2020
Non-AUG start codons: Expanding and regulating the small and alternative ORFeome
Cao X, Slavoff SA. Non-AUG start codons: Expanding and regulating the small and alternative ORFeome. Experimental Cell Research 2020, 391: 111973. PMID: 32209305, PMCID: PMC7256928, DOI: 10.1016/j.yexcr.2020.111973.Peer-Reviewed Original ResearchConceptsSmall open reading framesFunctional small open reading framesStart codonClasses of genesImportant biological processesNon-AUG start codonsOpen reading frameNon-AUG codonsStart codon usageAUG start codonEukaryotic genomesGenomic toolsRibosome profilingNovel genesCodon usageReading frameProteomic studiesBiological processesSequence propertiesCodonGenesPresence of thousandsEukaryotesProkaryotes
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
The Discovery of Human sORF‐Encoded Polypeptides (SEPs) in Cell Lines and Tissue
Ma J, Ward C, Jungreis I, Slavoff S, Schwaid A, Neveu J, Budnik B, Kellis M, Saghatelian A. The Discovery of Human sORF‐Encoded Polypeptides (SEPs) in Cell Lines and Tissue. The FASEB Journal 2015, 29 DOI: 10.1096/fasebj.29.1_supplement.567.21.Peer-Reviewed Original ResearchShort open reading framesNon-AUG start codonsOpen reading frameCell linesHuman genomeMammalian cellsReading frameStart codonAdditional cell linesPolypeptide productsMolecular biologyUbiquitous classK562 cellsGenomeProteomeHuman SEPsPolypeptideHuman tissuesNew SEPCellsCodonDiscoveryBiologyTissueLines
2014
Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue
Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A. Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue. Journal Of Proteome Research 2014, 13: 1757-1765. PMID: 24490786, PMCID: PMC3993966, DOI: 10.1021/pr401280w.Peer-Reviewed Original ResearchConceptsShort open reading framesNon-AUG start codonsOpen reading frameCell linesHuman genomeMammalian cellsReading frameStart codonAdditional cell linesPolypeptide productsMolecular biologyUbiquitous classK562 cellsGenomeProteomeHuman SEPsPolypeptideHuman tissuesNew SEPCellsCodonDiscoveryBiologyTissueLines