2024
An efficient multiplex approach to CRISPR/Cas9 gene editing in citrus
Sagawa C, Thomson G, Mermaz B, Vernon C, Liu S, Jacob Y, Irish V. An efficient multiplex approach to CRISPR/Cas9 gene editing in citrus. Plant Methods 2024, 20: 148. PMID: 39342225, PMCID: PMC11438372, DOI: 10.1186/s13007-024-01274-4.Peer-Reviewed Original ResearchSimultaneous editing of multiple genesMultiple genesGene editingEudicot plant speciesPol III promotersTarget multiple genesGenus fallRPS5A promoterCRISPR/Cas9 gene editingCRISPR/Cas9-mediated gene editingMultiplex gene editingGenome engineeringIII promotersGenetic screeningPlant speciesCas9 endonucleaseEditing efficiencyGene editing efficiencySgRNAGenesArabidopsisUBQ10SpeciesSimultaneous editingPromoterTopologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk
Nakamura T, Ueda J, Mizuno S, Honda K, Kazuno A, Yamamoto H, Hara T, Takata A. Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk. Cell Genomics 2024, 4: 100488. PMID: 38280381, PMCID: PMC10879036, DOI: 10.1016/j.xgen.2024.100488.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingASD genesWhole-genome sequencing dataTopologically associating domainsInfluence multiple genesGene regulatory mechanismsASD-associated genesGenetic architectureASD heritabilityMultiple genesASD probandsPromoter variantsGenesAutism spectrum disorder riskHuman induced pluripotent stem cellsPromoterPluripotent stem cellsTADStudies of autism spectrum disorderVariantsAutism spectrum disorderStem cellsSequenceProbandsHeritabilityStructural basis for transcription activation by the nitrate-responsive regulator NarL
Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B. Structural basis for transcription activation by the nitrate-responsive regulator NarL. Nucleic Acids Research 2024, 52: 1471-1482. PMID: 38197271, PMCID: PMC10853779, DOI: 10.1093/nar/gkad1231.Peer-Reviewed Original ResearchTranscription activation complexC-terminal domainTranscription activationAlpha C-terminal domainStructural basisGlobal transcription factorCryo-EM structureDetailed mechanistic understandingPromoter DNATranscription initiationBinds DNATranscription assaysTranscription factorsActivation complexÅ resolutionNarLDimer bindsMolecular mechanismsNovel mechanismActivation mechanismMechanistic understandingDNAStress factorsPromoterActivation
2023
Transposable elements cause the loss of self‐incompatibility in citrus
Hu J, Liu C, Du Z, Guo F, Song D, Wang N, Wei Z, Jiang J, Cao Z, Shi C, Zhang S, Zhu C, Chen P, Larkin R, Lin Z, Xu Q, Ye J, Deng X, Bosch M, Franklin‐Tong V, Chai L. Transposable elements cause the loss of self‐incompatibility in citrus. Plant Biotechnology Journal 2023, 22: 1113-1131. PMID: 38038155, PMCID: PMC11022811, DOI: 10.1111/pbi.14250.Peer-Reviewed Original ResearchConceptsMiniature inverted-repeat transposable elementsMiniature inverted-repeat transposable element insertionSelf-incompatibilityTransposable elementsS-locusS-RNaseS-RNase-based SI systemPromoter regionLoss of self-incompatibilityPromote genetic diversityS-RNase allelesPrezygotic mechanismsGenetic diversityInbreeding depressionSelf-compatibleNucleotide mutationsFlowering plantsLoss of SiTransgenic experimentsBreeding strategiesCitrus genusAllelesSI phenotypePromoterCitrusChromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy
Poulet A, Kratkiewicz A, Li D, van Wolfswinkel J. Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy. Science Advances 2023, 9: eadh4887. PMID: 37801496, PMCID: PMC10558129, DOI: 10.1126/sciadv.adh4887.Peer-Reviewed Original ResearchConceptsAdult pluripotent stem cellsPluripotent stem cellsStem cell genesStem cellsCell genesPluripotency-related gene expressionStem cell-specific genesTissue-specific genesCell-specific genesTissue-specific promotersChromatin stateChromatin organizationRegenerative organismsChromatin analysisConstitutive genesRegulatory logicTranscription factorsGene expressionSequence featuresGenesDefault statePromoterLong-term maintenanceCellsISWIChromatin expansion microscopy reveals nanoscale organization of transcription and chromatin
Pownall M, Miao L, Vejnar C, M'Saad O, Sherrard A, Frederick M, Benitez M, Boswell C, Zaret K, Bewersdorf J, Giraldez A. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin. Science 2023, 381: 92-100. PMID: 37410825, PMCID: PMC10372697, DOI: 10.1126/science.ade5308.Peer-Reviewed Original ResearchConceptsZygotic genome activationTranscriptional elongationExpansion microscopyRNA polymerase IIChromatin regulatory factorsEnhancer-promoter contactsGenome activationChromatin organizationNuclear organizationPolymerase IIPol IIFactor NanogTranscription factorsGene expressionRegulatory factorsChromatinNanoscale organizationNanogTranscriptionElongationNucleosomesUniversal processPromoterEmbryosEnhancerIRX5 promotes DNA damage repair and activation of hair follicle stem cells
Chen J, Wiedemann J, Nguyen L, Lin Z, Tahir M, Hui C, Plikus M, Andersen B. IRX5 promotes DNA damage repair and activation of hair follicle stem cells. Stem Cell Reports 2023, 18: 1227-1243. PMID: 37084727, PMCID: PMC10202659, DOI: 10.1016/j.stemcr.2023.03.013.Peer-Reviewed Original ResearchConceptsDNA damage repairDamage repairStem cellsDNA damageDNA damage repair genesCell cycle progressionHair follicle stem cellsEpidermal stem cellsFollicle stem cellsIrx genesChromatin regionsHFSC proliferationHFSC activationInterfollicular epidermal stem cellsDownstream targetsCycle progressionIRX5Molecular mechanismsRepair genesFGF18 expressionAnagen onsetBRCA1 expressionQuiescent phenotypeGenesPromoterDNA 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
Better late than never: A unique strategy for late gene transcription in the beta- and gammaherpesviruses
Dremel S, Didychuk A. Better late than never: A unique strategy for late gene transcription in the beta- and gammaherpesviruses. Seminars In Cell And Developmental Biology 2022, 146: 57-69. PMID: 36535877, PMCID: PMC10101908, DOI: 10.1016/j.semcdb.2022.12.001.Peer-Reviewed Original ResearchConceptsViral transcriptional activityViral preinitiation complexPol IITranscription of late genesGene transcriptionCellular RNA polymerase IITATA-binding proteinRNA polymerase IIModified TATA boxCis-acting elementsSubfamily of herpesvirusesPolymerase IITATA boxPreinitiation complexConsensus sequenceLate genesTranscriptional activityGene promoterLytic replicationGenesTemporal cascadeTranscriptionViral mimicPolPromoterVitamin C epigenetically controls osteogenesis and bone mineralization
Thaler R, Khani F, Sturmlechner I, Dehghani SS, Denbeigh JM, Zhou X, Pichurin O, Dudakovic A, Jerez SS, Zhong J, Lee JH, Natarajan R, Kalajzic I, Jiang YH, Deyle DR, Paschalis EP, Misof BM, Ordog T, van Wijnen AJ. Vitamin C epigenetically controls osteogenesis and bone mineralization. Nature Communications 2022, 13: 5883. PMID: 36202795, PMCID: PMC9537512, DOI: 10.1038/s41467-022-32915-8.Peer-Reviewed Original ResearchConceptsSevere skeletal defectsBone-specific genesEpigenetic functionsChromatin accessibilityHistone demethylationDNA hydroxymethylationTranscriptional activityPro-osteogenic genesCell differentiationOsteogenic cell differentiationOsteogenic differentiationGenesSkeletal defectsBone phenotypeMurine boneOsteoblastogenesisDifferentiationKnockout miceGulo knockout miceVitamin C deficiencyTET1Collagen maturationPromoterDemethylationVitamin CA noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation
Yanchus C, Drucker K, Kollmeyer T, Tsai R, Winick-Ng W, Liang M, Malik A, Pawling J, De Lorenzo S, Ali A, Decker P, Kosel M, Panda A, Al-Zahrani K, Jiang L, Browning J, Lowden C, Geuenich M, Hernandez J, Gosio J, Ahmed M, Loganathan S, Berman J, Trcka D, Michealraj K, Fortin J, Carson B, Hollingsworth E, Jacinto S, Mazrooei P, Zhou L, Elia A, Lupien M, He H, Murphy D, Wang L, Abyzov A, Dennis J, Maass P, Campbell K, Wilson M, Lachance D, Wrensch M, Wiencke J, Mak T, Pennacchio L, Dickel D, Visel A, Wrana J, Taylor M, Zadeh G, Dirks P, Eckel-Passow J, Attisano L, Pombo A, Ida C, Kvon E, Jenkins R, Schramek D. A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation. Science 2022, 378: 68-78. PMID: 36201590, PMCID: PMC9926876, DOI: 10.1126/science.abj2890.Peer-Reviewed Original ResearchConceptsNoncoding single nucleotide polymorphismSingle nucleotide polymorphismsCausal variantsMolecular pathwaysIsocitrate dehydrogenaseLethal gliomaHeritable predispositionGlioma formationTumor developmentLow-grade gliomasMutant lower grade gliomasPolymorphismMouse modelPromoterLociEnhancerSixfold greater riskRs55705857PathwayMechanisticallyDehydrogenaseDisruptsExpressionPenetranceCancer riskIdentification and Characterization of the Alternative σ28 Factor in Treponema denticola
Kurniyati K, Chang Y, Liu J, Li C. Identification and Characterization of the Alternative σ28 Factor in Treponema denticola. Journal Of Bacteriology 2022, 204: e00248-22. PMID: 36043861, PMCID: PMC9487585, DOI: 10.1128/jb.00248-22.Peer-Reviewed Original ResearchConceptsDependent promotersTranscription factorsSpirochete Treponema denticolaGene expressionOral spirochete Treponema denticolaCryo-electron tomography analysisFlagellin gene expressionExpression of flagellinSite-directed mutagenesisFlagellar regulationChemotaxis genesPeriplasmic flagellaRNA polymeraseFliABacterial motilityTranscriptional factorsLate promoterExternal flagellaLines of evidenceEscherichia coliPromoterT. denticolaBiochemical analysisEssential roleE. coli
2021
TAZ inhibits glucocorticoid receptor and coordinates hepatic glucose homeostasis in normal physiological states
Xu S, Liu Y, Hu R, Wang M, Stöhr O, Xiong Y, Chen L, Kang H, Zheng L, Cai S, He L, Wang C, Copps K, White M, Miao J. TAZ inhibits glucocorticoid receptor and coordinates hepatic glucose homeostasis in normal physiological states. ELife 2021, 10: e57462. PMID: 34622775, PMCID: PMC8555985, DOI: 10.7554/elife.57462.Peer-Reviewed Original ResearchConceptsGluconeogenic gene promotersBinding of GRGene promoterGlucocorticoid receptorGlucose homeostasisLigand-binding domainGlucose productionOverexpression of TAZHepatic glucose homeostasisWW domainsBlood glucose concentrationPhysiological fastingGluconeogenic genesGR response elementResponse elementNovel roleTAZNormal physiological stateGR transactivationPhysiological statePromoterMouse liverPericentral hepatocytesPathological statesGlucose concentrationA metabolic daylength measurement system mediates winter photoperiodism in plants
Liu W, Feke A, Leung CC, Tarté DA, Yuan W, Vanderwall M, Sager G, Wu X, Schear A, Clark DA, Thines BC, Gendron JM. A metabolic daylength measurement system mediates winter photoperiodism in plants. Developmental Cell 2021, 56: 2501-2515.e5. PMID: 34407427, PMCID: PMC8440495, DOI: 10.1016/j.devcel.2021.07.016.Peer-Reviewed Original ResearchConceptsPhotoperiodic floweringPlant fitnessCellular healthMetabolic networksStudy systemPhotoperiodic regulationWinter-like photoperiodsVegetative healthPhotoperiodic expressionsSucrose levelsPlantsStarch productionFloweringPhotoperiodismArabidopsisPhotosynthesisGenesPromoterFlowersBioinformaticsReporterLuciferaseFitnessRegulationPhotoperiodStructural visualization of transcription activated by a multidrug-sensing MerR family regulator
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B. Structural visualization of transcription activated by a multidrug-sensing MerR family regulator. Nature Communications 2021, 12: 2702. PMID: 33976201, PMCID: PMC8113463, DOI: 10.1038/s41467-021-22990-8.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsBacterial ProteinsBase SequenceBinding SitesCloning, MolecularCryoelectron MicroscopyCrystallography, X-RayDNA-Binding ProteinsDNA-Directed RNA PolymerasesDNA, BacterialEscherichia coliGene ExpressionGene Expression Regulation, BacterialGenetic VectorsModels, MolecularNucleic Acid ConformationPromoter Regions, GeneticProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein Interaction Domains and MotifsRecombinant ProteinsTranscription Elongation, GeneticTranscription Initiation, GeneticConceptsMerR family regulatorsFamily regulatorCryo-electron microscopy structureBacterial RNA polymerase holoenzymeRegulation of transcriptionRNA polymerase holoenzymePromoter openingTranscription regulationMicroscopy structureTranscription initiationPolymerase holoenzymeRNA elongationTranscriptional regulatorsMerR familyDNA remodelingSpacer DNAPromoter recognitionPromoter elementsCellular signalsSpacer promoterInitial transcriptionTranscription processTranscriptionPromoterRegulator
2020
Cutting, Amplifying, and Aligning Microtubules with Severing Enzymes
Kuo YW, Howard J. Cutting, Amplifying, and Aligning Microtubules with Severing Enzymes. Trends In Cell Biology 2020, 31: 50-61. PMID: 33183955, PMCID: PMC7749064, DOI: 10.1016/j.tcb.2020.10.004.Peer-Reviewed Original ResearchConceptsAAA ATPasesTissue morphogenesisCellular processesMicrotubule cytoskeletonCell divisionGrowth promotionBiophysical advancesSevering enzymesMicrotubule networkMolecular mechanismsStrong promoterMicrotubule growthNeuronal developmentShort filamentsMicrotubulesSpastinEnzymeSeveringFidgetinKataninCytoskeletonMorphogenesisPromoterProteinRecent workHorizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence
Choi J, Groisman EA. Horizontally acquired regulatory gene activates ancestral regulatory system to promote Salmonella virulence. Nucleic Acids Research 2020, 48: 10832-10847. PMID: 33045730, PMCID: PMC7641745, DOI: 10.1093/nar/gkaa813.Peer-Reviewed Original ResearchConceptsPhoP/PhoQAncestral regulatorNucleoid structuring protein H-NSProtein H-NSS. bongoriSalmonella enterica serovar TyphimuriumAncestral genomesH-NSTarget promotersEnterica serovar TyphimuriumRegulatory genesBacterial virulenceSalmonella virulencePromoter regionSsrBOpposite regulationGenesS. typhimuriumPhoQRegulatory systemSerovar TyphimuriumVirulenceTranscriptionPromoterRegulatorFEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo
Duprey A, Groisman EA. FEDS: a Novel Fluorescence-Based High-Throughput Method for Measuring DNA Supercoiling In Vivo. MBio 2020, 11: 10.1128/mbio.01053-20. PMID: 32723920, PMCID: PMC7387798, DOI: 10.1128/mbio.01053-20.Peer-Reviewed Original ResearchConceptsDNA supercoilingFluorescent proteinDNA supercoiling resultsBacterial DNA supercoilingSingle-cell heterogeneityGreen fluorescent proteinRed fluorescent proteinCellular physiologyDNA processesHigh-throughput methodConstitutive promoterNovel regulatorNucleotide sequenceGenetic informationRegulatory loopHigh-throughput measurementsSupercoilingForms of lifeGenesSingle cellsTranscriptionPromoterProteinChemical supportNovel fluorescenceH3K4me1 Distribution Predicts Transcription State and Poising at Promoters
Bae S, Lesch BJ. H3K4me1 Distribution Predicts Transcription State and Poising at Promoters. Frontiers In Cell And Developmental Biology 2020, 8: 289. PMID: 32432110, PMCID: PMC7214686, DOI: 10.3389/fcell.2020.00289.Peer-Reviewed Original ResearchGerm cellsGene regulatory statesDifferent epigenetic marksTranscription start siteEmbryonic stem cellsMouse germ cellsGene expression levelsTranscription stateChromatin stateEpigenetic memoryEpigenetic stateEpigenetic marksLysine 4Histone H3Somatic cellsDistal enhancerStart siteActive promotersH3K4me1Transcriptional activityPromoter regionH3K4me3Possible rolePromoterCell types
2019
Deep Learning Implicitly Handles Tissue Specific Phenomena to Predict Tumor DNA Accessibility and Immune Activity
Wnuk K, Sudol J, Givechian K, Soon-Shiong P, Rabizadeh S, Szeto C, Vaske C. Deep Learning Implicitly Handles Tissue Specific Phenomena to Predict Tumor DNA Accessibility and Immune Activity. IScience 2019, 20: 119-136. PMID: 31563852, PMCID: PMC6823659, DOI: 10.1016/j.isci.2019.09.018.Peer-Reviewed Original ResearchDNA accessibilityChromatin stateOpen chromatin stateChromatin regulationSpecific tissue typesPromoter-flanking regionAccessibility landscapeCancer Genome AtlasTranscriptional eventsTissue-specific phenomenonDNA sequencesGenome AtlasTissue typesImmune pathwaysPromoterTumor progressionAccessibility patternsLung adenocarcinomaNew toolKey dynamic featuresTumor typesPathwayRegulationImmune activitySequence
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