2025
FAM72A promotes UNG2 degradation and mutagenesis in human cancer cells
Feng Y, Barbulescu P, Chana C, Shirdarreh M, Yang H, Wu L, Mamand S, Kashem M, Zia A, Han M, Tsao J, Pugh T, Cescon D, Schatz D, Sicheri F, Martin A, Pezo R. FAM72A promotes UNG2 degradation and mutagenesis in human cancer cells. Scientific Reports 2025, 15: 23467. PMID: 40604025, PMCID: PMC12223117, DOI: 10.1038/s41598-025-07723-x.Peer-Reviewed Original ResearchConceptsUracil DNA glycosylase 2Proteasomal degradationMutagenic repairMutagenic DNA repairFunctional roleTumorigenic tissuesBase excision repairHuman cancer cellsSubstrate adaptorHuman cell linesE3 ligaseBioinformatics studiesDNA repairGenetic lesionsExcision repairHuman cellsCancer cellsCell linesHuman biologyFAM72AMechanisms of carcinogenesisCancer developmentProtein levelsGenesFAM72Decoding the Complex Functional Landscape of the ykkC Riboswitches
Barth K, Hiller D, de Andrade G, Kavita K, Fernando C, Breaker R, Strobel S. Decoding the Complex Functional Landscape of the ykkC Riboswitches. Biochemistry 2025, 64: 1983-1995. PMID: 40254862, DOI: 10.1021/acs.biochem.4c00787.Peer-Reviewed Original ResearchConceptsTerminator hairpinSequence changesMutation analysisExtensive mutational analysisAssociated with genesSmall sequence changesBinding site positionsComplex functional landscapeRiboswitch classesPhylogenetic analysisChemically diverse ligandsVariant classesTranscriptional controlAptamer domainRiboswitchNatural riboswitchesLigand specificityFunctional roleFunctional landscapeGMP synthesisDiverse ligandsStructural studiesHairpinSite positionsSequenceCrystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling
Li T, Stayrook S, Li W, Wang Y, Li H, Zhang J, Liu Y, Klein D. Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling. Nature Communications 2025, 16: 3580. PMID: 40234450, PMCID: PMC12000326, DOI: 10.1038/s41467-025-58828-w.Peer-Reviewed Original ResearchConceptsThrombospondin type I repeatsIsthmin-1Pre-adipocytesType I repeatsBacterial streptavidinSurface helicesI repeatsMolecular detailsDiverse functionsFunctional studiesAkt phosphorylationFunctional roleStructural plasticityInsulin-like propertiesCrystal structureAMOPGrowth factorDomainPhosphorylationApoptosisLiver steatosisProteinHelixAktStreptavidin
2024
Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes
Peng X, Li S, Dou W, Li M, Gontcharov A, Peng Z, Qi B, Wang Q, Li Y. Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes. Microorganisms 2024, 12: 2540. PMID: 39770743, PMCID: PMC11677963, DOI: 10.3390/microorganisms12122540.Peer-Reviewed Original ResearchCommunity compositionMicrobial functional profilesHost-specific selectionMicrobial community compositionCharacteristics of microbiotaCulture-based studiesSpecies of bacteriaBacteria community compositionPhagocytosis of bacteriaFunctional traitsMetagenomic sequencingMyxomycete speciesAssociated microbiomeAmplicon sequencingFunctional redundancyMetagenomic insightsMicrobial communitiesMyxomycetesSpecies-specificBacteria speciesDominant bacteriaBacteriaFunctional roleFunctional analysisPlasmodiaX-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes
Hasenbein T, Hoelzl S, Smith Z, Gerhardinger C, Gonner M, Aguilar-Pimentel A, Amarie O, Becker L, Calzada-Wack J, Dragano N, da Silva-Buttkus P, Garrett L, Hölter S, Kraiger M, Östereicher M, Rathkolb B, Sanz-Moreno A, Spielmann N, Wurst W, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Meissner A, Engelhardt S, Rinn J, Andergassen D. X-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes. Nature Communications 2024, 15: 10631. PMID: 39638999, PMCID: PMC11621363, DOI: 10.1038/s41467-024-54673-5.Peer-Reviewed Original ResearchConceptsAutosomal gene regulationRegions genome-wideAllele-specific analysisSex-specific lociLoci in vivoX-linked genesRandom X-chromosome inactivationX-chromosome inactivationSex-specific phenotypesFirre locusGenome-wideIn vivo roleChromatin structureGene regulationX chromosomeEpigenetic featuresDXZ4Epigenetic profilesKnockout studiesLociDiverse phenotypesLncRNA FIRREFunctional roleCombinatorial effectsFIRRENeuronal parts list and wiring diagram for a visual system
Matsliah A, Yu S, Kruk K, Bland D, Burke A, Gager J, Hebditch J, Silverman B, Willie K, Willie R, Sorek M, Sterling A, Kind E, Garner D, Sancer G, Wernet M, Kim S, Murthy M, Seung H. Neuronal parts list and wiring diagram for a visual system. Nature 2024, 634: 166-180. PMID: 39358525, PMCID: PMC11446827, DOI: 10.1038/s41586-024-07981-1.Peer-Reviewed Original ResearchDoes Eosinophil Heterogeneity Translate into Functional Diversity? A Review of the Evolving Paradigm of Eosinophil Heterogeneity in Asthma
Wilson G, Gautam S, Chupp G. Does Eosinophil Heterogeneity Translate into Functional Diversity? A Review of the Evolving Paradigm of Eosinophil Heterogeneity in Asthma. Biomedicines 2024, 12: 2011. PMID: 39335525, PMCID: PMC11428232, DOI: 10.3390/biomedicines12092011.Peer-Reviewed Original ResearchType 2 inflammatory diseasesTreatment of patientsEosinophil subtypesEosinophilic phenotypeFunctional diversityClinical therapyEosinophil heterogeneityEosinophil subpopulationsBiological agentsEosinophilsPhenotypic changesFunctional roleAsthmaOverview of evidenceDiseaseSubpopulationsMepolizumabTherapyPatientsSubtypesReviewFunctional Roles of H3K4 Methylation in Transcriptional Regulation
Yu H, Lesch B. Functional Roles of H3K4 Methylation in Transcriptional Regulation. Molecular And Cellular Biology 2024, 44: 505-515. PMID: 39155435, PMCID: PMC11529435, DOI: 10.1080/10985549.2024.2388254.Peer-Reviewed Original ResearchTranscriptional regulationAssociated with active transcriptionHistone 3 lysine 4 methylationFunctional roleTranscribed lociOpen chromatinActivate transcriptionChromatin modificationsH3K4 methylationRegulatory elementsHistone methyltransferaseEpigenetic editingTranscriptional activityResidue mutationsMammalian systemsCell differentiationHistoneH3K4me1H3K4meH3K4me3ChromatinRegulationH3K4YeastLociGene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging
Occean J, Yang N, Sun Y, Dawkins M, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price N, Kim J, Cui C, Fan J, Bhattacharyya M, De S, Maragkakis M, de Cabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. Nature Communications 2024, 15: 6357. PMID: 39069555, PMCID: PMC11284234, DOI: 10.1038/s41467-024-50725-y.Peer-Reviewed Original ResearchConceptsTissue-specific functionsDNA hydroxymethylationMagnitude of transcriptional changesAlternative splicing eventsMagnitude of gene expression changesTissue-specific genesGene expression changesGene bodiesSplicing eventsDNA methylationModel organismsTranscriptional changesExpression changesGenesAge-related diseasesFunctional roleMouse liverHuman tissuesProlonged quiescenceRestriction functionSplicingDNAMiceAge-related contextSenescenceThe West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles
Huston N, Tsao L, Brackney D, Pyle A. The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2312080121. PMID: 38985757, PMCID: PMC11260092, DOI: 10.1073/pnas.2312080121.Peer-Reviewed Original ResearchConceptsWest Nile virus genomeWest Nile virusPositive-sense RNA virusesFunctional roleArthropod cell linesRiboregulatory elementsGenome foldingFlaviviral genomeRNA genomeIncreasing global threatVirus genomeGenomeRNA virusesStructural homologyHost-dependentSecondary structureLack of effective therapeuticsFunctional validationLocked nucleic acidStructural insightsRNA drugsCell linesArthropod-borneNucleic acidsAntisense locked nucleic acidAbundant extrasynaptic expression of α3β4-containing nicotinic acetylcholine receptors in the medial habenula–interpeduncular nucleus pathway in mice
Tsuzuki A, Yamasaki M, Konno K, Miyazaki T, Takei N, Tomita S, Yuzaki M, Watanabe M. Abundant extrasynaptic expression of α3β4-containing nicotinic acetylcholine receptors in the medial habenula–interpeduncular nucleus pathway in mice. Scientific Reports 2024, 14: 14193. PMID: 38902419, PMCID: PMC11189931, DOI: 10.1038/s41598-024-65076-3.Peer-Reviewed Original ResearchConceptsMHb-IPN pathwayMHb neuronsNicotine dependenceNicotinic acetylcholine receptorsAcetylcholine receptorsNicotine-related behaviorsCell surfaceImmunoelectron microscopySubunitAxonal compartmentFunctional roleNeurotransmitter releasePresynaptic terminalsSubcellular expressionPathwaySimultaneous detectionDistribution patternsSynaptic junctionsNAChRsAnatomical basisExpressionNegative controlReceptorsNeuronsAntibodies
2023
Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora
Wang Z, Wang Y, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend J. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. PLOS Genetics 2023, 19: e1011019. PMID: 37934795, PMCID: PMC10684091, DOI: 10.1371/journal.pgen.1011019.Peer-Reviewed Original ResearchConceptsLineage-specific genesHET domain genesSexual reproductionFunctional roleUnusual carbon sourcesPotential functional roleMating lociAsexual growthGenetic mutantsNeurospora crassaPossible functional roleSexual phaseGenetic manipulationTranscriptomic profilingReproduction regulationGene knockoutPP-1ADV-1Environmental alterationsGenesSexual developmentNeurosporaReproductionCarbon sourceGenetic barrier56. USING HIPSC-NEURONS AND CRISPR TO UNCOVER NON-ADDITIVE EFFECTS OF SCZ RISK GENES
Deans M, Seah C, Johnson J, García-González J, Townsley K, Cao E, Schrode N, Stahl E, O'Reilly P, Huckins L, Brennand K. 56. USING HIPSC-NEURONS AND CRISPR TO UNCOVER NON-ADDITIVE EFFECTS OF SCZ RISK GENES. European Neuropsychopharmacology 2023, 75: s86. DOI: 10.1016/j.euroneuro.2023.08.162.Peer-Reviewed Original ResearchSCZ risk genesNon-additive effectsRisk genesCombinatorial perturbationsTranscriptomic effectsFunctional roleRisk variantsGene expression changesBulk RNA-seqMultiple functional rolesSynaptic functionHigh-throughput imagingFunctional redundancyTranscriptional regulatorsRNA-seqCRISPR activationCellular phenotypesRNA interferenceEGenesGene expressionExpression changesHiPSC neuronsPolygenic risk scoresGenetic studiesGenesDeleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality
Hong Y, Battle S, Shi W, Puiu D, Pillalamarri V, Xie J, Pankratz N, Lake N, Lek M, Rotter J, Rich S, Kooperberg C, Reiner A, Auer P, Heard-Costa N, Liu C, Lai M, Murabito J, Levy D, Grove M, Alonso A, Gibbs R, Dugan-Perez S, Gondek L, Guallar E, Arking D. Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality. Nature Communications 2023, 14: 6113. PMID: 37777527, PMCID: PMC10542802, DOI: 10.1038/s41467-023-41785-7.Peer-Reviewed Original ResearchConceptsSingle nucleotide variantsOwn circular genomeState of heteroplasmyAging-related diseasesNuclear genomeMitochondrial genomeCircular genomeMtDNA single nucleotide variantsMitochondrial DNASomatic cellsMitochondrial mutationsMtDNA heteroplasmyGenomeNucleotide variantsHeteroplasmyDNA moleculesFunctional roleMitochondriaUK BiobankCertain cancersVariantsDNAMutationsCopiesCellsNew insights into programmed cell death protein 1 blockade-associated cutaneous immune-related adverse events
Micevic G, Daniels A, Flavell R. New insights into programmed cell death protein 1 blockade-associated cutaneous immune-related adverse events. British Journal Of Dermatology 2023, 189: 355-357. PMID: 37471669, PMCID: PMC10503525, DOI: 10.1093/bjd/ljad236.Peer-Reviewed Original ResearchConceptsCutaneous immune-related adverse eventsImmune-related adverse eventsSelf-reactive T cellsCheckpoint receptor PD-1PD-1 inhibitorsHalf of patientsImmune checkpoint blockadeAntitumor immune responseReceptor PD-1Adverse eventsCheckpoint blockadePD-1Immune toleranceCTLA-4T cellsImmune responseLandmark studiesMolecular mechanismsFunctional roleCritical functional rolePatientsBlockadeDermatologistsImportant cluesTopology of the lateral visual system: The fundus of the superior temporal sulcus and parietal area H connect nonvisual cerebrum to the lateral occipital lobe
Dadario N, Tanglay O, Stafford J, Davis E, Young I, Fonseka R, Briggs R, Yeung J, Teo C, Sughrue M. Topology of the lateral visual system: The fundus of the superior temporal sulcus and parietal area H connect nonvisual cerebrum to the lateral occipital lobe. Brain And Behavior 2023, 13: e2945. PMID: 36912573, PMCID: PMC10097165, DOI: 10.1002/brb3.2945.Peer-Reviewed Original ResearchConceptsActivation likelihood estimationHub-like regionsLateral occipital lobeOccipital lobeVisual networkSuperior temporal sulcusTask-based functional MRI studiesTemporal sulcusTemporo-occipital regionsFunctional MRI studyCortical parcellation schemeMeta-analytic softwareClinical significanceFunctional roleLanguage cortexMRI studiesAbnormal activationCortical regionsVisual systemFunctional coactivationCerebrumCortexPossible important roleParcellation schemesStructural connectivity
2022
Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function
Lyon S, Harris K, Odzer N, Wilkins S, Breaker R. Ornate, large, extremophilic (OLE) RNA forms a kink turn necessary for OapC protein recognition and RNA function. Journal Of Biological Chemistry 2022, 298: 102674. PMID: 36336078, PMCID: PMC9723947, DOI: 10.1016/j.jbc.2022.102674.Peer-Reviewed Original ResearchConceptsOLE RNARNP complexesRNA-protein binding assaysPrecise biochemical functionRNA structural motifsInability of cellsNatural binding sitesRibonucleoprotein complexesRNA functionBiochemical functionsExhibit phenotypesBacterial proteinsK-turnKink turnBacillus haloduransDisruptive mutationsSame proteinBacterial speciesProtein recognitionAnaerobic bacterial speciesFunctional roleSecondary structureRNAProteinOapBProteotype coevolution and quantitative diversity across 11 mammalian species
Ba Q, Hei Y, Dighe A, Li W, Maziarz J, Pak I, Wang S, Wagner GP, Liu Y. Proteotype coevolution and quantitative diversity across 11 mammalian species. Science Advances 2022, 8: eabn0756. PMID: 36083897, PMCID: PMC9462687, DOI: 10.1126/sciadv.abn0756.Peer-Reviewed Original ResearchConceptsMammalian speciesRNA metabolic processesCommon mammalian speciesUbiquitin-proteasome systemEvolutionary profilingMammalian lineagesProteomic methodsProtein degradationProtein abundanceGene expressionProtein expression levelsHigh interspeciesMetabolic processesCovariation analysisFunctional roleNucleotide levelExpression levelsQuantitative diversityCoevolutionMammalsSpeciesRemarkable variationExpressionTranscriptomeBiological variabilityCoupled fibromodulin and SOX2 signaling as a critical regulator of metastatic outgrowth in melanoma
Oria VO, Zhang H, Zito CR, Rane CK, Ma XY, Provance OK, Tran TT, Adeniran A, Kluger Y, Sznol M, Bosenberg MW, Kluger HM, Jilaveanu LB. Coupled fibromodulin and SOX2 signaling as a critical regulator of metastatic outgrowth in melanoma. Cellular And Molecular Life Sciences 2022, 79: 377. PMID: 35737114, PMCID: PMC9226089, DOI: 10.1007/s00018-022-04364-5.Peer-Reviewed Original ResearchConceptsTumor suppressor Hippo pathwayNovel regulatory mechanismTumor vasculogenic mimicryMetastatic outgrowthExtracellular matrix componentsHippo pathwayRegulatory mechanismsMolecular eventsTumor-stroma interactionsCritical regulatorMetastatic competenceProgenitor markersProliferative stateFunctional roleFunctional studiesSOX2Vasculogenic mimicryDistinct phenotypesMatrix componentsEarly developmentFmodHigh expressionCritical processOutgrowthImportant roleInvestigating DNA methylation as a mediator of genetic risk in childhood acute lymphoblastic leukemia
Xu K, Li S, Pandey P, Kang AY, Morimoto LM, Mancuso N, Ma X, Metayer C, Wiemels JL, de Smith AJ. Investigating DNA methylation as a mediator of genetic risk in childhood acute lymphoblastic leukemia. Human Molecular Genetics 2022, 31: 3741-3756. PMID: 35717575, PMCID: PMC9616572, DOI: 10.1093/hmg/ddac137.Peer-Reviewed Original ResearchConceptsEpigenome-wide association studiesSingle nucleotide polymorphismsGenetic risk lociDNA methylationRisk single nucleotide polymorphismsRisk lociAssociation studiesHeritable genetic variationGenome-wide association studiesMost single nucleotide polymorphismsDNA methylation differencesNon-European populationsEpigenetic mechanismsGenetic variationMethylation differencesSignificant DMPsPromoter regionFunctional pathwaysCpG positionsAssociation analysisFunctional roleMethylationNucleotide polymorphismsLociBlood DNA
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