2022
mRNA 5′ terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay
van den Elzen A, Watson M, Thoreen C. mRNA 5′ terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay. PLOS Genetics 2022, 18: e1010532. PMID: 36441824, PMCID: PMC9731452, DOI: 10.1371/journal.pgen.1010532.Peer-Reviewed Original ResearchConceptsTerminal sequenceGene expressionKey post-transcriptional regulatorsTerminal oligopyrimidine motifsCore promoter motifsPost-transcriptional regulatorsPromoter motifsMRNA decayTranslation initiationRegulatory sequencesReporter mRNAEfficient transcriptionLibrary sequencesEndogenous mRNARegulatory potentialNative mRNAHuman cellsTranscriptionMRNAHybrid sequencesSequenceExpressionMotifMRNA expressionTranslation
2020
Induced pluripotent stem cell reprogramming‐associated methylation at the GABRA2 promoter and chr4p12 GABAA subunit gene expression in the context of alcohol use disorder
Goetjen A, Watson M, Lieberman R, Clinton K, Kranzler H, Covault J. Induced pluripotent stem cell reprogramming‐associated methylation at the GABRA2 promoter and chr4p12 GABAA subunit gene expression in the context of alcohol use disorder. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2020, 183: 464-474. PMID: 33029895, PMCID: PMC8022112, DOI: 10.1002/ajmg.b.32824.Peer-Reviewed Original ResearchConceptsGene expressionSubunit gene expressionSubunit geneNeural culturesInduced pluripotent stem cellsReceptor subunit genesPluripotent stem cellsStochastic methylationGene clusterDNA methylationCpG methylationMethylation levelsReceptor subunit gene expressionMethylationSignificant genetic contributionGenesStem cellsGenetic contributionMolecular effectsIPSC linesGABRB1 geneExpressionGABRA2GenotypesAdditive effectGlobal analysis of LARP1 translation targets reveals tunable and dynamic features of 5′ TOP motifs
Philippe L, van den Elzen AMG, Watson MJ, Thoreen CC. Global analysis of LARP1 translation targets reveals tunable and dynamic features of 5′ TOP motifs. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 5319-5328. PMID: 32094190, PMCID: PMC7071917, DOI: 10.1073/pnas.1912864117.Peer-Reviewed Original ResearchConceptsTOP mRNAsTerminal oligopyrimidine motifsTranslation targetsAlternative transcription initiation sitesTOP mRNA translationRNA-binding proteinSpecific biological contextMTOR complex 1Transcription initiation siteTop sequenceTranscriptome scaleTranslation regulatorsMRNA translationRegulatory sequencesTranslation factorsTOP motifGene expressionMRNA regulationBiological contextMammalian tissuesInitiation siteProtein 1TranscriptomeLARP1MRNA
2012
Prevalence of Streptococci and Increased Polymicrobial Diversity Associated with Cystic Fibrosis Patient Stability
Filkins L, Hampton T, Gifford A, Gross M, Hogan D, Sogin M, Morrison H, Paster B, O'Toole G. Prevalence of Streptococci and Increased Polymicrobial Diversity Associated with Cystic Fibrosis Patient Stability. Journal Of Bacteriology 2012, 194: 4709-4717. PMID: 22753064, PMCID: PMC3415522, DOI: 10.1128/jb.00566-12.Peer-Reviewed Original ResearchConceptsDiverse microbial communitiesHigher bacterial diversityCystic fibrosis lung environmentQuantitative PCRGenomic DNA samplesCystic fibrosis patientsMicrobial communitiesRRNA geneBacterial communitiesBacterial diversityOverall diversityTaxonomic profilesGroup speciesMicroarray analysisDominant organismsPseudomonas aeruginosaPatient stabilityPredominant generaFibrosis patientsSpeciesHypervariable regionSpecies of StreptococcusCurrent dogmaStable lung diseaseDiversity
2011
Hemolytic Phospholipase C Inhibition Protects Lung Function during Pseudomonas aeruginosa Infection
Wargo M, Gross M, Rajamani S, Allard J, Lundblad L, Allen G, Vasil M, Leclair L, Hogan D. Hemolytic Phospholipase C Inhibition Protects Lung Function during Pseudomonas aeruginosa Infection. American Journal Of Respiratory And Critical Care Medicine 2011, 184: 345-354. PMID: 21562128, PMCID: PMC3175536, DOI: 10.1164/rccm.201103-0374oc.Peer-Reviewed Original ResearchConceptsLung functionP. aeruginosa infectionAeruginosa infectionSignificant lung function impairmentLung function impairmentLung function declineBronchoalveolar lavage fluidPseudomonas aeruginosa infectionChronic lung infectionVirulence factorsP. aeruginosaP. aeruginosa virulence factorsPulmonary surfactant functionSingle virulence factorFunction declineMechanical ventilationFunction impairmentLavage fluidRespiratory endpointsSurfactant dysfunctionComputer-controlled ventilatorLung infectionAeruginosa virulence factorsStrain infectionLung physiology