2024
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders
Lee A, Ayers L, Kosicki M, Chan W, Fozo L, Pratt B, Collins T, Zhao B, Rose M, Sanchis-Juan A, Fu J, Wong I, Zhao X, Tenney A, Lee C, Laricchia K, Barry B, Bradford V, Jurgens J, England E, Lek M, MacArthur D, Lee E, Talkowski M, Brand H, Pennacchio L, Engle E. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. Nature Communications 2024, 15: 8268. PMID: 39333082, PMCID: PMC11436875, DOI: 10.1038/s41467-024-52463-7.Peer-Reviewed Original ResearchConceptsNon-coding variantsCranial motor neuronsMendelian disordersIn vivo transgenic assayPredictor of enhancer activityCis-regulatory elementsMulti-omic frameworkWhole-genome sequencingEnhanced activityVariant discoveryGenome sequenceChromatin accessibilityPutative enhancersHistone modificationsRegulatory elementsGene expression assaysGene predictionTransgenic assaysEpigenomic profilingMendelian casesExpression assaysMutational enhancementCongenital cranial dysinnervation disordersCell typesFunctional impact
2023
SLC26A1 is a major determinant of sulfate homeostasis in humans
Pfau A, López-Cayuqueo K, Scherer N, Wuttke M, Wernstedt A, Fassrainer D, Smith D, van de Kamp J, Ziegeler K, Eckardt K, Luft F, Aronson P, Köttgen A, Jentsch T, Knauf F. SLC26A1 is a major determinant of sulfate homeostasis in humans. Journal Of Clinical Investigation 2023, 133: e161849. PMID: 36719378, PMCID: PMC9888379, DOI: 10.1172/jci161849.Peer-Reviewed Original ResearchConceptsSulfate homeostasisIntervertebral disc disordersWhole-exome sequencingMajor determinantBack painPatient presentingMusculoskeletal healthDisc disordersPlasma sulfateSulfate reabsorptionFunctional expression assaysCartilage healthHomozygous mutationPotential targetPopulation studiesNumerous physiological processesRecent evidenceExome analysisHomeostasisHyposulfatemiaExpression assaysPivotal roleClinical geneticsAdditional variantsHumans
2020
Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency
Chu JH, Zang W, Vukmirovic M, Yan X, Adams T, DeIuliis G, Hu B, Mihaljinec A, Schupp JC, Becich MJ, Hochheiser H, Gibson KF, Chen ES, Morris A, Leader JK, Wisniewski SR, Zhang Y, Sciurba FC, Collman RG, Sandhaus R, Herzog EL, Patterson KC, Sauler M, Strange C, Kaminski N. Gene coexpression networks reveal novel molecular endotypes in alpha-1 antitrypsin deficiency. Thorax 2020, 76: 134-143. PMID: 33303696, PMCID: PMC10794043, DOI: 10.1136/thoraxjnl-2019-214301.Peer-Reviewed Original ResearchConceptsWeighted gene co-expression network analysisAlpha-1 antitrypsin deficiencyGene modulesGene co-expression network analysisDifferential gene expression analysisCo-expression network analysisPeripheral blood mononuclear cellsGene expression patternsPBMC gene expression patternsGene coexpression networksAATD individualsGene expression profilesGene expression analysisBronchoalveolar lavageAugmentation therapyClinical variablesAntitrypsin deficiencyGene expression assaysRNA-seqCoexpression networkGene validationExpression analysisExpression assaysWGCNA modulesExpression patterns
2016
Risk Stratification of Newly Diagnosed Prostate Cancer with Genomic Platforms
Leapman M, Carroll P. Risk Stratification of Newly Diagnosed Prostate Cancer with Genomic Platforms. Urology Practice 2016, 4: 322-328. PMID: 37592678, DOI: 10.1016/j.urpr.2016.06.008.Peer-Reviewed Original Research
2015
Isolation and characterization of a poplar d-type cyclin gene associated with the SHORT-ROOT/SCARECROW network
Xu M, Liu S, Xuan L, Huang M, Wang Z. Isolation and characterization of a poplar d-type cyclin gene associated with the SHORT-ROOT/SCARECROW network. Trees 2015, 30: 255-263. DOI: 10.1007/s00468-015-1296-y.Peer-Reviewed Original ResearchAdventitious root developmentRegulatory networksCyclin genesProtoplast transient expression assaysRoot developmentD-type cyclin genesRoot radial patterningGFP fusion proteinBiomolecular fluorescence complementationTransient expression assaysCortex cell layersD-type cyclinsRoot patterningArabidopsis rootsFluorescence complementationRadial patterningCell specificationModel organismsCycle genesDaughter cellsExpression assaysKey regulatorFusion proteinGenesPericlinal divisions
2010
Multi-targeted priming for genome-wide gene expression assays
Adomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP. Multi-targeted priming for genome-wide gene expression assays. BMC Genomics 2010, 11: 477. PMID: 20716356, PMCID: PMC3091673, DOI: 10.1186/1471-2164-11-477.Peer-Reviewed Original ResearchMeSH KeywordsDNA PrimersGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalMetabolic Networks and PathwaysMyceliumNeurospora crassaNitrogenOligonucleotide Array Sequence AnalysisReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionReverse TranscriptionRNA, FungalRNA, MessengerSaccharomyces cerevisiaeSequence Analysis, RNAConceptsGene expressionGene expression assaysNeurospora crassaRibosomal RNAExpression assaysMost protein-coding genesEarly sexual developmentGenome-wide gene expressionTransfer RNA genesProtein-coding genesNitrogen starvation responseGenome of SaccharomycesPreponderance of genesGlobal gene expressionResponse of SaccharomycesCommon sequence motifsSexual developmentDetailed expression profilesReverse transcriptionRNA genesStarvation responseTag sequencingSequence motifsTransfer RNATranscriptomic assays
2003
Genetic Variability at the Human FMO1 Locus: Significance of a Basal Promoter Yin Yang 1 Element Polymorphism (FMO1*6)
Hines R, Luo Z, Hopp K, Cabacungan E, Koukouritaki S, McCarver D. Genetic Variability at the Human FMO1 Locus: Significance of a Basal Promoter Yin Yang 1 Element Polymorphism (FMO1*6). Journal Of Pharmacology And Experimental Therapeutics 2003, 306: 1210-1218. PMID: 12829732, DOI: 10.1124/jpet.103.053686.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsFlavin-containing monooxygenasesGenetic variabilityIntron 1 splice donor siteElectrophoretic mobility shift assaysYin Yang 1 (YY1) transcription factorTransient expression assaysCore binding sequenceATG start codonMobility shift assaysSplice donor siteCommon single nucleotide polymorphismsYY1 bindingStructural geneTranscription factorsStart codonShift assaysExonic sequencesChromosome 1q23Binding sequenceExpression assaysPromoter activityVariety of toxicantsBase pairsNucleotide polymorphisms
2000
Activation of human γ-globin gene expression via triplex-forming oligonucleotide (TFO)-directed mutations in the γ-globin gene 5′ flanking region
Xu X, Glazer P, Wang G. Activation of human γ-globin gene expression via triplex-forming oligonucleotide (TFO)-directed mutations in the γ-globin gene 5′ flanking region. Gene 2000, 242: 219-228. PMID: 10721715, DOI: 10.1016/s0378-1119(99)00522-3.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBinding SitesCell LineDNADNA-Binding ProteinsGene Expression RegulationGlobinsHeLa CellsHost Cell Factor C1HumansK562 CellsMolecular Sequence DataMutagenesis, Site-DirectedMutationOctamer Transcription Factor-1OligonucleotidesProtein BindingRegulatory Sequences, Nucleic AcidTranscription FactorsTumor Cells, CulturedConceptsGamma-globin gene expressionGamma-globin geneGene expressionHuman γ-globin gene expressionVivo gene expression assaysΓ-globin gene expressionGenetic diseasesAgamma-globin geneMouse erythroleukemia cellsTarget gene expressionTarget siteBeta-globin disordersFetal hemoglobin (HPFH) conditionBeta-globin geneSingle base changeGene expression assaysProtein binding assaysTranscription factorsHuman normal fibroblast cellsDNA sequencing analysisCommon genetic diseaseFlanking regionsExpression assaysErythroleukemia cellsTriplex-forming oligonucleotides
1995
In vitro binding and functional studies comparing the human CYPIAI negative regulatory element with the orthologous sequences from rodent genes
Boucher P, Hines R. In vitro binding and functional studies comparing the human CYPIAI negative regulatory element with the orthologous sequences from rodent genes. Carcinogenesis 1995, 16: 383-392. PMID: 7859371, DOI: 10.1093/carcin/16.2.383.Peer-Reviewed Original ResearchConceptsNegative regulatory elementSpecific DNA-protein complexesDNA-protein complexesTransient expression assaysRegulatory elementsNuclear proteinsMouse fragmentsHeterologous promoterExpression assaysCell linesElectrophoretic mobility shift assaysMouse nuclear proteinMouse CYP1A1 geneSouthwestern blot analysisMobility shift assaysCYP1A1 geneNegative regulatory activitySimilar protection patternMouse hepatoma cell lineRodent cell linesCytosine-rich sequencesCytosine-rich regionsHuman CYP1A1 geneOrthologous sequencesRodent genes
1993
Targeted mutagenesis of simian virus 40 DNA mediated by a triple helix-forming oligonucleotide
Havre P, Glazer P. Targeted mutagenesis of simian virus 40 DNA mediated by a triple helix-forming oligonucleotide. Journal Of Virology 1993, 67: 7324-7331. PMID: 8230456, PMCID: PMC238196, DOI: 10.1128/jvi.67.12.7324-7331.1993.Peer-Reviewed Original ResearchConceptsTriple helix-forming oligonucleotidesTarget genesTranscription factor accessViral genomeTransient expression assaysSimian virus 40 DNASequence-specific mannerDNA sequence analysisGene functionFactor accessMammalian cellsGenetic manipulationHomopurine/homopyrimidineTargeted base pairsPromoter sitesTriple-helical DNAExpression assaysGenetic engineeringGene expressionTargeted mutationsSequence analysisMutagenesisHeritable effectsSV40 DNAGenome
1985
Synthesis of Predominantly Unspliced Cytoplasmic RNAs by Chimeric Herpes Simplex Virus Type 1 Thymidine Kinase-Human β-Globin Genes
Greenspan D, Weissman S. Synthesis of Predominantly Unspliced Cytoplasmic RNAs by Chimeric Herpes Simplex Virus Type 1 Thymidine Kinase-Human β-Globin Genes. Molecular And Cellular Biology 1985, 5: 1894-1900. DOI: 10.1128/mcb.5.8.1894-1900.1985.Peer-Reviewed Original Research
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