2024
The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis
McCool M, Bryant C, Abriola L, Surovtseva Y, Baserga S. The cytidine deaminase APOBEC3A regulates nucleolar function to promote cell growth and ribosome biogenesis. PLOS Biology 2024, 22: e3002718. PMID: 38976757, PMCID: PMC11257408, DOI: 10.1371/journal.pbio.3002718.Peer-Reviewed Original ResearchRibosome biogenesis factorsRibosome biogenesisBiogenesis factorsCell growthNucleolar functionRegulation of nucleolar functionHuman ribosome biogenesisProtein synthesisProduction of ribosomesFamily of proteinsSource of mutagenesisLevel of protein synthesisCytidine deaminase familyIncreased cell growthPromote cell growthPre-rRNAPotential direct rolePre-mRNATransient overexpressionRibosomeGenomic mutationsBiogenesisMCF10A cellsMaturation stepsAPOBEC3ADiscovery of novel microRNA mimic repressors of ribosome biogenesis
Bryant C, McCool M, González G, Abriola L, Surovtseva Y, Baserga S. Discovery of novel microRNA mimic repressors of ribosome biogenesis. Nucleic Acids Research 2024, 52: 1988-2011. PMID: 38197221, PMCID: PMC10899765, DOI: 10.1093/nar/gkad1235.Peer-Reviewed Original Research
2023
Nucleolar structure connects with global nuclear organization.
Wang C, Ma H, Baserga S, Pederson T, Huang S. Nucleolar structure connects with global nuclear organization. Molecular Biology Of The Cell 2023, 34: ar114. PMID: 37610836, PMCID: PMC10846622, DOI: 10.1091/mbc.e23-02-0062.Peer-Reviewed Original ResearchConceptsNucleolar structureGenomic lociNuclear domainsSpecific genomic lociGlobal nuclear organizationRNA processing factorsRNA polymerase ICajal bodiesNuclear organizationRibosome synthesisNuclear bodiesKnockdown cellsPerinucleolar compartmentPolymerase IIntranuclear locationHeLa cellsNucleolar segregationSpatial organizationNucleoliLociUtp4CellsRPA194SegregationCompositional changesHuman nucleolar protein 7 (NOL7) is required for early pre-rRNA accumulation and pre-18S rRNA processing
McCool M, Bryant C, Huang H, Ogawa L, Farley-Barnes K, Sondalle S, Abriola L, Surovtseva Y, Baserga S. Human nucleolar protein 7 (NOL7) is required for early pre-rRNA accumulation and pre-18S rRNA processing. RNA Biology 2023, 20: 257-271. PMID: 37246770, PMCID: PMC10228412, DOI: 10.1080/15476286.2023.2217392.Peer-Reviewed Original ResearchConceptsPre-rRNA accumulationRibosome biogenesisNonessential roleEukaryotic ribosome biogenesisEssential cellular processesNucleolar stress responsePre-rRNA levelsRRNA processingLikely orthologCellular processesAssociated proteinsTumor suppressorStress responseHuman cellsProtein synthesisProtein 7Human counterpartBiogenesisYeastOrthologsHomologSubcomplexAccumulationRRNATranscription
2022
Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing
McCool M, Buhagiar A, Bryant C, Ogawa L, Abriola L, Surovtseva Y, Baserga S. Human pre-60S assembly factors link rRNA transcription to pre-rRNA processing. RNA 2022, 29: rna.079149.122. PMID: 36323459, PMCID: PMC9808572, DOI: 10.1261/rna.079149.122.Peer-Reviewed Original ResearchRRNA transcriptionRRNA processingRibosomal subunit biogenesisRNA polymerase IRibosome biosynthesisSubunit biogenesisRibosome biogenesisRibosome assemblyAssembly factorsTranscription controlBiogenesis factorsRRNA productionSteady-state levelsRNA transcriptionPolymerase IComplex membersHuman cellsProtein synthesisP53 stabilizationTranscriptionEssential processBiogenesisCell proliferationDual roleRegulatory details
2020
Ribosome Biogenesis and its Role in Cell Growth and Proliferation in the Liver
Farley‐Barnes K, Baserga S. Ribosome Biogenesis and its Role in Cell Growth and Proliferation in the Liver. 2020, 174-182. DOI: 10.1002/9781119436812.ch15.ChaptersRibosome biogenesisBiogenesis of ribosomesProduction of ribosomesHuman ribosome biogenesisCell growthTumor suppressor p53Cellular cuesNumerous proteinsNucleolar stressRegulated processTranscription factorsBiogenesisNutrient availabilityKey regulatorMechanistic targetSuppressor p53Rapamycin (mTOR) pathwayRibosomesRegulationProliferationSuch diseasesMYCRegulatorCytoplasmProtein
2018
799 Exome, genome, and cDNA sequencing reveal KDSR mutations cause two forms of ichthyosis and identify retinoids as pathogenesis-directed therapy
Boyden L, Vincent N, Zhou J, Hu R, Paller A, Lifton R, Baserga S, Choate K. 799 Exome, genome, and cDNA sequencing reveal KDSR mutations cause two forms of ichthyosis and identify retinoids as pathogenesis-directed therapy. Journal Of Investigative Dermatology 2018, 138: s136. DOI: 10.1016/j.jid.2018.03.809.Peer-Reviewed Original ResearchHigh throughput discovery of novel regulators of human ribosome biogenesis
Baserga S, Farley‐Barnes K, McCann K, Ogawa L, Merkel J, Surovtseva Y. High throughput discovery of novel regulators of human ribosome biogenesis. The FASEB Journal 2018, 32: 526.25-526.25. DOI: 10.1096/fasebj.2018.32.1_supplement.526.25.Peer-Reviewed Original ResearchRibosome biogenesisNucleolar functionNumber of nucleoliMammalian cellsGenome-wide siRNA screenRNA polymerase I transcriptionHuman ribosome biogenesisPre-ribosomal RNAPolymerase I transcriptionExperimental Biology 2018 MeetingHigh-throughput discoveryNucleolar proteinsRibosomal DNAProtein regulatorsI transcriptionNew regulatorNovel regulatorSiRNA screenBiogenesisHuman cellsProteinRegulatorNucleoliFASEB JournalThroughput discovery
2017
Using Cryo‐electron Microscopy to Discover Box C/D s(no)RNP Structure
Baserga S, Yip W, Shigematsu H, Taylor D. Using Cryo‐electron Microscopy to Discover Box C/D s(no)RNP Structure. The FASEB Journal 2017, 31 DOI: 10.1096/fasebj.31.1_supplement.910.2.Peer-Reviewed Original ResearchBox C/DArchaeal box C/D sRNPsBox C/D sRNAsBox C/D sRNPRibosomal RNA modificationsElectron microscopy modelCryo-electron microscopyCryo-EM reconstructionCellular organismsRRNA modificationRibosome functionRNA modificationsSRNAsSRNPStructural techniquesEukaryaPotential interactionsArchaeaStructural analysisStem endClose proximityOrganismsNuclear magnetic resonance studiesStemInteraction
2016
Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis
Robson A, Owens ND, Baserga SJ, Khokha MK, Griffin JN. Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC Developmental Biology 2016, 16: 38. PMID: 27784267, PMCID: PMC5081970, DOI: 10.1186/s12861-016-0138-5.Peer-Reviewed Original ResearchConceptsRibosome biogenesis factorsBiogenesis factorsVentral blood islandsHuman congenital diseasesCranial neural crestRNA-seq dataAntisense mRNA probesBlood islandsEmbryonic developmentDistinct tissuesNeural crestProtein productionDifferential expressionTranscript numbersMachinery componentsSpecific tissuesSpecific phenotypesRibosomopathiesSitu hybridizationMRNA probesRibosomesExpressionTissue localizationPhenotypeFactor expressionNop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA
Zhang J, McCann KL, Qiu C, Gonzalez LE, Baserga SJ, Hall TM. Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA. Nature Communications 2016, 7: 13085. PMID: 27725644, PMCID: PMC5062617, DOI: 10.1038/ncomms13085.Peer-Reviewed Original ResearchConceptsEukaryotic ribosome biogenesisCorrect subcellular locationRibosome assembly factorsPre-ribosomal RNAPumilio repeatsRibosome biogenesisHuman ribosomopathiesAssembly factorsBiogenesis factorsRepeat proteinsMature rRNASubcellular locationNop9RNA complexCleavage siteRRNATimely cleavageProteinStructural featuresFinal processing stepRibosomopathiesBiogenesisCleavageYeastNucleaseProbing the mechanisms underlying human diseases in making ribosomes.
Farley KI, Baserga SJ. Probing the mechanisms underlying human diseases in making ribosomes. Biochemical Society Transactions 2016, 44: 1035-44. PMID: 27528749, PMCID: PMC5360156, DOI: 10.1042/bst20160064.Peer-Reviewed Original ResearchThe Contributions of the Ribosome Biogenesis Protein Utp5/WDR43 to Craniofacial Development
Sondalle SB, Baserga SJ, Yelick PC. The Contributions of the Ribosome Biogenesis Protein Utp5/WDR43 to Craniofacial Development. Journal Of Dental Research 2016, 95: 1214-1220. PMID: 27221611, PMCID: PMC5076753, DOI: 10.1177/0022034516651077.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsRibosomal proteinsCraniofacial developmentRibosome biogenesis proteinsRibosomal protein functionHuman craniofacial developmentTissue-specific defectsDiverse cell typesHuman ribosomopathiesBiogenesis proteinsTranslational machineryProtein functionDistinct functionsTranslational mechanismsTissue differentiationCell typesWDR43Global defectsProteinExciting researchSurprising similaritiesUnderstanding of rolesRibosomopathiesBiogenesisMachineryMutationsBox C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs
Yip WS, Shigematsu H, Taylor DW, Baserga SJ. Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs. Nucleic Acids Research 2016, 44: 8976-8989. PMID: 27342279, PMCID: PMC5062973, DOI: 10.1093/nar/gkw576.Peer-Reviewed Original ResearchConceptsBox C/DArchaeal box C/D sRNPsBox C/D sRNAsBox C/D sRNPRibosomal RNA modificationsElectron microscopy modelCryo-EM reconstructionCellular organismsRibosome functionRNA modificationsSRNAsSRNPModification typesStructural techniquesEukaryaPotential interactionsStemArchaeaStructural analysisStem endClose proximityOrganismsNuclear magnetic resonance studiesCatalyseInteractionThe molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome
McCann KL, Teramoto T, Zhang J, Hall T, Baserga SJ. The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome. ELife 2016, 5: e16381. PMID: 27077951, PMCID: PMC4859800, DOI: 10.7554/elife.16381.Peer-Reviewed Original ResearchMeSH KeywordsAlopeciaCircular DichroismEndocrine System DiseasesHumansIntellectual DisabilityMagnetic Resonance SpectroscopyModels, BiologicalMutant ProteinsProtein BindingProtein FoldingProtein Interaction MapsRibonucleoproteins, Small NucleolarRibosome Subunits, LargeRNA PrecursorsRNA Processing, Post-TranscriptionalRNA-Binding ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsProtein-protein interactionsANE syndromeMolecular basisDefective protein foldingRRNA processing defectsRNA recognition motifMature ribosomesRibosome assemblyHub proteinsRRNA processingNucleolar proteinsDomain foldingProtein foldingRecognition motifHuman diseasesProcessing defectsInteractomeMutationsCircular dichroismHub functionModel systemYeastFoldingProteinNOP4Discovery of mammalian regulators of ribosome biogenesis
Farley K, McCann K, Merkel J, Surovtseva Y, Baserga S. Discovery of mammalian regulators of ribosome biogenesis. The FASEB Journal 2016, 30 DOI: 10.1096/fasebj.30.1_supplement.594.1.Peer-Reviewed Original ResearchRibosome biogenesisNucleolar functionNumber of nucleoliGenome-wide siRNA screenRNA polymerase I transcriptionPre-ribosomal RNAPolymerase I transcriptionMammalian regulatorsChromatin stateNucleolar proteinsRibosomal DNAMammalian cellsProtein regulatorsI transcriptionNew regulatorSiRNA screenBiogenesisNucleolar numberHuman cellsProteinRegulatorNucleoliNew roleCellsNew pathwayWhen Good Ribosomes Go Bad
Baserga S, McCann K, Teramoto T, Zhang J, Tanaka Hall T. When Good Ribosomes Go Bad. The FASEB Journal 2016, 30 DOI: 10.1096/fasebj.30.1_supplement.387.1.Peer-Reviewed Original ResearchProtein-protein interactionsRNA recognition motifANE syndromeRibosome biogenesisRRNA processingProtein functionMolecular basisPre-rRNA processing defectThird RNA recognition motifDefective protein foldingHuman genetic diseasesFull-length proteinSingle amino acid substitutionNumerous human disordersAmino acid substitutionsYeast orthologMature ribosomesEukaryotic cellsGood ribosomeRibosome synthesisHub proteinsNucleolar proteinsNucleolar functionDomain foldingNucleolar dysfunction
2015
A protein interaction map of the LSU processome
McCann KL, Charette JM, Vincent NG, Baserga SJ. A protein interaction map of the LSU processome. Genes & Development 2015, 29: 862-875. PMID: 25877921, PMCID: PMC4403261, DOI: 10.1101/gad.256370.114.Peer-Reviewed Original ResearchConceptsLarge ribosomal subunitBiogenesis factorsRibosome biogenesis factorsTwo-hybrid assayProtein interaction mapsProtein-protein interactionsSystems biology approachInteractome mapHub proteinsBiology approachProcessomeProtein pairsRibosomal subunitInteraction mapCoordinated processConcerted actionCurrent knowledgeEukaryotesNOP4SubcomplexSubunitsProteinFourfold increaseMaturationAssemblyDeterminants of mammalian nucleolar architecture
Farley KI, Surovtseva Y, Merkel J, Baserga SJ. Determinants of mammalian nucleolar architecture. Chromosoma 2015, 124: 323-331. PMID: 25670395, PMCID: PMC4534358, DOI: 10.1007/s00412-015-0507-z.Peer-Reviewed Original ResearchConceptsNucleolar formationNucleolar architectureNucleolar structureNucleolar organizer regionsProduction of ribosomesRibosome biogenesisFunctional nucleoliHuman nucleoliCell divisionOrganizer regionsNucleoliEssential machineFunction manifestBiogenesisIntricate relationshipMinimal requirementsCellsRibosomesOrganellesProteinFunctionFormationDivisionDeterminants
2014
Cryo-Electron Microscopic Study of the Enzymatic Mechanism of the RNA 2'-O-Methyltransferase Box C\D sRNP
Yip W, Shigematsu H, Taylor D, Wang H, Baserga S. Cryo-Electron Microscopic Study of the Enzymatic Mechanism of the RNA 2'-O-Methyltransferase Box C\D sRNP. Microscopy And Microanalysis 2014, 20: 1284-1285. DOI: 10.1017/s1431927614008150.Peer-Reviewed Original Research