2024
Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape
Boddu P, Gupta A, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer J, Chandhok N, King D, Nannya Y, Ogawa S, Lin H, Simon M, Dray E, Kupfer G, Verma A, Neugebauer K, Pillai M. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Molecular Cell 2024, 84: 1475-1495.e18. PMID: 38521065, PMCID: PMC11061666, DOI: 10.1016/j.molcel.2024.02.032.Peer-Reviewed Original ResearchRate of RNA polymerase IIChromatin landscapeElongation defectsElongation rate of RNA polymerase IIImpaired protein-protein interactionsSplicing of pre-messenger RNATranscription elongation defectsRNA polymerase IIProtein-protein interactionsPre-messenger RNACancer-associated mutationsIsogenic cell linesSin3/HDAC complexGene bodiesPolymerase IIChromatin accessibilityH3K4me3 markChromatin changesMutant SF3B1ChromatinMutant mouse modelsEpigenetic disordersEpigenetic factorsHuman diseasesMutant stateAn epigenetic timer regulates the transition from cell division to cell expansion during Arabidopsis petal organogenesis
Huang R, Irish V. An epigenetic timer regulates the transition from cell division to cell expansion during Arabidopsis petal organogenesis. PLOS Genetics 2024, 20: e1011203. PMID: 38442104, PMCID: PMC10942257, DOI: 10.1371/journal.pgen.1011203.Peer-Reviewed Original ResearchConceptsCell division to cell expansionCell divisionCell expansionRemodeling of chromatin accessibilityResponse to environmental changesRNA polymerase activityPlant developmental timingRegulate developmental eventsMultiple cell divisionsDownstream direct targetsCorepressor TOPLESSArabidopsis petalsChromatin accessibilityHistone modificationsPetal developmentEpigenetic stateTranscriptional repressorPetal organogenesisPolymerase activityEpigenetic memoryPetal primordiaPlant organogenesisCell cycleEpigenetic factorsControl organogenesisGenetic and epigenetic determinants of non-alcoholic fatty liver disease (NAFLD) in lean individuals: a systematic review
Njei B, Al-Ajlouni Y, Ugwendum D, Abdu M, Forjindam A, Mohamed M. Genetic and epigenetic determinants of non-alcoholic fatty liver disease (NAFLD) in lean individuals: a systematic review. Translational Gastroenterology And Hepatology 2024, 9: 11-11. PMID: 38317742, PMCID: PMC10838615, DOI: 10.21037/tgh-23-31.Peer-Reviewed Original ResearchNewcastle Ottawa ScaleLean non-alcoholic fatty liver diseaseNon-alcoholic fatty liver diseaseSystematic reviewDeterminants of non-alcoholic fatty liver diseaseAscertainment of exposureLean individualsEpigenetic factorsModerate overall qualityFatty liver diseaseRisk of biasGene variantsPeer-reviewed studiesLiver diseaseQuality assessmentFrequent genetic risk factorGenetic risk factorsOttawa ScaleHistone variantsQualitative synthesisStudy designNAFLD riskPRISMA guidelinesEpigenetic determinantsEpigenetic contributions
2023
Genetic Variation and Sensory Perception of a Pediatric Formulation of Ibuprofen: Can a Medicine Taste Too Good for Some?
Mennella J, Kan M, Lowenthal E, Saraiva L, Mainland J, Himes B, Pepino M. Genetic Variation and Sensory Perception of a Pediatric Formulation of Ibuprofen: Can a Medicine Taste Too Good for Some? International Journal Of Molecular Sciences 2023, 24: 13050. PMID: 37685855, PMCID: PMC10487938, DOI: 10.3390/ijms241713050.Peer-Reviewed Original ResearchConceptsGenetic ancestryEuropean genetic ancestryTaste receptor genesIndependent of ancestryAfrican genetic ancestryGenetic variationFormulations of ibuprofenEpigenetic factorsAncestryReceptor geneDouble-blind cohort studyUrge to coughPerception of palatabilityRisk of accidental ingestionPersonality variationCohort studyPediatric formulationsSensory phenotypesThroat sensationChemesthetic sensationsMedicinal tasteTingling sensationPanelistsAdult panelistsDiverse populationsDysregulated MicroRNAs in the Pathogenesis of Systemic Lupus Erythematosus: A Comprehensive Review
Choi D, Kim J, Yang J, Kim J, Park S, Shin J. Dysregulated MicroRNAs in the Pathogenesis of Systemic Lupus Erythematosus: A Comprehensive Review. International Journal Of Biological Sciences 2023, 19: 2495-2514. PMID: 37215992, PMCID: PMC10197884, DOI: 10.7150/ijbs.74315.Peer-Reviewed Original ResearchConceptsSystemic lupus erythematosusLupus erythematosusPathogenesis of systemic lupus erythematosusComparison to healthy controlsPathogenesis of lupusSevere renal diseaseChronic autoimmune diseaseClinical presentationLupus patientsPotential roleDisease activitySLE pathogenesisAutoimmune diseasesOrgan damageRenal diseaseHealthy controlsPathogenic roleTherapeutic potentialTreatment goalsGenetic factorsPathogenesisPathogenic processesErythematosusEpigenetic factorsLupusDNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ
Pramio D, Vieceli F, Varella-Branco E, Goes C, Kobayashi G, da Silva Pelegrina D, de Moraes B, El Allam A, De Kumar B, Jara G, Farfel J, Bennett D, Kundu S, Viapiano M, Reis E, de Oliveira P, Dos Santos E Passos-Bueno M, Rothlin C, Ghosh S, Schechtman D. DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ. Biochimica Et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2023, 1866: 194909. PMID: 36682583, PMCID: PMC10037092, DOI: 10.1016/j.bbagrm.2023.194909.Peer-Reviewed Original ResearchConceptsInduced pluripotent stem cellsInternal promoterNeuronal differentiationEpigenetic mechanismsDNA methylationUpstream promoterProtein kinase C ζHuman neuronal differentiationSite-specific hypermethylationAberrant DNA hypermethylationPluripotent stem cellsEpigenetic regulationSame epigenetic mechanismsLong-term memory formationDNA hypermethylationDemethylated regionsEpigenetic factorsPromoter regionTissue specificityMolecular mechanismsPRKCZ geneDifferentiated neuronsPromoterProtein kinase M zetaLong-term potentiation
2022
Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia
Farrelly L, Zheng S, Schrode N, Topol A, Bhanu N, Bastle R, Ramakrishnan A, Chan J, Cetin B, Flaherty E, Shen L, Gleason K, Tamminga C, Garcia B, Li H, Brennand K, Maze I. Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia. Nature Communications 2022, 13: 2195. PMID: 35459277, PMCID: PMC9033776, DOI: 10.1038/s41467-022-29922-0.Peer-Reviewed Original ResearchConceptsHistone posttranslational modificationsPosttranslational modificationsUnbiased proteomic approachPluripotent stem cellsPatient-derived neuronsH2A.Z acetylationChromatin profilingHyperacetylated histonesFamily proteinsProteomic approachProtein interactionsHistone acetylationTranscriptional abnormalitiesEpigenetic factorsExtraterminal (BET) proteinsSZ casesRisk variantsHuman neuronsStem cellsAberrant roleProtein inhibitionBona fideTreatment of schizophreniaPostmortem human brainCritical role
2021
Do Epigenetic Timers Control Petal Development?
Huang R, Huang T, Irish V. Do Epigenetic Timers Control Petal Development? Frontiers In Plant Science 2021, 12: 709360. PMID: 34295349, PMCID: PMC8290480, DOI: 10.3389/fpls.2021.709360.Peer-Reviewed Original ResearchGene expressionEpigenetic factorsSuch regulatory mechanismsPetal developmentPlant organogenesisHeritable changesChromatin structureDNA accessibilityEpigenetic controlHistone modificationsEpigenetic modificationsPetal growthDNA methylationDevelopmental timingDevelopmental eventsRegulatory mechanismsDevelopmental transitionsMolecular mechanismsCell typesEnvironmental changesDevelopmental progressionOrganogenesisSuch modificationsRecent studiesExpression
2018
The Role of Maternal HP1a in Early Drosophila Embryogenesis via Regulation of Maternal Transcript Production
Park AR, Liu N, Neuenkirchen N, Guo Q, Lin H. The Role of Maternal HP1a in Early Drosophila Embryogenesis via Regulation of Maternal Transcript Production. Genetics 2018, 211: 201-217. PMID: 30442760, PMCID: PMC6325692, DOI: 10.1534/genetics.118.301704.Peer-Reviewed Original ResearchConceptsHeterochromatin protein 1aMaternal transcriptsEarly Drosophila embryogenesisGermline developmentDrosophila embryogenesisMRNA splicingCell divisionTranscript productionProtein 1AEpigenetic factorsDownregulates genesEmbryogenesisGenesTranscriptsSplicingOogenesisTranscriptionOrganogenesisRegulationRoleProductionNeurogenesisDivisionDevelopmentTranslation
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
Myh 11 R 247 C / R 247 C mutations increase thoracic aorta vulnerability to intramural damage despite a general biomechanical adaptivity
Bellini C, Wang S, Milewicz DM, Humphrey JD. Myh 11 R 247 C / R 247 C mutations increase thoracic aorta vulnerability to intramural damage despite a general biomechanical adaptivity. Journal Of Biomechanics 2014, 48: 113-121. PMID: 25433566, PMCID: PMC4283495, DOI: 10.1016/j.jbiomech.2014.10.031.Peer-Reviewed Original ResearchConceptsThoracic aortaSevere vascular phenotypeAortic aneurysmContractile proteinsLocalized poolsMedial smooth muscle cellsEpigenetic factorsGenetic studiesThoracic aortic diseaseThoracic aortic aneurysmSmooth muscle cellsSuch mutationsMutationsC mutationAortic dissectionAortic diseaseHistopathologic characteristicsMuscle cellsRisk factorsGlycosaminoglycans/proteoglycansNormal adaptationMouse modelNormal biomechanicsAortic structureAortaPharmacogenetics of nicotine addiction: role of dopamine
Herman AI, DeVito EE, Jensen KP, Sofuoglu M. Pharmacogenetics of nicotine addiction: role of dopamine. Pharmacogenomics 2014, 15: 221-234. PMID: 24444411, PMCID: PMC4154357, DOI: 10.2217/pgs.13.246.Peer-Reviewed Original ResearchAntiviral Agents☆
Paintsil E, Cheng Y. Antiviral Agents☆. 2014, 176-225. PMCID: PMC7150273, DOI: 10.1016/b978-0-12-801238-3.02387-4.Peer-Reviewed Original ResearchAntiviral agentsViral life cycleAntiviral drugsAvailable antiviral agentsCurrent antiviral agentsNovel antiviral agentsDevelopment of resistanceViral infectionRelevant pharmacologicDrug AdministrationClinical propertiesFree virusViral attachmentNew viral proteinsViral RNADrugsViral proteinsVirusHost cellsEpigenetic factorsAgentsViral mRNAsMRNABody fluidsPharmacologic
2013
A Major Epigenetic Programming Mechanism Guided by piRNAs
Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H. A Major Epigenetic Programming Mechanism Guided by piRNAs. Developmental Cell 2013, 24: 502-516. PMID: 23434410, PMCID: PMC3600162, DOI: 10.1016/j.devcel.2013.01.023.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Genetically ModifiedArgonaute ProteinsChromatinChromatin ImmunoprecipitationChromobox Protein Homolog 5Chromosomal Proteins, Non-HistoneDNA Transposable ElementsDrosophilaDrosophila ProteinsEpigenomicsGenomeGenomicsMethyltransferasesMutationReal-Time Polymerase Chain ReactionReverse Transcriptase Polymerase Chain ReactionRNA Polymerase IIRNA, MessengerRNA, Small InterferingConceptsSpecific genomic sitesEpigenetic factorsGenomic sitesRNA polymerase II associationPiwi-piRNA complexDrosophila genomeEpigenetic stateEpigenetic landscapeComplex associatesPiwiGenomePiRNAsCentral enigmaMajor mechanismEctopic sitesSequenceHP1aDrosophilaPiRNASitesEpigeneticsMechanismProgramming mechanismAssociatesRecruitmentFunction of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity
Darricarrère N, Liu N, Watanabe T, Lin H. Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 1297-1302. PMID: 23297219, PMCID: PMC3557079, DOI: 10.1073/pnas.1213283110.Peer-Reviewed Original ResearchConceptsPIWI proteinsPiRNA biogenesisSlicer activityPIWI-interacting RNA (piRNA) biogenesisEndonuclease activityFunction of PiwiNuclear Piwi proteinSecondary piRNA biogenesisGerm line developmentPiwi functionPiwi membersArgonaute proteinsRNA biogenesisArgonaute 3Transgenic fliesPiwiSomatic cellsCatalytic triadEpigenetic factorsRegulatory functionsBiogenesisOnly memberProteinTransposonRecent evidence
2012
Fibrosis in systemic sclerosis: common and unique pathobiology
Bhattacharyya S, Wei J, Tourtellotte WG, Hinchcliff M, Gottardi CG, Varga J. Fibrosis in systemic sclerosis: common and unique pathobiology. Fibrogenesis & Tissue Repair 2012, 5: s18. PMID: 23259815, PMCID: PMC3368774, DOI: 10.1186/1755-1536-5-s1-s18.Peer-Reviewed Original ResearchReactive oxygen speciesMesenchymal progenitor cell differentiationCellular differentiation programsProgenitor cell differentiationSystemic sclerosisTranscriptional activatorComplex polygenic diseaseDifferentiation programEpigenetic factorsFibroblast activationCell differentiationInnate immune receptorsImmune receptorsPolygenic diseaseBone marrow-derived fibrocytesUnique pathobiologyOxygen speciesGrowth factorOxidative stressSelective targetingDifferentiationObliterative vasculopathyPathobiologic featuresUncontrolled progressionFibrotic response
2011
The microRNA regulation of stem cells
Huang XA, Lin H. The microRNA regulation of stem cells. Wiley Interdisciplinary Reviews Membrane Transport And Signalling 2011, 1: 83-95. PMID: 23024929, PMCID: PMC3459065, DOI: 10.1002/wdev.5.Peer-Reviewed Original ResearchStem cellsMore mRNA targetsAdult tissue stem cellsDistinct expression profilesEmbryonic stem cellsTissue stem cellsMiRNA pathwayNegative feedback loopGene regulationMicroRNA regulationMRNA targetsTranscription factorsGene expressionRegulatory mechanismsEpigenetic factorsExpression profilesBiological processesDifferent miRNAsConcerted controlRegulatory roleIPS cellsMiRNAsSuch regulationRegulationCellsEpigenetic Regulation of Transcription and Virulence in Trypanosoma cruzi by O-Linked Thymine Glucosylation of DNA
Ekanayake D, Minning T, Weatherly B, Gunasekera K, Nilsson D, Tarleton R, Ochsenreiter T, Sabatini R. Epigenetic Regulation of Transcription and Virulence in Trypanosoma cruzi by O-Linked Thymine Glucosylation of DNA. Molecular And Cellular Biology 2011, 31: 1690-1700. PMID: 21321080, PMCID: PMC3126337, DOI: 10.1128/mcb.01277-10.Peer-Reviewed Original ResearchConceptsPolycistronic unitsBase JTranscription initiationPol II transcription initiationSite of transcription initiationGene expressionEpigenetic regulation of transcriptionPolycistronic gene clustersProtein-coding genesPol II transcriptionGenome-wide increaseRegulation of transcriptionHost cell invasionRegulate gene expressionDNA basePolymerase IIVirulence genesGene clusterPol IIII transcriptionAffected genesPosttranscriptional processesEpigenetic regulationBiological roleEpigenetic factors
2008
Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression
Hua S, Kallen CB, Dhar R, Baquero MT, Mason CE, Russell BA, Shah PK, Liu J, Khramtsov A, Tretiakova MS, Krausz TN, Olopade OI, Rimm DL, White KP. Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. Molecular Systems Biology 2008, 4: msb200825. PMID: 18414489, PMCID: PMC2394496, DOI: 10.1038/msb.2008.25.Peer-Reviewed Original ResearchConceptsHistone variant H2A.ZVariant H2A.ZBreast cancer progressionTranscription factor-binding sitesTranscriptional regulatory cascadeCancer progressionGenome tiling arraysWhole-genome mappingFactor-binding sitesRegulatory cascadeTiling arraysChromatin immunoprecipitationGenome mappingGenomic analysisH2A.Z levelsRNA interferenceGene targetsGene expressionEpigenetic factorsMicroarray screeningH2A.ZCell proliferationLymph node metastasisBreast cancer survivalHigh expression
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