2019
Proteomic Detection and Validation of Translated Small Open Reading Frames
Khitun A, Slavoff SA. Proteomic Detection and Validation of Translated Small Open Reading Frames. Current Protocols In Chemical Biology 2019, 11: e77. PMID: 31750990, PMCID: PMC6878975, DOI: 10.1002/cpch.77.Peer-Reviewed Original ResearchConceptsSiRNA-based silencingSmall open reading framesNon-AUG start codonsOpen reading frameStandard proteomic methodsSpecific transcript isoformsCultured human cellsUnique tryptic peptidesGenomic lociShorter proteinTranscript isoformsProtein databaseProteomic methodsNovel regulatorReading frameProteomic detectionStart codonFunctional characterizationMass spectrometry-based detectionComplete annotationSmall proteinsHuman cellsTryptic peptidesProtein extractionSmORFs
2015
Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry
Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD. Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. Molecular Cell 2015, 59: 858-866. PMID: 26340425, PMCID: PMC4560836, DOI: 10.1016/j.molcel.2015.07.023.Peer-Reviewed Original ResearchConceptsDynamic transcriptome analysisReversible covalent chemistryGlobal miRNA levelsMiRNA processing machineryTissue-specific transcriptionCovalent chemistryCultured human cellsChemical methodsImproved chemistryRNA turnoverRNA populationsTranscriptome analysisMethanethiosulfonate reagentsProcessing machineryHuman cellsHPDP-biotinHigh yieldsDisulfide bondsChemistryMiRNA levelsRNADifferent populationsTurnoverBondsReagents
2013
Arterial territory-specific phosphorylated retinoblastoma protein species and CDK2 promote differences in the vascular smooth muscle cell response to mitogens
Lange M, Fujikawa T, Koulova A, Kang S, Griffin M, Lassaletta A, Erat A, Tobiash E, Bianchi C, Elmadhun N, Sellke F, Usheva A. Arterial territory-specific phosphorylated retinoblastoma protein species and CDK2 promote differences in the vascular smooth muscle cell response to mitogens. Cell Cycle 2013, 13: 315-323. PMID: 24240190, PMCID: PMC3906247, DOI: 10.4161/cc.27056.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell MovementCell ProliferationCoronary VesselsCulture Media, Serum-FreeCyclin-Dependent Kinase 2Cyclin-Dependent Kinase 4Cyclin-Dependent Kinase Inhibitor p15Gene Knockdown TechniquesHumansMaleMammary ArteriesMitogensMyocytes, Smooth MusclePhosphorylationPrimary Cell CultureRetinoblastoma ProteinSerumSwineYY1 Transcription FactorConceptsCyclin-dependent kinase 2Internal mammary arteryCoronary artery SMCsDisease resistanceRb phosphorylationRetinoblastoma tumor suppressor proteinTumor suppressor proteinMammary arteryCoronary arteryCultured human cellsVascular smooth muscle cell responsesProtein speciesPhosphorylation profileSmooth muscle cell dedifferentiationSuppressor proteinPrevalence of restenosisKinase 2Serum stimulationMolecular mechanismsSmooth muscle cell responseMuscle cell dedifferentiationHuman cellsSMC populationCause of mortalitySiRNA knockdown
2008
Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region
Jiang YH, Wauki K, Liu Q, Bressler J, Pan Y, Kashork CD, Shaffer LG, Beaudet AL. Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region. BMC Genomics 2008, 9: 50. PMID: 18226259, PMCID: PMC2268926, DOI: 10.1186/1471-2164-9-50.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAngelman SyndromeAnimalsAutoantigensChromosome BreakageChromosome DeletionChromosomes, Human, Pair 15Conserved SequenceContig MappingCpG IslandsDNA MethylationElectrophoresis, Gel, Pulsed-FieldExonsGenomic ImprintingGenomicsHumansIntronsMiceOpen Reading FramesPrader-Willi SyndromeRNA, MessengerTranscription, GeneticWiskott-Aldrich Syndrome Protein FamilyConceptsLow-copy repeatsHuman genomeAllele-specific expression patternsProtein-coding genesHuman genome sequenceComplex chromosomal regionsCoiled-coil proteinsUCSC Genome BrowserCharacterization of transcriptsPolymorphic regionSequence-based physical mapProximal breakpoint regionCultured human cellsExtensive sequence analysisCopy number variationsGenomic orientationGene organizationNovel genesCentromeric deletion breakpointGenome sequenceSubfamily proteinsGenome browserGenomic analysisPhysical mapExact protein
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