2024
A Unified Post-Transcriptional Mechanism Regulates Intron Retention in Splicing Factor-Mutant MDS
Boddu P, Roy R, Baumgartner F, Hutter S, Haferlach T, Pillai M. A Unified Post-Transcriptional Mechanism Regulates Intron Retention in Splicing Factor-Mutant MDS. Blood 2024, 144: 2732-2732. DOI: 10.1182/blood-2024-211458.Peer-Reviewed Original ResearchRNA-binding proteinsIntron retentionAlternative splicing patternsPost-transcriptional mechanismsIR eventsSF mutationsSR proteinsSF3B1 mutantsAnalyzed RNA-seq datasetsMyelodysplastic syndromeCo-transcriptional splicingCo-transcriptional mechanismsRNA-seq datasetsPost-transcriptional splicingWild-typeSub-compartmentsNuclear sub-compartmentsHEK293T cellsGene expression analysisWild-type K562 cellsRNA processingMutant cellsPhospho-proteomicsExon featuresAS eventsImmunometabolism of CD8+ T cell differentiation in cancer
Shi H, Chen S, Chi H. Immunometabolism of CD8+ T cell differentiation in cancer. Trends In Cancer 2024, 10: 610-626. PMID: 38693002, PMCID: PMC11342304, DOI: 10.1016/j.trecan.2024.03.010.Peer-Reviewed Original ResearchCD8<sup>+</sup> cytotoxic T lymphocytesT cell receptorImmune signalingCD8+ T cell differentiationMediators of tumor immunityTumor antigen recognitionCytotoxic T lymphocytesT cell differentiationTumor-immune interactionsTumor immunityNovel immunotherapiesT lymphocytesIntracellular metabolic pathwaysCo-StimulationAntigen recognitionMetabolic programmingDesign novel immunotherapiesImmunotherapyCentral mediatorsMetabolic landscapePost-transcriptional mechanismsTumorBidirectional regulationSignaling eventsMetabolic processes
2019
GIGANTEA recruits the UBP12 and UBP13 deubiquitylases to regulate accumulation of the ZTL photoreceptor complex
Lee CM, Li MW, Feke A, Liu W, Saffer AM, Gendron JM. GIGANTEA recruits the UBP12 and UBP13 deubiquitylases to regulate accumulation of the ZTL photoreceptor complex. Nature Communications 2019, 10: 3750. PMID: 31434902, PMCID: PMC6704089, DOI: 10.1038/s41467-019-11769-7.Peer-Reviewed Original ResearchConceptsDeubiquitylating enzymesCircadian clockTarget proteinsE3 ubiquitin ligase activityPlant circadian clockUbiquitin-specific protease 12Post-transcriptional mechanismsUbiquitin ligase activityPhotoreceptor complexZTL proteinProtein ubiquitylationInteracting partnerProtein complexesLigase activityZEITLUPEUBP12Gi protein levelsUBP13Enzyme typeLight conditionsGiganteaProtein levelsProteinEnzymeDay light conditionsA novel, noncoding-RNA-mediated, post-transcriptional mechanism of anti-Mullerian hormone regulation by the H19/let-7 axis
Qin C, Xia X, Fan Y, Jiang Y, Chen Y, Zhang N, Uslu B, Johnson J, Kallen AN. A novel, noncoding-RNA-mediated, post-transcriptional mechanism of anti-Mullerian hormone regulation by the H19/let-7 axis. Biology Of Reproduction 2019, 101: 257-257. PMID: 31286140, PMCID: PMC6614579, DOI: 10.1093/biolre/ioz046.Peer-Reviewed Original ResearchHistone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally
Huang H, Weng H, Zhou K, Wu T, Zhao BS, Sun M, Chen Z, Deng X, Xiao G, Auer F, Klemm L, Wu H, Zuo Z, Qin X, Dong Y, Zhou Y, Qin H, Tao S, Du J, Liu J, Lu Z, Yin H, Mesquita A, Yuan CL, Hu YC, Sun W, Su R, Dong L, Shen C, Li C, Qing Y, Jiang X, Wu X, Sun M, Guan JL, Qu L, Wei M, Müschen M, Huang G, He C, Yang J, Chen J. Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally. Nature 2019, 567: 414-419. PMID: 30867593, PMCID: PMC6438714, DOI: 10.1038/s41586-019-1016-7.Peer-Reviewed Original ResearchConceptsM6A methyltransferase complexHistone H3 trimethylationH3 trimethylationHistone modificationsImportant post-transcriptional mechanismMouse embryonic stem cellsGene expression regulationRNA polymerase IIPrevalent internal modificationPost-transcriptional mechanismsEmbryonic stem cellsN6-methyladenosine (m<sup>6</sup>A) mRNA modificationM6A depositionTranscription elongationNascent RNAMethyltransferase complexPolymerase IIExpression regulationGene expression1RNA methylationMRNA modificationMETTL14 knockdownH3K36me3M6A modificationCell stemness
2016
Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition
Bazzini AA, del Viso F, Moreno‐Mateos M, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition. The EMBO Journal 2016, 35: 2087-2103. PMID: 27436874, PMCID: PMC5048347, DOI: 10.15252/embj.201694699.Peer-Reviewed Original ResearchConceptsZygotic transitionMRNA stabilityTranslation efficiencyMRNA clearanceMaternal mRNAsCodon identityCodon compositionGene expressionMaternal mRNA clearanceRegulated mRNA decayPost-transcriptional mechanismsAmino acid sequenceTranscript decayMRNA decayPolyadenylation statusAmino acid compositionCodon tripletsGenetic codeSynonymous codonsAcid sequenceCellular transitionsRegulatory informationNew transcriptionDevelopmental progressionMRNA
2015
Increased abundance of translation machinery in stem cell–derived neural progenitor cells from four schizophrenia patients
Topol A, English J, Flaherty E, Rajarajan P, Hartley B, Gupta S, Desland F, Zhu S, Goff T, Friedman L, Rapoport J, Felsenfeld D, Cagney G, Mackay-Sim A, Savas J, Aronow B, Fang G, Zhang B, Cotter D, Brennand K. Increased abundance of translation machinery in stem cell–derived neural progenitor cells from four schizophrenia patients. Translational Psychiatry 2015, 5: e662-e662. PMID: 26485546, PMCID: PMC4930118, DOI: 10.1038/tp.2015.118.Peer-Reviewed Original ResearchConceptsHiPSC neural progenitor cellsNeural progenitor cellsNovel post-transcriptional mechanismProtein synthesisGlobal protein translationElongation factor proteinGlobal protein synthesisPost-transcriptional mechanismsProgenitor cellsHuman-induced pluripotent stem cellsPluripotent stem cellsMass spectrometry evidenceTranslation machineryTranslation initiationProtein translationEpigenetic factorsFactor proteinStem cellsProtein levelsTotal protein levelsCellsUnaffected controlsMachineryProteinAbundance
2014
The emerging role of RNA‐binding proteins in the life cycle of Trypanosoma brucei
Kolev NG, Ullu E, Tschudi C. The emerging role of RNA‐binding proteins in the life cycle of Trypanosoma brucei. Cellular Microbiology 2014, 16: 482-489. PMID: 24438230, PMCID: PMC3974610, DOI: 10.1111/cmi.12268.Peer-Reviewed Original ResearchConceptsParasitic protozoan Trypanosoma bruceiIdentification of RBPsTargets of RBPsSpecific gene networksProtozoan Trypanosoma bruceiPost-transcriptional mechanismsGene regulatory networksGene expression patternsRelated trypanosomatidsTranscriptional machineryCellular fateGene networksRegulatory networksTrypanosoma bruceiExpression patternsRegulatory mechanismsDifferent hostsRBPsLife cyclePathogenic organismsRNAOrganismsProteinDifferent environmentsCrucial role
2013
Human embryonic poly(A)-binding protein (EPAB) alternative splicing is differentially regulated in human oocytes and embryos
Guzeloglu-Kayisli O, Lalioti MD, Babayev E, Torrealday S, Karakaya C, Seli E. Human embryonic poly(A)-binding protein (EPAB) alternative splicing is differentially regulated in human oocytes and embryos. Molecular Human Reproduction 2013, 20: 59-65. PMID: 24002949, DOI: 10.1093/molehr/gat061.Peer-Reviewed Original ResearchConceptsZygotic genome activationEarly embryo developmentEarly embryosTranslational activationSomatic tissuesSpliced formsEmbryo developmentEmbryo-specific expressionPost-transcriptional mechanismsOocyte maturationHuman somatic tissuesFull-length formGenome activationExon 8Transcriptional regulationAlternative splicingTranscriptional activityGene expressionHuman oocytesEPABAmino acidsXenopusEmbryosMRNAOocytes
2012
The miR-35-41 Family of MicroRNAs Regulates RNAi Sensitivity in Caenorhabditis elegans
Massirer K, Perez S, Mondol V, Pasquinelli A. The miR-35-41 Family of MicroRNAs Regulates RNAi Sensitivity in Caenorhabditis elegans. PLOS Genetics 2012, 8: e1002536. PMID: 22412382, PMCID: PMC3297572, DOI: 10.1371/journal.pgen.1002536.Peer-Reviewed Original ResearchConceptsLin-35/RbSmall interfering RNADouble-stranded RNAMir-35RNA interferenceEndo-RNAiRNA pathwaysCaenorhabditis elegansSources of double-stranded RNASmall RNA pathwaysC. elegans homologGenome-wide microarray analysisRNA interference sensitivitySilencing of genesInactivation of genesRegulates RNA interferencePost-transcriptional mechanismsTargeting specific mRNAsEndo-siRNAsRNAi sensitivityExo-RNAiRNAi responseRetinoblastoma geneMaternal contributionSpecific mRNAs
2004
Small Interfering Double-Stranded RNAs as Therapeutic Molecules to Restore Chemosensitivity to Thymidylate Synthase Inhibitor Compounds
Schmitz JC, Chen TM, Chu E. Small Interfering Double-Stranded RNAs as Therapeutic Molecules to Restore Chemosensitivity to Thymidylate Synthase Inhibitor Compounds. Cancer Research 2004, 64: 1431-1435. PMID: 14973067, DOI: 10.1158/0008-5472.can-03-1203.Peer-Reviewed Original ResearchConceptsTS expressionRKO cellsDose-dependent inhibitionCellular drug resistanceHuman colon cancer RKO cellsSynthase inhibitorColon cancer RKO cellsTherapeutic potentialDrug resistanceRNA interferenceMRNA levelsCell linesI. InhibitionProtein inductionSynthase mRNAChemosensitivityRaltitrexedDouble-stranded RNAInhibitor compoundsTherapeutic moleculesThymidylate synthase mRNATS mRNAPost-transcriptional mechanismsSiRNAEffective inhibitor
2003
Making informed decisions: regulatory interactions between two-component systems
Bijlsma JJ, Groisman EA. Making informed decisions: regulatory interactions between two-component systems. Trends In Microbiology 2003, 11: 359-366. PMID: 12915093, DOI: 10.1016/s0966-842x(03)00176-8.Peer-Reviewed Original ResearchConceptsTwo-component systemTwo-component regulatory systemPost-transcriptional mechanismsMultitude of stressesResponse regulatorBacterial adaptationRegulatory interactionsComplex nichePhosphoryl transferMolecular levelRegulatory systemSpecific signalsMultiple signalsPhosphorelayMultifaceted environmentNicheRegulatorBacteriaPhosphataseMechanismStressAdaptation
1998
Myb-dependent Regulation of Thrombospondin 2 Expression ROLE OF mRNA STABILITY*
Bein K, Ware J, Simons M. Myb-dependent Regulation of Thrombospondin 2 Expression ROLE OF mRNA STABILITY*. Journal Of Biological Chemistry 1998, 273: 21423-21429. PMID: 9694906, DOI: 10.1074/jbc.273.33.21423.Peer-Reviewed Original ResearchConceptsNIH 3T3 cellsC-MybWild-type NIH 3T3 cellsTranscription factor c-MybEndogenous target genesPost-transcriptional mechanismsPromoter-reporter assaysMRNA stability studiesDifferential display analysisSimilar transcriptional levelsTSP-2 expressionV-SrcHomology searchCDNA endsGene productsTarget genesTranscriptional levelMRNA stabilityV-mycCell cycleTSP-1C-JunHematopoietic cellsDNA probesHomologous products
1993
Expression of endogenous NMDAR1 transcripts without receptor protein suggests post-transcriptional control in PC12 cells.
Sucher N, Brose N, Deitcher D, Awobuluyi M, Gasic G, Bading H, Cepko C, Greenberg M, Jahn R, Heinemann S, Lipton S. Expression of endogenous NMDAR1 transcripts without receptor protein suggests post-transcriptional control in PC12 cells. Journal Of Biological Chemistry 1993, 268: 22299-22304. PMID: 8226739, DOI: 10.1016/s0021-9258(18)41528-1.Peer-Reviewed Original ResearchMeSH KeywordsAlternative SplicingAnimalsAstrocytesBase SequenceCell DifferentiationCell LineCells, CulturedDimethylphenylpiperazinium IodideDNA PrimersGene ExpressionGene Expression Regulation, NeoplasticGenetic VariationHippocampusHumansKidneyMacromolecular SubstancesMembrane PotentialsMolecular Sequence DataMolecular WeightNerve Growth FactorsN-MethylaspartatePC12 CellsPolymerase Chain ReactionReceptors, N-Methyl-D-AspartateRNA, MessengerSynaptic MembranesTranscription, GeneticTransfectionConceptsNMDAR1 proteinPC12 cellsPost-transcriptional controlPost-transcriptional mechanismsNative PC12 cellsParticular cell typeUndifferentiated rat pheochromocytoma (PC12) cellsExpression of RNAPC12 cell lineTranslational regulationIsoform CRat pheochromocytoma cellsNorthern hybridizationExpression vectorReceptor proteinCell typesIon channelsProteinFunctional NMDACell linesPheochromocytoma cellsCytomegalovirus promoterModel systemRNAExpression
1989
Post‐transcriptional mechanisms of deregulation of MYC following conversion of a human B cell line by Epstein‐Barr virus.
Lacy J, Summers W, Summers W. Post‐transcriptional mechanisms of deregulation of MYC following conversion of a human B cell line by Epstein‐Barr virus. The EMBO Journal 1989, 8: 1973-1980. PMID: 2551670, PMCID: PMC401064, DOI: 10.1002/j.1460-2075.1989.tb03603.x.Peer-Reviewed Original ResearchConceptsEpstein-Barr virusB cell linesBJAB cellsNegative Burkitt lymphoma linesPresence of EBVLymphoma linesBurkitt lymphoma linesCell linesNormal human B cellsHuman B cell linesHuman B cellsMYC mRNAEBV genomeVitro infectionMyc transcriptsB cellsEBVLymphoblastoid linesMYC expressionVirusMechanism of deregulationCellsPost-transcriptional mechanismsMYC
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