2024
CasRx-based Wnt activation promotes alveolar regeneration while ameliorating pulmonary fibrosis in a mouse model of lung injury
Shen S, Wang P, Wu P, Huang P, Chi T, Xu W, Xi Y. CasRx-based Wnt activation promotes alveolar regeneration while ameliorating pulmonary fibrosis in a mouse model of lung injury. Molecular Therapy 2024 PMID: 39245939, DOI: 10.1016/j.ymthe.2024.09.008.Peer-Reviewed Original ResearchWnt/b-catenin signalingStem cell activityLung epitheliumAlveolar regenerationPulmonary fibrosisLung fibrosisWnt signalingCell activationMouse models of lung injuryModel of lung injuryWnt activityAlveolar type II cell proliferationBleomycin-induced injuryAmeliorated pulmonary fibrosisActivation of Wnt signalingType II cell proliferationInhibit lung fibrosisRegenerative medicineAnti-fibrotic effectsTreating pulmonary fibrosisActivated Wnt signalingLung injuryMouse modelFibrosisWnt/b-cateninExpanding RNA editing toolkit using an IDR-based strategy
Di M, Lv J, Jing Z, Yang Y, Yan K, Wu J, Ge J, Rauch S, Dickinson B, Chi T. Expanding RNA editing toolkit using an IDR-based strategy. Molecular Therapy - Nucleic Acids 2024, 35: 102190. PMID: 38721279, PMCID: PMC11077028, DOI: 10.1016/j.omtn.2024.102190.Peer-Reviewed Original Research
2022
iMAPping the Perturb-Atlas
Sun Y, Lin W, Kaundal R, Chi T. iMAPping the Perturb-Atlas. Life Medicine 2022, 2: lnac057. DOI: 10.1093/lifemedi/lnac057.Peer-Reviewed Original ResearchPPARγ phase separates with RXRα at PPREs to regulate target gene expression
Li Z, Luo L, Yu W, Li P, Ou D, Liu J, Ma H, Sun Q, Liang A, Huang C, Chi T, Huang X, Zhang Y. PPARγ phase separates with RXRα at PPREs to regulate target gene expression. Cell Discovery 2022, 8: 37. PMID: 35473936, PMCID: PMC9043196, DOI: 10.1038/s41421-022-00388-0.Peer-Reviewed Original ResearchPPAR response elementNuclear condensatesTranscriptional activationPPRE siteZinc finger motifsDNA binding domainsKey transcription activatorSpecific transcriptional activationTarget gene expressionPPARγ/RXRαRetinoid X receptor αPPARγ target genesFinger motifPhase-separated dropletsTranscription activatorTranscriptional responseObligate heterodimersTarget genesX receptor αBinding domainsGene expressionResponse elementPeroxisome proliferator-activated receptorNovel mechanismProliferator-activated receptor
2021
EasyCatch, a convenient, sensitive and specific CRISPR detection system for cancer gene mutations
Liu Y, Chen Y, Dang L, Liu Y, Huang S, Wu S, Ma P, Jiang H, Li Y, Pan Y, Wei Y, Ma X, Liu M, Ji Q, Chi T, Huang X, Wang X, Zhou F. EasyCatch, a convenient, sensitive and specific CRISPR detection system for cancer gene mutations. Molecular Cancer 2021, 20: 157. PMID: 34856977, PMCID: PMC8638196, DOI: 10.1186/s12943-021-01456-x.Peer-Reviewed Original Research
2017
Chapter 15 Mouse Models of Epigenetic Inheritance: Classification, Mechanisms, and Experimental Strategies
Mao S, Li Y, Liu B, Chi T. Chapter 15 Mouse Models of Epigenetic Inheritance: Classification, Mechanisms, and Experimental Strategies. 2017, 231-243. DOI: 10.1016/b978-0-12-805388-1.00015-8.Peer-Reviewed Original ResearchEpigenetic inheritanceChromatin modificationsHeritable chromatin modificationsHeritable epigenetic statesSimple reporter geneEpigenetic stateExperimental strategiesEpigenetic mechanismsMolecular basisReporter geneMouse modelInheritanceInheritance modelEnvironmental factorsCompelling evidenceMechanistic studiesEmbryogenesisExtensive contributionsGenesTraitsMechanismMechanistic problemsModificationInducerOffspring
2014
Chapter 8 Towards the Molecular Mechanisms of Transgenerational Epigenetic Inheritance Insights from Transgenic Mice
Kaundal R, Yang Y, Nottoli T, Chi T. Chapter 8 Towards the Molecular Mechanisms of Transgenerational Epigenetic Inheritance Insights from Transgenic Mice. 2014, 75-85. DOI: 10.1016/b978-0-12-405944-3.00008-8.Peer-Reviewed Original ResearchTransgenerational epigenetic inheritanceChromatin marksChromatin modificationsEpigenetic inheritanceGlobal epigenetic reprogrammingTraditional transgenic miceCopy numberGene-targeting methodsSite-specific integrationMitotic inheritanceHeritable perturbationsEpigenetic reprogrammingTransgenerational inheritanceTractable systemEpigenetic modificationsUnderlying genesEpigenetic perturbationsCpG methylationTransgenic miceGenetic strategiesReporter geneCOL1A1 locusMolecular mechanismsSubsequent embryogenesisGermline transmission
2013
Inducible mouse models illuminate parameters influencing epigenetic inheritance
Wan M, Gu H, Wang J, Huang H, Zhao J, Kaundal RK, Yu M, Kushwaha R, Chaiyachati BH, Deerhake E, Chi T. Inducible mouse models illuminate parameters influencing epigenetic inheritance. Development 2013, 140: 843-852. PMID: 23325759, PMCID: PMC3557779, DOI: 10.1242/dev.088229.Peer-Reviewed Original ResearchConceptsTransgenerational inheritanceEpigenetic perturbationsModification patternsChromatin modification patternsRepressive chromatin modificationsAberrant epigenetic modificationsTarget gene sequenceMitotic inheritanceChromatin modificationsEpigenetic inheritanceEpigenetic stateMetastable epiallelesEpigenetic modificationsTranscription factorsGene sequencesDNA sequencesEpigenetic programmingTarget genesCOL1A1 locusFetal epigenomeExtraordinary malleabilityPleiotropic effectsInducible mouse modelEpigenomeTransient manipulationA General Approach for Controlling Transcription and Probing Epigenetic Mechanisms: Application to the Cd4 Locus
Wan M, Kaundal R, Huang H, Zhao J, Yang X, Chaiyachati BH, Li S, Chi T. A General Approach for Controlling Transcription and Probing Epigenetic Mechanisms: Application to the Cd4 Locus. The Journal Of Immunology 2013, 190: 737-747. PMID: 23293358, PMCID: PMC3744393, DOI: 10.4049/jimmunol.1201278.Peer-Reviewed Original ResearchBRG1‐mediated immune tolerance: facilitation of Treg activation and partial independence of chromatin remodelling
Chaiyachati BH, Jani A, Wan Y, Huang H, Flavell R, Chi T. BRG1‐mediated immune tolerance: facilitation of Treg activation and partial independence of chromatin remodelling. The EMBO Journal 2013, 32: 395-408. PMID: 23321680, PMCID: PMC3567501, DOI: 10.1038/emboj.2012.350.Peer-Reviewed Original ResearchConceptsTreg activationRegulatory T cellsSeverity of inflammationChemokine receptor genesT-cell lineageΑβ T cell lineagesCD4 cellsSuppress autoimmunityProinflammatory roleImmune toleranceFatal inflammationT cellsInflammatory cuesTregsInflammationBrg1 deletionReceptor geneChromatin-remodelling factor BRG1Activation levelsActivationCell lineagesTarget genesATPase activityPoint mutationsCells
2012
LoxP-FRT Trap (LOFT): a simple and flexible system for conventional and reversible gene targeting
Chaiyachati BH, Kaundal RK, Zhao J, Wu J, Flavell R, Chi T. LoxP-FRT Trap (LOFT): a simple and flexible system for conventional and reversible gene targeting. BMC Biology 2012, 10: 96. PMID: 23198860, PMCID: PMC3529186, DOI: 10.1186/1741-7007-10-96.Peer-Reviewed Original ResearchEssential Roles of the Chromatin Remodeling Factor Brg1 in Spermatogenesis in Mice1
Wang J, Gu H, Lin H, Chi T. Essential Roles of the Chromatin Remodeling Factor Brg1 in Spermatogenesis in Mice1. Biology Of Reproduction 2012, 86: 186, 1-10. PMID: 22495890, PMCID: PMC3386149, DOI: 10.1095/biolreprod.111.097097.Peer-Reviewed Original ResearchConceptsMeiotic recombinationSomatic cellsDNA repairMeiotic sex chromosome inactivationChromatin Remodeling Factor BRG1Sex chromosome inactivationChromatin-remodeling complexBAF chromatin-remodeling complexImpaired homologous recombinationEssential roleRole of BRG1Chromatin regulationChromatin structureFactor BRG1Male germlineMammalian spermatogenesisSpatiotemporal regulationChromosome inactivationCatalytic subunitHomologous recombinationMidpachytene stageBRG1Expression patternsGene expressionGerm cells
2009
Molecular basis of CD4 repression by the Swi/Snf‐like BAF chromatin remodeling complex
Wan M, Zhang J, Lai D, Jani A, Prestone‐Hurlburt P, Zhao L, Ramachandran A, Schnitzler GR, Chi T. Molecular basis of CD4 repression by the Swi/Snf‐like BAF chromatin remodeling complex. European Journal Of Immunology 2009, 39: 580-588. PMID: 19180471, PMCID: PMC2774848, DOI: 10.1002/eji.200838909.Peer-Reviewed Original ResearchConceptsCD4 repressionCD4 silencerDominant negative mutantBAF complexNegative mutantSWI/SNF-like BAF chromatinBRG1/BRM-associated factor (BAF) chromatinCD4 silencer functionLinker histone H1Factor (BAF) chromatinT cell developmentKey repressorBAF chromatinSilencer functionBAF57Histone H1ChromatinMolecular basisFlanking regionsRepressionTranslational frameCD4 transcriptionSilencerEarly thymocytesMutantsInduction of TLR4-target genes entails calcium/calmodulin-dependent regulation of chromatin remodeling
Lai D, Wan M, Wu J, Preston-Hurlburt P, Kushwaha R, Grundström T, Imbalzano AN, Chi T. Induction of TLR4-target genes entails calcium/calmodulin-dependent regulation of chromatin remodeling. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 1169-1174. PMID: 19164553, PMCID: PMC2633529, DOI: 10.1073/pnas.0811274106.Peer-Reviewed Original ResearchConceptsCalcium/CaMChromatin remodelingBAF complexSWI/SNF-like BAF chromatinTarget genesDominant negative mutantCalcium/calmodulinCalmodulin-dependent regulationHMG domainBAF chromatinCaM-binding peptideNegative mutantGene expressionCaM antagonistsGenesToll-like receptor 4ChromatinRegulationRemodelingRecruitmentComplexesBAF57RNAiMutantsInduction
2008
A novel genetic strategy reveals unexpected roles of the Swi–Snf–like chromatin-remodeling BAF complex in thymocyte development
Jani A, Wan M, Zhang J, Cui K, Wu J, Preston-Hurlburt P, Khatri R, Zhao K, Chi T. A novel genetic strategy reveals unexpected roles of the Swi–Snf–like chromatin-remodeling BAF complex in thymocyte development. Journal Of Cell Biology 2008, 183: i7-i7. DOI: 10.1083/jcb1833oia7.Peer-Reviewed Original ResearchA novel genetic strategy reveals unexpected roles of the Swi–Snf–like chromatin-remodeling BAF complex in thymocyte development
Jani A, Wan M, Zhang J, Cui K, Wu J, Preston-Hurlburt P, Khatri R, Zhao K, Chi T. A novel genetic strategy reveals unexpected roles of the Swi–Snf–like chromatin-remodeling BAF complex in thymocyte development. Journal Of Experimental Medicine 2008, 205: 2813-2825. PMID: 18955569, PMCID: PMC2585832, DOI: 10.1084/jem.20080938.Peer-Reviewed Original ResearchConceptsPoint mutantsUnexpected roleImportant gene functionsThymocyte developmentNovel genetic strategyPoint mutationsEarly thymocyte developmentMammalian geneticsChromatin templatesSWI-SNFBAF complexGene functionATPase subunitsDeletion mutantsFactor complexCD4 locusTarget genesGenetic strategiesCD4 activationMutantsNovel activityPhysical interactionDeletionBRGMutationsNucleoprotein structure of the CD4 locus: Implications for the mechanisms underlying CD4 regulation during T cell development
Yu M, Wan M, Zhang J, Wu J, Khatri R, Chi T. Nucleoprotein structure of the CD4 locus: Implications for the mechanisms underlying CD4 regulation during T cell development. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 3873-3878. PMID: 18322012, PMCID: PMC2268827, DOI: 10.1073/pnas.0800810105.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCD4 AntigensChromatin ImmunoprecipitationEnhancer Elements, GeneticGene DeletionGene Expression RegulationHistonesLymphocyte SubsetsMiceMice, Inbred C57BLModels, BiologicalNucleoproteinsPromoter Regions, GeneticProtein BindingSilencer Elements, TranscriptionalT-LymphocytesTranscription FactorsConceptsT cell developmentCell developmentNucleoprotein structuresCD4 locusHeterochromatin-like structureOpen chromatin configurationStage-specific mannerSame regulatory elementsDP cellsRepression patternsTranscription activatorCD4 silencerP300 recruitmentChromatin configurationRegulatory elementsDN cellsMolecular basisMolecular mechanismsCD4 enhancerCD4 transcriptionMature T cellsCD4 regulationCD4 geneCD4 promoterSilencer
2004
A BAF-centred view of the immune system
Chi T. A BAF-centred view of the immune system. Nature Reviews Immunology 2004, 4: 965-977. PMID: 15573131, DOI: 10.1038/nri1501.Peer-Reviewed Original ResearchConceptsChromatin-remodelling complexBAF complexRepressive chromatin structureStructure of chromatinHistone-DNA contactsTranscription factor complexPost-translational modificationsTranscriptional start siteIFN-β geneTranscriptional machineryChromatin structureTranscriptional activatorTranscriptional repressorHuman genesResponsive genesExpression of CIITAStart siteDNA sequencesFactor complexHistone octamerNucleosomesOwn replicationGene expressionGenomic DNAIFN-β expression
2002
Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes
Chi TH, Wan M, Zhao K, Taniuchi I, Chen L, Littman DR, Crabtree GR. Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes. Nature 2002, 418: 195-199. PMID: 12110891, DOI: 10.1038/nature00876.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCD4 AntigensCD8 AntigensChromatinCross-Linking ReagentsDNA HelicasesDNA-Binding ProteinsFlow CytometryGene Expression RegulationGene SilencingMacromolecular SubstancesMiceMice, TransgenicMutationNuclear ProteinsProtein BindingProtein Structure, TertiaryProtein SubunitsThymus GlandTranscription FactorsConceptsBAF complexCD4 silencerYeast SWI/SNF complexSWI/SNF-like BAF complexHigh mobility group domainSWI/SNF complexLineage-specific genesDNA-binding subunitLineage bifurcationChromatin remodellingHMG domainChromatin lociSNF complexDNA bendingReciprocal regulationGroup domainCD4/CD8 expressionCell killingThymic developmentSilencerMutationsComplexesExpressionBAF57BRG
2000
Perspectives: signal transduction. Inositol phosphates in the nucleus.
Chi T, Crabtree G. Perspectives: signal transduction. Inositol phosphates in the nucleus. Science 2000, 287: 1937-9. PMID: 10755944, DOI: 10.1126/science.287.5460.1937.Peer-Reviewed Original ResearchArginineCell NucleusDNA-Binding ProteinsFungal ProteinsGene Expression Regulation, FungalInositol PhosphatesMinichromosome Maintenance 1 ProteinNuclear EnvelopePhosphotransferases (Alcohol Group Acceptor)Phytic AcidRNA, FungalRNA, MessengerSaccharomyces cerevisiaeSignal TransductionTranscription FactorsTranscription, Genetic