2025
Integration of metabolite and transcriptome profiles of cultivated and wild rice to unveil gene regulatory networks and key genes determining rice source and sink strength
Singh A, Mathan J, Dwivedi A, Rani R, Ranjan A. Integration of metabolite and transcriptome profiles of cultivated and wild rice to unveil gene regulatory networks and key genes determining rice source and sink strength. Functional & Integrative Genomics 2025, 25: 97. PMID: 40310586, DOI: 10.1007/s10142-025-01606-0.Peer-Reviewed Original ResearchConceptsWild rice accessionsWild riceCultivated varietiesSink strengthRice accessionsHub genesGene co-expression modulesPathways related to photosynthesisGene co-expression networksGene regulatory networksAmino acidsZinc finger proteinCo-expression modulesHigher photosynthesis rateCrop yield increasesCo-expression networkFatty acid metabolismFinger proteinRegulatory networksTranscriptional regulationTranscriptome comparisonFlag leavesPhotosynthesis ratePhotosynthetic leavesRice varieties
2022
MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression
Jaudal M, Mayo‐Smith M, Poulet A, Whibley A, Peng Y, Zhang L, Thomson G, Trimborn L, Jacob Y, van Wolfswinkel J, Goldstone D, Wen J, Mysore K, Putterill J. MtING2 encodes an ING domain PHD finger protein which affects Medicago growth, flowering, global patterns of H3K4me3, and gene expression. The Plant Journal 2022, 112: 1029-1050. PMID: 36178149, PMCID: PMC9828230, DOI: 10.1111/tpj.15994.Peer-Reviewed Original ResearchConceptsGene-edited mutantsGene expressionWinter-annual ArabidopsisWild-type plantsPlant homeodomain (PHD) fingerStrong mutant phenotypePHD finger proteinChIP-seq analysisRNA sequencing experimentsExpression of activatorsPHD fingerMutant phenotypeFinger proteinMedicago truncatulaImportant physiological roleAbnormal leavesInsertion mutantsMutant studiesEpigenetic mechanismsMost plantsSmall seedsGrowth genesKey regulatorWild typeMutants
2015
De novo pathogenic variants in CHAMP1 are associated with global developmental delay, intellectual disability, and dysmorphic facial features
Tanaka AJ, Cho MT, Retterer K, Jones JR, Nowak C, Douglas J, Jiang YH, McConkie-Rosell A, Schaefer GB, Kaylor J, Rahman OA, Telegrafi A, Friedman B, Douglas G, Monaghan KG, Chung WK. De novo pathogenic variants in CHAMP1 are associated with global developmental delay, intellectual disability, and dysmorphic facial features. Molecular Case Studies 2015, 2: a000661. PMID: 27148580, PMCID: PMC4849844, DOI: 10.1101/mcs.a000661.Peer-Reviewed Original ResearchDysmorphic facial featuresZinc finger proteinGlobal developmental delayDevelopmental delayIntellectual disabilityFinger proteinSignificant global developmental delayMicrotubule attachmentChromosome alignmentCell divisionDe novo mutationsDe novo pathogenic variantsNovo pathogenic variantsCHAMP1Phosphoprotein 1De novoNovo mutationsUnrelated individualsFunction variantsPathogenic variantsBrain developmentMutations
2008
NAC1, a POZ/BTB protein that functions as a corepressor
Korutla L, Wang P, Jackson T, Mackler S. NAC1, a POZ/BTB protein that functions as a corepressor. Neurochemistry International 2008, 54: 245-252. PMID: 19121354, DOI: 10.1016/j.neuint.2008.12.008.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineCentral Nervous SystemGenes, ReporterHumansKruppel-Like Transcription FactorsMiceNeoplasm ProteinsNerve Tissue ProteinsPromyelocytic Leukemia Zinc Finger ProteinProtein IsoformsProtein Structure, TertiaryProto-Oncogene ProteinsRecombinant Fusion ProteinsRepressor ProteinsTranscription, GeneticConceptsPOZ/BTB proteinBTB proteinsPOZ/BTB domainFusion proteinVP16 activation domainGST pulldown assaysGAL4 fusion proteinsTranscriptional repressor proteinZinc finger proteinProtein-protein interactionsB fusion proteinFinger proteinActivation domainTransient assaysNAC1 functionPulldown assaysRepressor proteinBTB domainNon-neuronal cellsTranscriptional inhibitionCorepressorNeuronal cellsProteinMature CNSSelective interaction
2006
Alterations in Expression and Chromatin Configuration of the Alpha Hemoglobin-Stabilizing Protein Gene in Erythroid Krüppel-Like Factor-Deficient Mice
Pilon AM, Nilson DG, Zhou D, Sangerman J, Townes TM, Bodine DM, Gallagher PG. Alterations in Expression and Chromatin Configuration of the Alpha Hemoglobin-Stabilizing Protein Gene in Erythroid Krüppel-Like Factor-Deficient Mice. Molecular And Cellular Biology 2006, 26: 4368-4377. PMID: 16705186, PMCID: PMC1489081, DOI: 10.1128/mcb.02216-05.Peer-Reviewed Original ResearchConceptsErythroid Krüppel-like factorAlpha-hemoglobin-stabilizing proteinWild-type chromatinAHSP promoterCACCC siteBeta-globin gene transcriptionDNase I hypersensitive sitesLocal chromatin structureZinc finger proteinBeta-globin promoterKrüppel-like factorMobility shift assaysBeta-globin geneErythroid genesCACCC sequenceChromatin modulatorsFinger proteinChromatin structureSubtractive hybridizationChromatin statusCACCC boxTranscription factorsProtein geneChromatin configurationHypersensitive sites
2000
Epsin 1 Undergoes Nucleocytosolic Shuttling and Its Eps15 Interactor Nh2-Terminal Homology (Enth) Domain, Structurally Similar to Armadillo and Heat Repeats, Interacts with the Transcription Factor Promyelocytic Leukemia Zn2+ Finger Protein (Plzf)
Hyman J, Chen H, Di Fiore P, De Camilli P, Brunger A. Epsin 1 Undergoes Nucleocytosolic Shuttling and Its Eps15 Interactor Nh2-Terminal Homology (Enth) Domain, Structurally Similar to Armadillo and Heat Repeats, Interacts with the Transcription Factor Promyelocytic Leukemia Zn2+ Finger Protein (Plzf). Journal Of Cell Biology 2000, 149: 537-546. PMID: 10791968, PMCID: PMC2174850, DOI: 10.1083/jcb.149.3.537.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Vesicular TransportAmino Acid SequenceAnimalsArmadillo Domain Proteinsbeta CateninCalcium-Binding ProteinsCarrier ProteinsCell LineCell NucleusCrystallography, X-RayCytoskeletal ProteinsCytosolDNA-Binding ProteinsDrosophila ProteinsFluorescent Antibody TechniqueInsect ProteinsModels, MolecularMolecular Sequence DataNeuropeptidesPhosphoproteinsProtein BindingRatsSequence AlignmentTrans-ActivatorsTranscription FactorsVesicular Transport ProteinsZinc FingersConceptsENTH domainFinger proteinCRM1-dependent nuclear export pathwayClathrin adaptor AP-2Nuclear export pathwayAdaptor AP-2HEAT repeatsEndocytic machineryNuclear functionsHomology domainExport pathwayLeptomycin BEpsin 1AP-2Cytosolic proteinsUnknown functionDirect interactionEpsinTerminal portionClathrinProteinArmadillosAntifungal antibioticsPathwayDomain
1998
Identification of candidate target genes for EVI-1, a zinc finger oncoprotein, using a novel selection strategy
Kim J, Hui P, Yue D, Aycock J, Leclerc C, Bjoring A, Perkins A. Identification of candidate target genes for EVI-1, a zinc finger oncoprotein, using a novel selection strategy. Oncogene 1998, 17: 1527-1538. PMID: 9794230, DOI: 10.1038/sj.onc.1202331.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAnimalsBase SequenceBinding SitesCalcium ChannelsDNA, ComplementaryDNA-Binding ProteinsEscherichia coliExonsGenomic LibraryHaploidyHumansInositol 1,4,5-Trisphosphate ReceptorsMDS1 and EVI1 Complex Locus ProteinMiceMolecular Sequence DataOncogene ProteinsProto-OncogenesReceptors, Cytoplasmic and NuclearRecombinant Fusion ProteinsSequence AlignmentTranscription FactorsTumor Cells, CulturedZinc FingersConceptsGenomic fragmentEvi-1Target genesZinc finger proteinHybrid selectionCandidate target genesTetracycline-regulated systemChimeric activatorFinger proteinHaploid genomeMouse cDNAMouse genomeGene sequencesMouse DNAFusion proteinTwo-step selectionGenesGenomeProteinCDNANovel selection strategyFragmentsHigh affinitySublibrariesITPR2
1995
Cloning of a New "Finger" Protein Gene (ZNF173) within the Class I Region of the Human MHC
Chu T, Capossela A, Coleman R, Goei V, Nallur G, Gruen J. Cloning of a New "Finger" Protein Gene (ZNF173) within the Class I Region of the Human MHC. Genomics 1995, 29: 229-239. PMID: 8530076, DOI: 10.1006/geno.1995.1236.Peer-Reviewed Original ResearchMeSH Keywordsalpha-FetoproteinsAmino Acid SequenceAnimalsBase SequenceCloning, MolecularConsensus SequenceConserved SequenceDNA, ComplementaryDNA-Binding ProteinsGene LibraryGenes, MHC Class IHominidaeHumansKidneyMajor Histocompatibility ComplexMiceMolecular Sequence DataRestriction MappingSequence Homology, Amino AcidZinc FingersConceptsFull-length cDNA cloneClass I regionHuman coding regionsPartial genomic cloneHuman MHCConceptual proteinFinger proteinGenomic clonesPositional cloningCDNA clonesCDNA sequenceProtein genePolyglutamic acid regionCarboxyl terminusI regionBiological roleCoding regionsAcid regionRelated sequencesGenesMultiple tissuesProteinMajor histocompatability complexCloningNucleic acids
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