberrant splicingExon 1Antisense oligonucleotidesRNAFactor 1IsoformsLateral sclerosis
2024
Mice deficient in TWIK-1 are more susceptible to kainic acid-induced seizures
Kim A, Bae Y, Gadhe C, Jung H, Yang E, Kim H, Lee J, Shim C, Sung Y, Noh J, Kim E, Kang D, Pae A, Hwang E, Park J. Mice deficient in TWIK-1 are more susceptible to kainic acid-induced seizures. IScience 2024, 28: 111587. PMID: 39811670, PMCID: PMC11732521, DOI: 10.1016/j.isci.2024.111587.Peer-Reviewed Original Research
2022
Functional elements of the cis-regulatory lincRNA-p21
Winkler L, Jimenez M, Zimmer JT, Williams A, Simon MD, Dimitrova N. Functional elements of the cis-regulatory lincRNA-p21. Cell Reports 2022, 39: 110687. PMID: 35443176, PMCID: PMC9118141, DOI: 10.1016/j.celrep.2022.110687.Peer-Reviewed Original ResearchConceptsGene expression controlFull-length transcriptionDNA regulatory elementsCell cycle genesCDKN1A/p21P53-dependent expressionFunctional elementsChromatin organizationLncRNA lociNascent transcriptionRegulatory lociExpression controlCycle genesLncRNA transcriptsRegulatory elementsMolecular mechanismsTranscriptionExon 1LincRNA-p21LociP21 expressionGenetic modelsAccumulationExpressionSplicing
2016
T Cell Receptor Mediated Calcium Entry Requires Alternatively Spliced Cav1.1 Channels
Matza D, Badou A, Klemic KG, Stein J, Govindarajulu U, Nadler MJ, Kinet JP, Peled A, Shapira OM, Kaczmarek LK, Flavell RA. T Cell Receptor Mediated Calcium Entry Requires Alternatively Spliced Cav1.1 Channels. PLOS ONE 2016, 11: e0147379. PMID: 26815481, PMCID: PMC4729531, DOI: 10.1371/journal.pone.0147379.Peer-Reviewed Original Research
2011
Striatal-Enriched Protein Tyrosine Phosphatase Expression and Activity in Huntington's Disease: A STEP in the Resistance to Excitotoxicity
Saavedra A, Giralt A, Rué L, Xifró X, Xu J, Ortega Z, Lucas JJ, Lombroso PJ, Alberch J, Pérez-Navarro E. Striatal-Enriched Protein Tyrosine Phosphatase Expression and Activity in Huntington's Disease: A STEP in the Resistance to Excitotoxicity. Journal Of Neuroscience 2011, 31: 8150-8162. PMID: 21632937, PMCID: PMC3472648, DOI: 10.1523/jneurosci.3446-10.2011.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBrainCalcineurinCell DeathDisease Models, AnimalGene Expression RegulationGene Products, tatHuntingtin ProteinHuntington DiseaseMiceMice, Neurologic MutantsMice, TransgenicMicroinjectionsNerve Tissue ProteinsNuclear ProteinsPhosphorylationProtein Tyrosine Phosphatases, Non-ReceptorQuinolinic AcidSignal TransductionConceptsStriatal-enriched protein tyrosine phosphataseCell deathSTEP expressionPhosphorylation levelsProtein Tyrosine Phosphatase ExpressionProtein tyrosine phosphataseSTEP phosphorylationTyrosine phosphataseProtein kinasePhosphorylated ERK2Phosphatase expressionHuntington's diseaseSTEP proteinMutant huntingtinCalcineurin activityPhosphorylationExon 1STEP protein levelsDisease mouse modelProtein levelsMouse modelMouse striatumTAT-STEPHuntington's disease mouse modelExpressionAnalysis of the Oxidative Damage Repair Genes NUDT1, OGG1, and MUTYH in Patients from Mismatch Repair Proficient HNPCC Families (MSS-HNPCC)
Garre P, Briceño V, Xicola RM, Doyle BJ, de la Hoya M, Sanz J, Llovet P, Pescador P, Puente J, Díaz-Rubio E, Llor X, Caldés T. Analysis of the Oxidative Damage Repair Genes NUDT1, OGG1, and MUTYH in Patients from Mismatch Repair Proficient HNPCC Families (MSS-HNPCC). Clinical Cancer Research 2011, 17: 1701-1712. PMID: 21355073, DOI: 10.1158/1078-0432.ccr-10-2491.Peer-Reviewed Original ResearchMeSH KeywordsCase-Control StudiesColorectal Neoplasms, Hereditary NonpolyposisDisease-Free SurvivalDNA DamageDNA GlycosylasesDNA Mismatch RepairDNA Repair EnzymesFemaleGene DosageGene FrequencyGenetic Association StudiesGenotypeHumansMaleMiddle AgedMutation, MissenseOxidation-ReductionPhosphoric Monoester HydrolasesPoint MutationRestriction MappingSequence Analysis, DNAConceptsRepair pathwaysOxidative DNA damageMajor DNA repair pathwaysDNA damageBase excision repair pathwayAmino acid conservationDNA repair pathwaysExcision repair pathwayRare variantsSplicing alterationsBER pathwayI familySplicing donorMolecular differencesTransversion mutationsExon 1OGG1Mutational screeningCancer susceptibilityPathwayNUDT1Segregation studiesMutationsSilico programsCommon polymorphisms
2008
An 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 mutationsA GC Box Element Is Critical for Transcriptional Regulation of the K-Cl Cotransporter Isoform KCC3a in Hematopoetic Cells.
Crable S, Joiner C, Gallagher P. A GC Box Element Is Critical for Transcriptional Regulation of the K-Cl Cotransporter Isoform KCC3a in Hematopoetic Cells. Blood 2007, 110: 1712. DOI: 10.1182/blood.v110.11.1712.1712.Peer-Reviewed Original ResearchUntranslated sequenceInitiator methionineErythroid cellsNovel transcriptsPromoter activityExon 1Cell RNATerminal truncationExon 1DTrans-regulatory factorsMajor splicing isoformsPotential phosphorylation sitesErythroid K562 cellsGC-box elementsFull promoter activityPrimer extension analysisTranslation initiation siteLate erythroid cellsFurther deletion analysisVolume regulationKCl cotransporterLuciferase promoter constructsBone marrow RNATranscriptional regulationEST databaseA Novel CaV1.2 N Terminus Expressed in Smooth Muscle Cells of Resistance Size Arteries Modifies Channel Regulation by Auxiliary Subunits*
Cheng X, Liu J, Asuncion-Chin M, Blaskova E, Bannister J, Dopico A, Jaggar J. A Novel CaV1.2 N Terminus Expressed in Smooth Muscle Cells of Resistance Size Arteries Modifies Channel Regulation by Auxiliary Subunits*. Journal Of Biological Chemistry 2007, 282: 29211-29221. PMID: 17699517, PMCID: PMC2276565, DOI: 10.1074/jbc.m610623200.Peer-Reviewed Original ResearchConceptsExon 1cN-terminusExon 1bAuxiliary subunitsRich N-terminusCysteine-rich N-terminusNovel alternative splicingResistance-size cerebral arteriesPlasma membrane insertionExon 1Arterial myocytesMultiple vascular functionsIsoform-dependent differencesWhole-cell current densityN-terminal variantsAlternative splicingMembrane insertionChannel regulationExon 1AMolecular identityHuman diseasesSubunitsTerminusEntry pathwaySmooth muscle cells
2006
Alternative Splicing within Exon 1 of the KCl Cotransporter-3 (KCC3) Gene Results in Novel Transcripts in Erythroid Cells.
Joiner C, Crable S, Gallagher P. Alternative Splicing within Exon 1 of the KCl Cotransporter-3 (KCC3) Gene Results in Novel Transcripts in Erythroid Cells. Blood 2006, 108: 1564. DOI: 10.1182/blood.v108.11.1564.1564.Peer-Reviewed Original ResearchUntranslated sequenceNovel transcriptsInitiator methionineErythroid cellsAlternative splicingPromoter activityExon 1Cell RNATerminal truncationPotential phosphorylation sitesMajor splicing isoformsErythroid K562 cellsPrimer extension analysisTranslation initiation siteVolume regulationNegative regulatory elementKCl cotransporterLuciferase promoter constructsBone marrow RNAEST databaseTranscriptional controlGenomic regionsPhosphorylation sitesSplicing isoformsDifferent transcripts
2005
Chicken TAP genes differ from their human orthologues in locus organisation, size, sequence features and polymorphism
Walker B, van Hateren A, Milne S, Beck S, Kaufman J. Chicken TAP genes differ from their human orthologues in locus organisation, size, sequence features and polymorphism. Immunogenetics 2005, 57: 232-247. PMID: 15900495, DOI: 10.1007/s00251-005-0786-2.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAnimalsATP-Binding Cassette TransportersBase SequenceCell LineChickensChromosome MappingConserved SequenceDNA, ComplementaryExonsGenes, MHC Class IHaplotypesInterferon-gammaMajor Histocompatibility ComplexMolecular Sequence DataPolymorphism, GeneticPolymorphism, Single-Stranded ConformationalPromoter Regions, GeneticRecombinant ProteinsRNA, MessengerSequence Homology, Amino AcidSpecies SpecificityUp-RegulationConceptsTAP genesClass I genesSequence featuresI geneTranscription Factor Binding SitesProtein sequence featuresLevel of polymorphismFactor binding sitesChicken major histocompatibility complexEndoplasmic reticulum retentionBi-directional promoterClass I gene promoterInbred lines of chickensGene sizeGene structureBind ATPHuman orthologueProcessing genesExon 1Tapasin bindingHeterodimer formationTransporters associated with antigen processing genesLines of chickensHuman TAPInbred lines
2004
Sequences Downstream of the Erythroid Promoter Promote High-Level Expression of the Human α-Spectrin Gene by Providing Boundary Activity and Positive Regulatory Elements.
Gallagher P, Nilson D, Lin J, Bodine D. Sequences Downstream of the Erythroid Promoter Promote High-Level Expression of the Human α-Spectrin Gene by Providing Boundary Activity and Positive Regulatory Elements. Blood 2004, 104: 1572. DOI: 10.1182/blood.v104.11.1572.1572.Peer-Reviewed Original ResearchPositive regulatory elementGATA-1 sitesAγ-globin geneRegulatory elementsIntron 1Exon 1Gene expressionLuc activitySplice siteGATA-1 activityErythroid-specific expressionHypersensitive site mappingΒ-globin promoterΑ-spectrin geneK562 cellsTransient transfection assaysMutant exon 1Γ-globin proteinMouse linesHigh-level expressionChromatin modificationsChromatin Remodeling of the Mouse AHSP Gene Requires EKLF.
Pilon A, Wong C, Garrett-Beal L, Weiss M, Gallagher P, Bodine D. Chromatin Remodeling of the Mouse AHSP Gene Requires EKLF. Blood 2004, 104: 375. DOI: 10.1182/blood.v104.11.375.375.Peer-Reviewed Original ResearchAlpha-Hemoglobin Stabilizing ProteinDNase I hypersensitive sitesAHSP geneAHSP gene expressionHypersensitive sitesWild typeΓ-globin mRNAFetal liver cellsHistone H3Human γ-globin genesGene expressionStrong DNase I hypersensitive siteIntron 1Wild-type chromatinChromatin Remodeling ComplexErythroid-specific proteinΓ-globin genePutative promoter sequencesTranscription factor EKLFExon 1Non-coding exonsΑ-globin mRNAPosition-independent expressionMRNA initiation siteRNase protection analysis
2001
Rapid, Efficient Genotyping of Clinical Tumor Samples by Laser-Capture Microdissection/PCR/SSCP
Dillon D, Zheng K, Costa J. Rapid, Efficient Genotyping of Clinical Tumor Samples by Laser-Capture Microdissection/PCR/SSCP. Experimental And Molecular Pathology 2001, 70: 195-200. PMID: 11417998, DOI: 10.1006/exmp.2001.2362.Peer-Reviewed Original ResearchConceptsLaser capture microdissectionP53 exons 5PCR/SSCPTumor genotypingPure tumor cell populationsSSCP/sequencingSurgical pathology reportsRoutine clinical useClinical tumor samplesExon 5Colorectal adenocarcinomaTherapeutic responsePathology reportsTumor cell populationLaser-microdissected samplesClinical practiceTumor samplesClinical useSporadic mutationsExon 1Molecular analysisCell populationsDirect sequencingMutation analysisPCR productsAccelerated age-related CpG island methylation in ulcerative colitis.
Issa JP, Ahuja N, Toyota M, Bronner MP, Brentnall TA. Accelerated age-related CpG island methylation in ulcerative colitis. Cancer Research 2001, 61: 3573-7. PMID: 11325821.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAdultAge FactorsAgedCarrier ProteinsChondroitin Sulfate ProteoglycansColitis, UlcerativeColonic NeoplasmsCpG IslandsDNA MethylationGenes, p16HumansIntestinal MucosaLectins, C-TypeMiddle AgedMutL Protein Homolog 1MyoD ProteinNeoplasm ProteinsNuclear ProteinsPrecancerous ConditionsReceptors, EstrogenVersicansConceptsMechanism of geneP16 exon 1Exon 1CpG island hypermethylationCpG island methylationMethylation marksMethylation patternsUndesirable genesColorectal epithelial cellsIsland hypermethylationIsland methylationGenesMethylationPremature agingMyoDColon cancerHigh-grade dysplasiaEpithelial cellsCell turnoverHypermethylationNon-UC controlsNormal appearing epitheliumUlcerative colitisHigh levelsCSPG2
2000
Variant detection at the δ opioid receptor (OPRD1) locus and population genetics of a novel variant affecting protein sequence
Gelernter J, Kranzler H. Variant detection at the δ opioid receptor (OPRD1) locus and population genetics of a novel variant affecting protein sequence. Human Genetics 2000, 107: 86-88. PMID: 10982041, DOI: 10.1007/s004390000340.Peer-Reviewed Original ResearchConceptsPopulation geneticsProtein sequencesPopulation genetic dataAmino acid sequenceNovel variantsΔ locusAcid sequenceGenetic dataReceptor locusExon 1LociReceptor geneOpioid receptor geneCommon variantsEuropean populationsAllele frequenciesGeneticsVariant detectionSequenceAllelesOpioid dependenceVariantsPhysiologic effectsG alleleSubstance dependenceEvolution of exon 1 of the dopamine D4 receptor (DRD4) gene in primates
Seaman M, Chang F, Deinard A, Quiñones A, Kidd K. Evolution of exon 1 of the dopamine D4 receptor (DRD4) gene in primates. Journal Of Experimental Zoology 2000, 288: 32-38. PMID: 10750051, DOI: 10.1002/(sici)1097-010x(20000415)288:1<32::aid-jez4>3.0.co;2-g.Peer-Reviewed Original ResearchConceptsHigh conservationOld World monkeysWorld monkeysTandem repeatsPrimate speciesExon 1Amino acid sequenceReceptor geneGreat apesRelaxed selectionEvolutionary historyD4 receptor geneHomologous exonsInterspecific differencesNew World monkeysDopamine D4 receptor geneAcid sequenceSelective pressureFirst exonTandem duplicationExonsExon 3SpeciesGenesRepeats
1998
Somatic Inactivation of Pkd2 Results in Polycystic Kidney Disease
Wu G, D'Agati V, Cai Y, Markowitz G, Park J, Reynolds D, Maeda Y, Le T, Hou H, Kucherlapati R, Edelmann W, Somlo S. Somatic Inactivation of Pkd2 Results in Polycystic Kidney Disease. Cell 1998, 93: 177-188. PMID: 9568711, DOI: 10.1016/s0092-8674(00)81570-6.Peer-Reviewed Original ResearchConceptsCellular recessive mechanismIntragenic homologous recombinationExon 1True null alleleMutant exon 1Somatic inactivationPkd2 resultsRenal cyst formationPKD2 proteinPolycystic kidney diseaseHomologous recombinationNull allelesHuman phenotypesPKD2 expressionUnstable alleleSomatic lossPKD2Autosomal dominant polycystic kidney diseaseDominant polycystic kidney diseaseMutationsGermline mutationsRecessive mechanismAllelesInactivationCyst formation
1997
Characterization of the Exon Structure of the Polycystic Kidney Disease 2 Gene (PKD2)
Hayashi T, Mochizuki T, Reynolds D, Wu G, Cai Y, Somlo S. Characterization of the Exon Structure of the Polycystic Kidney Disease 2 Gene (PKD2). Genomics 1997, 44: 131-136. PMID: 9286709, DOI: 10.1006/geno.1997.4851.Peer-Reviewed Original ResearchConceptsAG/GT rulePolycystic kidney disease 2 (PKD2) geneExon-intron structureIntegral membrane proteinsAutosomal dominant polycystic kidney diseaseTranslation start siteExon structurePositional cloningMembrane proteinsStart siteGenomic DNASplice acceptorPKD2 geneGenesExon 1Oligonucleotide primersHeteroduplex analysisPKD2Dominant polycystic kidney diseasePolycystic kidney diseaseMutation analysisCalcium channelsCloningSecond formExons
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