2024
Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions
Lee P, Sun Y, Soares A, Fai C, Picciotto M, Guo J. Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions. Molecular Cell 2024, 84: 3967-3978.e8. PMID: 39317199, PMCID: PMC11490368, DOI: 10.1016/j.molcel.2024.08.032.Peer-Reviewed Original ResearchTranslation initiation siteNeuronal pentraxin receptorAUG translational initiation siteAlternative translation initiation sitesN-terminal signal sequenceN-terminal transmembrane domainRNA secondary structureAlternative translation initiationN-terminal extensionTranslation initiationSignal sequenceProtein isoformsProtein localizationAUG initiatorTransmembrane domainWidespread mechanismSecondary structureInitiation siteAlternative usageAMPA-type glutamate receptorsProteoformsSecreted factorsProteinReduced AMPA receptorMRNA
2022
MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles
He L, Gao M, Pratt H, Weng Z, Struhl K. MafB, WDR77, and ß-catenin interact with each other and have similar genome association profiles. PLOS ONE 2022, 17: e0264799. PMID: 35482762, PMCID: PMC9049301, DOI: 10.1371/journal.pone.0264799.Peer-Reviewed Original Research
2020
Global analysis of LARP1 translation targets reveals tunable and dynamic features of 5′ TOP motifs
Philippe L, van den Elzen AMG, Watson MJ, Thoreen CC. Global analysis of LARP1 translation targets reveals tunable and dynamic features of 5′ TOP motifs. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 5319-5328. PMID: 32094190, PMCID: PMC7071917, DOI: 10.1073/pnas.1912864117.Peer-Reviewed Original ResearchConceptsTOP mRNAsTerminal oligopyrimidine motifsTranslation targetsAlternative transcription initiation sitesTOP mRNA translationRNA-binding proteinSpecific biological contextMTOR complex 1Transcription initiation siteTop sequenceTranscriptome scaleTranslation regulatorsMRNA translationRegulatory sequencesTranslation factorsTOP motifGene expressionMRNA regulationBiological contextMammalian tissuesInitiation siteProtein 1TranscriptomeLARP1MRNA
2010
The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution
Kolev NG, Franklin JB, Carmi S, Shi H, Michaeli S, Tschudi C. The Transcriptome of the Human Pathogen Trypanosoma brucei at Single-Nucleotide Resolution. PLOS Pathogens 2010, 6: e1001090. PMID: 20838601, PMCID: PMC2936537, DOI: 10.1371/journal.ppat.1001090.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceGene Expression ProfilingGenome, BacterialHigh-Throughput Nucleotide SequencingHumansMolecular Sequence DataRNA Polymerase IIRNA PrecursorsRNA, BacterialSequence Homology, Nucleic AcidTranscription Initiation SiteTranscription, GeneticTrypanosoma brucei bruceiTrypanosomiasis, AfricanConceptsGene clusterNew transcriptsHigh-throughput RNA sequencingInitiation siteOrganization of genesRNA polymerase IISimilar genome organizationPutative initiation siteSingle-nucleotide resolutionTranscription initiation siteGene expression patternsPre-mRNA processingNon-coding RNAsGenome organizationPolymerase IIGenomic mapTranscription initiationInsect vectorsEukaryotic promotersMass spectrometry analysisImportant human pathogenMammalian hostsRNA sequencingTrypanosoma bruceiT. brucei
2006
Rab33A: Characterization, Expression, and Suppression by Epigenetic Modification
Cheng E, Trombetta SE, Kovacs D, Beech RD, Ariyan S, Reyes-Mugica M, McNiff JM, Narayan D, Kluger HM, Picardo M, Halaban R. Rab33A: Characterization, Expression, and Suppression by Epigenetic Modification. Journal Of Investigative Dermatology 2006, 126: 2257-2271. PMID: 16810302, DOI: 10.1038/sj.jid.5700386.Peer-Reviewed Original ResearchConceptsX chromosome-linked geneSpecific gene expressionTranscription initiation siteSpecific promoter regionsMelanoma cellsGTPase mutantsEpigenetic modificationsSmall GTPaseDNA methylationVesicular transportRab33AGene expressionPromoter regionMelanosomal proteinsInitiation siteNormal melanocytesAberrant downregulationGenesEarly eventsAberrant processesMelanocytesExpressionGTPaseImportant roleNormal process
2005
A dinucleotide deletion in the ankyrin promoter alters gene expression, transcription initiation and TFIID complex formation in hereditary spherocytosis
Gallagher PG, Nilson DG, Wong C, Weisbein JL, Garrett-Beal LJ, Eber SW, Bodine DM. A dinucleotide deletion in the ankyrin promoter alters gene expression, transcription initiation and TFIID complex formation in hereditary spherocytosis. Human Molecular Genetics 2005, 14: 2501-2509. PMID: 16037067, DOI: 10.1093/hmg/ddi254.Peer-Reviewed Original ResearchMeSH KeywordsAnkyrinsBase CompositionDNA PrimersErythrocyte MembraneGene Expression RegulationGenes, ReporterHumansPeptide Chain Initiation, TranslationalPolymerase Chain ReactionPolymorphism, Single-Stranded ConformationalPromoter Regions, GeneticSequence DeletionSpherocytosis, HereditaryTATA BoxTranscription Factor TFIIDTranscription, GeneticConceptsTFIID complex formationTATA-binding proteinTranscription initiation siteGene expressionAnkyrin promoterCis elementsInitiation siteCore promoter DNAMultiple transcription initiation sitesPreinitiation complex formationStart site utilizationComplex formationSite utilizationAlters gene expressionTFIID complexFunctional Sp1Promoter DNATranscription initiationTypes of promotersErythroid promoterMammalian promotersGene transcriptionTG deletionMutant promotersReporter gene
2001
Flanking regulatory sequences of the locus encoding the murine GDNF receptor, c‐ret, directs lac Z (β‐galactosidase) expression in developing somatosensory system
Sukumaran M, Waxman S, Wood J, Pachnis V. Flanking regulatory sequences of the locus encoding the murine GDNF receptor, c‐ret, directs lac Z (β‐galactosidase) expression in developing somatosensory system. Developmental Dynamics 2001, 222: 389-402. PMID: 11747074, DOI: 10.1002/dvdy.1192.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornBase SequenceChromosome MappingCloning, MolecularConsensus SequenceDrosophila ProteinsEmbryo, MammalianGanglia, SensoryGene ExpressionGene Expression Regulation, DevelopmentalGenes, RegulatorGlial Cell Line-Derived Neurotrophic Factor ReceptorsLac OperonLectinsMiceMice, TransgenicNeurons, AfferentNociceptorsPromoter Regions, GeneticProtein Structure, TertiaryProto-Oncogene ProteinsProto-Oncogene Proteins c-retReceptor Protein-Tyrosine KinasesSpinal CordTranscription Initiation SiteConceptsRegulatory domainLac Z expressionZ expressionCell type-specific expressionDistal regulatory domainEndogenous gene expressionCis-regulatory domainsTranscription initiation siteEntire structural geneSpecific regulatory domainsLac Z reporter geneStructural geneMouse genomeLateral mesodermRegulatory sequencesCpG islandsDNA sequencesPrimitive streakReporter geneFlanking sequencesCosmid contigGene expressionSpecific expressionTransgenic mouse lineInitiation site
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
1996
Genomic structure and regulation of Kcn1, a cGMP-gated potassium channel
Yao X, Liu Y, Tung F, Desir GV. Genomic structure and regulation of Kcn1, a cGMP-gated potassium channel. American Journal Of Physiology 1996, 271: f37-f41. PMID: 8760241, DOI: 10.1152/ajprenal.1996.271.1.f37.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsPromoter regionEnhancer elementsNovel potassium channel geneMajor transcription initiation siteTypical TATA boxTranscription initiation sitePhorbol esterPotassium channel genesLuciferase reporter constructsPotassium channelsGenomic structurePorcine kidney cell lineDeletion analysisRabbit geneTATA boxAcid proteinGene transcriptionKidney cell lineReporter constructsChannel genesSequence analysisPrimer extensionInitiation siteNorthern blot
1995
Structure, Organization, and Expression of the Human Band 7.2b Gene, a Candidate Gene for Hereditary Hydrocytosis (∗)
Gallagher P, Forget B. Structure, Organization, and Expression of the Human Band 7.2b Gene, a Candidate Gene for Hereditary Hydrocytosis (∗). Journal Of Biological Chemistry 1995, 270: 26358-26363. PMID: 7592848, DOI: 10.1074/jbc.270.44.26358.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAmino Acid SequenceAnemia, HemolyticAnimalsBase SequenceBlood ProteinsBlotting, NorthernCell LineConsensus SequenceDNA PrimersDNA, ComplementaryExonsGene ExpressionGenetic VariationHominidaeHumansIntronsLeukemia, Erythroblastic, AcuteMembrane ProteinsMiceMolecular Sequence DataPolymerase Chain ReactionPolymorphism, GeneticPromoter Regions, GeneticRecombinant Fusion ProteinsRegulatory Sequences, Nucleic AcidRestriction MappingRNA, MessengerTransfectionTumor Cells, CulturedConceptsSingle transcription initiation siteSimple sequence repeat polymorphismKilobases of DNATranscription initiation siteAlternative polyadenylation signalsFurther genetic studiesHigh-level expressionNorthern blot analysisPattern of expressionWide tissue distributionGenomic structureRich promoterNonerythroid cellsChromosomal genesPolyadenylation signalMembrane skeletonGene cDNAGene promoterReporter geneCandidate genesRecognition sequenceGenetic studiesInitiation siteGenesBase pairs
1986
Identification of a cyclic-AMP-responsive element within the rat somatostatin gene.
Montminy M, Sevarino K, Wagner J, Mandel G, Goodman R. Identification of a cyclic-AMP-responsive element within the rat somatostatin gene. Proceedings Of The National Academy Of Sciences Of The United States Of America 1986, 83: 6682-6686. PMID: 2875459, PMCID: PMC386573, DOI: 10.1073/pnas.83.18.6682.Peer-Reviewed Original ResearchConceptsRat somatostatin geneSomatostatin geneCAMP responsivenessReporter gene encoding chloramphenicolTranscriptional initiation siteProtein kinase 2Promoter deletion mutantsSimian virus 40 promoterSomatostatin gene promoterCAMP-responsive elementPC12 rat pheochromocytoma cellsKinase 2 activityGene encoding chloramphenicolTranscriptional regulationDeletion mutantsChimeric genePromoter elementsGene promoterGene expressionKinase 2Rat pheochromocytoma cellsInitiation siteResponsive elementGenesBase pairsRat growth hormone gene expression is correlated with an unmethylated CGCG sequence near the transcription initiation site.
Strobl J, Dannies P, Thompson E. Rat growth hormone gene expression is correlated with an unmethylated CGCG sequence near the transcription initiation site. Biochemistry 1986, 25: 3640-8. PMID: 3013292, DOI: 10.1021/bi00360a025.Peer-Reviewed Original ResearchConceptsTranscription initiation siteInitiation siteGene expressionRat growth hormone gene expressionMethylation-sensitive restriction enzymesRat growth hormone geneHybrid cellsGene control regionsGrowth hormone geneThai sitesGrowth hormone gene expressionGH3 cellsCGCG sequenceControl regionDNA methylationBp 5Gene regionGH geneHormone geneHormone gene expressionRestriction enzymesMethylation statusRestriction sitesMouse fibroblastsGH gene expression
1985
A wheat HMW glutenin subunit gene reveals a highly repeated structure
Sugiyama T, Rafalski A, Peterson D, Söll D. A wheat HMW glutenin subunit gene reveals a highly repeated structure. Nucleic Acids Research 1985, 13: 8729-8737. PMID: 3001648, PMCID: PMC318947, DOI: 10.1093/nar/13.24.8729.Peer-Reviewed Original ResearchConceptsTypical eukaryotic promoterWheat genomic libraryHMW glutenin subunit genesRNA initiation siteGlutenin subunit genesPartial cDNA cloneAmino acid sequenceMature proteinGenomic libraryGlutenin genesEukaryotic promotersCDNA clonesGene sequencesProline contentSubunit geneAcid sequenceGrain endospermInitiation siteQuality of wheatGenesSynthetic oligonucleotidesHigh glutamineMolecular weightProteinClones
1983
Each element of the Drosophila tRNA Arg gene split promoter directs transcription in Xenopus oocytes
Sharp S, Dingermann T, Schaack J, Sharp J, Burke D, DeRobertis E, Söll D. Each element of the Drosophila tRNA Arg gene split promoter directs transcription in Xenopus oocytes. Nucleic Acids Research 1983, 11: 8677-8690. PMID: 6561520, PMCID: PMC326616, DOI: 10.1093/nar/11.24.8677.Peer-Reviewed Original ResearchConceptsD-control regionDrosophila tRNAArg geneTRNAArg geneEukaryotic tRNA gene transcriptionXenopus oocytesRNA polymerase III transcription factorT-control regionEukaryotic tRNA genesTRNA gene transcriptionIntragenic control regionTranscription initiation siteSpecific DNA sequencesTRNA genesTranscription initiationArg genesControl regionTranscription factorsGene transcriptionDNA sequencesMutant formsOocyte nucleusSequence 5Initiation siteGenesTranscription
1977
Characterization of two mRNA · rRNA complexes implicated in the initiation of protein biosynthesis
Steitz J, Steege D. Characterization of two mRNA · rRNA complexes implicated in the initiation of protein biosynthesis. Journal Of Molecular Biology 1977, 114: 545-558. PMID: 335077, DOI: 10.1016/0022-2836(77)90177-2.Peer-Reviewed Original ResearchConceptsProtein biosynthesisEscherichia coli 16 S ribosomal RNAS ribosomal RNABase pair regionNuclease digestion studiesFragment complexAssignment of residuesRibosomal RNARRNA complexLambda PRBacteriophage lambdaMolecular understandingInitiation siteInitiation eventsStrong experimental supportMessenger RNABiosynthesisThermal denaturation studiesDenaturation studiesRNAPR transcriptsPR regionDigestion studiesMRNAComplexes
1974
Specific recognition of the isolated R17 replicase initiator region by R17 coat protein
STEITZ J. Specific recognition of the isolated R17 replicase initiator region by R17 coat protein. Nature 1974, 248: 223-225. PMID: 4819415, DOI: 10.1038/248223a0.Peer-Reviewed Original Research
1972
Oligonucleotide Sequence of Replicase Initiation Site in Qβ RNA
STEITZ J. Oligonucleotide Sequence of Replicase Initiation Site in Qβ RNA. Nature 1972, 236: 71-75. PMID: 4502455, DOI: 10.1038/newbio236071a0.Peer-Reviewed Original ResearchConceptsReplicase geneQβ RNAMajor coat proteinN-terminal sequenceCoat cistronTermination signalReplicase cistronNucleotide sequenceCoat proteinRNA genomeInitiator codonInitiation siteQβ replicaseGenesProteinBacteriophage QβCistronUGA suppressorRNAVirus particlesSequenceOligonucleotide sequencesProtein7GenomeReplicase
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