2020
Global Profiling of Cellular Substrates of Human Dcp2
Luo Y, Schofield J, Simon MD, Slavoff SA. Global Profiling of Cellular Substrates of Human Dcp2. Biochemistry 2020, 59: 4176-4188. PMID: 32365300, PMCID: PMC7641959, DOI: 10.1021/acs.biochem.0c00069.Peer-Reviewed Original ResearchConceptsDecapping enzymeFirst committed stepCellular transcriptsP-bodiesRNA decayCommitted stepHuman transcriptomeMammalian cellsMolecular marksKnockout cellsGlobal profilingConsensus sequenceCellular substratesDCP2Human cellsTranscriptsEnzymeEnzyme substrateCellsDistinct subsetsTranscriptomeAdditive effectEnrichmentRNACytoplasm
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
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