2020
Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation
Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain P, Zhou H, Hodny Z, Reiter L, Liu Y. Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation. Molecular Systems Biology 2020, 16: msb199170. PMID: 32175694, PMCID: PMC7073818, DOI: 10.15252/msb.20199170.Peer-Reviewed Original ResearchConceptsProtein degradationGenome-wide correlation analysisGene dosage variationProtein abundance levelsStable isotope-labeled amino acidsIndividual protein isoformsSpecific biological processesAlternative splicing isoformsData-independent acquisition mass spectrometryIsotope-labeled amino acidsAcquisition mass spectrometryProtein degradation ratesIntron retentionCellular functionsProtein isoformsSplicing isoformsCellular organellesTranscriptome variabilitySame geneTurnover controlRegulatory mechanismsBiological processesSpecific mRNAsTight associationAbundance levels
2019
Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins
Shao W, Guo T, Toussaint N, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser C, Poyet C, Ljubicic J, Rupp N, Rüschoff J, Zhong Q, Beyer A, Ji J, Collins B, Liu Y, Rätsch G, Wild P, Aebersold R. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature Communications 2019, 10: 2524. PMID: 31175306, PMCID: PMC6555818, DOI: 10.1038/s41467-019-10513-5.Peer-Reviewed Original ResearchConceptsProtein degradationMass spectrometric methodDegradation of mRNAAnalysis of mRNASpectrometric methodStability of proteinsMass spectrometryRNA-seqIndicator of sample qualitySWATH mass spectrometryDegree of protein degradationMRNA degradationClinical sample cohortsProteomic analysisClinical tissuesProteinMRNAMolecular measurementsConfounding conclusions
2017
Impact of Alternative Splicing on the Human Proteome
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Impact of Alternative Splicing on the Human Proteome. Cell Reports 2017, 20: 1229-1241. PMID: 28768205, PMCID: PMC5554779, DOI: 10.1016/j.celrep.2017.07.025.Peer-Reviewed Original ResearchConceptsProteomic diversityAlternative splicingAlternative splicing eventsDifferential transcript usageIntron retentionSplicing eventsHuman transcriptomeHuman proteomeTranscript usageRNA sequencingProtein abundanceTranscript levelsHuman diseasesProteomeSWATH-MSSplicingQuantitative snapshotIntegrative approachCritical determinantDiversityTranscriptomeSequencingAbundanceMRNAQuantitative manner
2016
On the Dependency of Cellular Protein Levels on mRNA Abundance
Liu Y, Beyer A, Aebersold R. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell 2016, 165: 535-550. PMID: 27104977, DOI: 10.1016/j.cell.2016.03.014.Peer-Reviewed Original ResearchConceptsProtein levelsGene expression regulationCellular protein levelsLong‐term state changeGenotype-phenotype relationshipsExpression regulationMRNA fluctuationsProtein biosynthesisGenomic informationProteomic profilingTranscript levelsGene expressionBiological processesMRNA abundanceLife science researchMRNA levelsShort-term adaptationComplete understandingProtein concentrationBiosynthesisCentral importanceLocal availabilityTranscriptsTemporal variationProtein
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