2019
Small open reading frames and cellular stress responses
Khitun A, Ness TJ, Slavoff SA. Small open reading frames and cellular stress responses. Molecular Omics 2019, 15: 108-116. PMID: 30810554, PMCID: PMC6662920, DOI: 10.1039/c8mo00283e.Peer-Reviewed Original ResearchConceptsSmall open reading framesOpen reading frameUpstream ORFsReading frameStress responseCellular stress responseEukaryotic cellsGenome annotationCellular homeostasisDownstream cistronEvolutionary spaceFunctional polypeptidesAmino acidsEukaryotesSmORFsPolypeptideProkaryotesGenomeCistronGenomicsORFRecent advancesProteomicsFootprintingRegulator
2018
The translation of non-canonical open reading frames controls mucosal immunity
Jackson R, Kroehling L, Khitun A, Bailis W, Jarret A, York AG, Khan OM, Brewer JR, Skadow MH, Duizer C, Harman CCD, Chang L, Bielecki P, Solis AG, Steach HR, Slavoff S, Flavell RA. The translation of non-canonical open reading frames controls mucosal immunity. Nature 2018, 564: 434-438. PMID: 30542152, PMCID: PMC6939389, DOI: 10.1038/s41586-018-0794-7.Peer-Reviewed Original ResearchConceptsNon-canonical open reading framesOpen reading frameProtein-coding genomeReading frameNew open reading framesProtein-coding genesNon-protein codingNon-coding RNAsUnbiased transcriptomics approachTranscriptomic approachMethionine codonDistinct proteinsFunctional proteinsImportant transcriptsEssential roleGenomeAbsolute requirementGenesRNABacterial infectionsProteinaceous productsProteinTranslationMisannotationsCodon
2017
Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli
D’Lima N, Khitun A, Rosenbloom AD, Yuan P, Gassaway BM, Barber KW, Rinehart J, Slavoff SA. Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli. Journal Of Proteome Research 2017, 16: 3722-3731. PMID: 28861998, PMCID: PMC5647875, DOI: 10.1021/acs.jproteome.7b00419.Peer-Reviewed Original ResearchConceptsCold shock proteinsComparative proteomicsShock proteinsRelated Gram-negative bacteriaMass spectrometry-based proteomicsSmall open reading framesMolecular genetic approachesWhole genome databaseSpectrometry-based proteomicsOpen reading frameE. coliEukaryotic genomesGram-negative bacteriaCellular functionsDifferent organismsGenetic approachesReading frameBiological roleProteomicsMicroproteinsEnable identificationProteinColiGenomeRecent advances
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
2013
Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames
Schwaid AG, Shannon DA, Ma J, Slavoff SA, Levin JZ, Weerapana E, Saghatelian A. Chemoproteomic Discovery of Cysteine-Containing Human Short Open Reading Frames. Journal Of The American Chemical Society 2013, 135: 16750-16753. PMID: 24152191, PMCID: PMC3868496, DOI: 10.1021/ja406606j.Peer-Reviewed Original ResearchConceptsShort open reading framesOpen reading frameReading frameProtein-coding genesProtein-coding potentialGene-finding algorithmsAffinity-based approachRibosome profilingNew genesHuman proteomeMass spectrometry technologyEndogenous RNASpectrometry technologyLabeling approachGenesHuman SEPsPotential importanceInvaluable insightsExperimental approachGenomeProteomeDiscoveryRNABiologyPolypeptide