2025
Effect of Dietary Salt Excess on DNA Methylation and Transcriptional Regulation of Human Angiotensinogen Gene Expression
Perla S, Garcia-Milan R, Mopidevi B, Jain S, Kumar A. Effect of Dietary Salt Excess on DNA Methylation and Transcriptional Regulation of Human Angiotensinogen Gene Expression. American Journal Of Hypertension 2025, hpaf150. PMID: 40808626, DOI: 10.1093/ajh/hpaf150.Peer-Reviewed Original ResearchGenome-wide association studiesDNA methylation patternsHap-IITranscriptional regulationHap-IHuman AGTMethylation patternsBinding of transcription factorsGene expressionHuman AGT genePotential gene targetsHigh-salt dietRNA-seqAssociation studiesIntron IDNA demethylationDNA methylationCpG sitesTranscriptional analysisExpressed genesTranscription factorsRisk haplotypeRNA sequencingCanonical pathwaysGene targetingA tgl-Dependent Adipocyte Lipolysis Promotes Lipodystrophy and Restrains Fibrogenic Responses during Skin Fibrosis
Caves E, Jussila A, Forni M, Benvie A, Lei V, King D, Edelman H, Hamdan M, Odell I, Hinchcliff M, Atit R, Horsley V. A tgl-Dependent Adipocyte Lipolysis Promotes Lipodystrophy and Restrains Fibrogenic Responses during Skin Fibrosis. Journal Of Investigative Dermatology 2025, 145: 1896-1909.e5. PMID: 39884454, DOI: 10.1016/j.jid.2024.12.022.Peer-Reviewed Original ResearchLipid storageAdipocyte lipolysisExtracellular matrix proteinsFatty acidsTranscriptional analysisSkin fibrosisAdipocyte lipid storageTranscriptional changesSkin fibrosis developmentExtracellular matrix remodelingFibrosis developmentLipid-filled adipocytesDermal extracellular matrixHuman diseasesTreating fibrotic diseasesMouse modelMatrix proteinsDermal adipocytesFibrogenic responseGenetic modelsExtracellular matrixAdipocytesLoss of adipose tissueBleomycin-treated miceFibrotic mouse model
2021
Methylation of dual-specificity phosphatase 4 controls cell differentiation
Su H, Jiang M, Senevirathne C, Aluri S, Zhang T, Guo H, Xavier-Ferrucio J, Jin S, Tran NT, Liu SM, Sun CW, Zhu Y, Zhao Q, Chen Y, Cable L, Shen Y, Liu J, Qu CK, Han X, Klug CA, Bhatia R, Chen Y, Nimer SD, Zheng YG, Iancu-Rubin C, Jin J, Deng H, Krause DS, Xiang J, Verma A, Luo M, Zhao X. Methylation of dual-specificity phosphatase 4 controls cell differentiation. Cell Reports 2021, 36: 109421. PMID: 34320342, PMCID: PMC9110119, DOI: 10.1016/j.celrep.2021.109421.Peer-Reviewed Original ResearchMeSH KeywordsAdultAnimalsArginineCell DifferentiationCell LineChildDual-Specificity PhosphatasesEnzyme StabilityFemaleHEK293 CellsHumansMaleMAP Kinase Signaling SystemMegakaryocytesMethylationMice, Inbred C57BLMiddle AgedMitogen-Activated Protein Kinase PhosphatasesMyelodysplastic Syndromesp38 Mitogen-Activated Protein KinasesPolyubiquitinProtein-Arginine N-MethyltransferasesProteolysisRepressor ProteinsUbiquitinationYoung AdultConceptsDual-specificity phosphataseCell differentiationSingle-cell transcriptional analysisP38 MAPKControls cell differentiationE3 ligase HUWE1Knockdown screeningMK differentiationTranscriptional analysisMegakaryocyte differentiationProtein kinaseP38 axisP38 activationPRMT1Transcriptional signatureContext of thrombocytopeniaMK cellsMechanistic insightsPharmacological inhibitionDifferentiationMethylationMAPKPhosphataseUbiquitinylationActivationIsolation of human ESC-derived cardiac derivatives and embryonic heart cells for population and single-cell RNA-seq analysis
Santoro F, Chien K, Sahara M. Isolation of human ESC-derived cardiac derivatives and embryonic heart cells for population and single-cell RNA-seq analysis. STAR Protocols 2021, 2: 100339. PMID: 33644774, PMCID: PMC7887647, DOI: 10.1016/j.xpro.2021.100339.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cell differentiationEmbryonic stem cell differentiationSingle-cell RNA-seq analysisSingle-cell RNA sequencing analysisComprehensive transcriptional analysisRNA-seq analysisStem cell differentiationRNA sequencing analysisCardiac derivativesFluorescence-activated cell sortingSmart-seq2Developmental tissuesTranscriptional analysisCombination of populationCDNA libraryMolecular atlasHuman embryogenesisHuman ESCsCell differentiationSequencing analysisComplete detailsCell sortingPowerful approachEmbryonic heart cellsDifferentiation
2020
The stress-responsive gene GDPGP1/mcp-1 regulates neuronal glycogen metabolism and survival
Schulz A, Sekine Y, Oyeyemi MJ, Abrams AJ, Basavaraju M, Han SM, Groth M, Morrison H, Strittmatter SM, Hammarlund M. The stress-responsive gene GDPGP1/mcp-1 regulates neuronal glycogen metabolism and survival. Journal Of Cell Biology 2020, 219: e201807127. PMID: 31968056, PMCID: PMC7041677, DOI: 10.1083/jcb.201807127.Peer-Reviewed Original ResearchConceptsNeuronal stress resistanceStress resistanceNovel cellular responsesMouse neuronsVariety of stressesCaenorhabditis elegansC. elegansTranscriptional analysisSingle homologueEnvironmental stressFunctional characterizationCellular responsesCell deathNeuronal cell deathNeuronal glycogenGlycogen metabolismWidespread neuronal cell deathElegansSurvival of animalsTauopathy modelMaladaptive responsesKey roleHomologuesGlycogen levelsKnockdown
2018
Innate Myeloid Cell Subset-Specific Gene Expression Patterns in the Human Colon are Altered in Crohn’s Disease Patients
Sekido Y, Yasumizu Y, Nishimura J, Kayama H, Matsuno H, Ogino T, Miyoshi N, Takahashi H, Haraguchi N, Hata T, Matsuda C, Doki Y, Mori M, Takeda K, Ohkura N, Sakaguchi S, Mizushima T. Innate Myeloid Cell Subset-Specific Gene Expression Patterns in the Human Colon are Altered in Crohn’s Disease Patients. Digestion 2018, 99: 194-204. PMID: 30343293, DOI: 10.1159/000490890.Peer-Reviewed Original ResearchConceptsGene expression patternsGO BP termsExpression patternsGene OntologyGut homeostasisMyeloid cell subsetsInnate myeloid cellsBiological processesCrohn's diseaseComprehensive gene expression profilesMaintenance of gut homeostasisCell type-specific mechanismsCell subsetsMyeloid cellsHuman colonGene expression profilesHuman intestinal lamina propriaInnate immune responseLamina propriaType-specific mechanismsTranscriptional analysisGO-BPRNA sequencingDisease patientsPathogenesis of Crohn's diseaseInteraction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn's disease
Liu TC, Kern JT, VanDussen KL, Xiong S, Kaiko GE, Wilen CB, Rajala MW, Caruso R, Holtzman MJ, Gao F, McGovern DP, Nunez G, Head RD, Stappenbeck TS. Interaction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn's disease. Journal Of Clinical Investigation 2018, 128: 5110-5122. PMID: 30137026, PMCID: PMC6205411, DOI: 10.1172/jci120453.Peer-Reviewed Original ResearchConceptsPaneth cell defectsCD susceptibility genesSusceptibility genesCell defectsDisease-relevant phenotypesTranscriptional analysisCellular phenotypesApoptosis inhibitorCell-specific knockoutDisease subjectsFull-thickness ileumDistinct pathwaysCrohn's disease subjectsComplex inflammatory diseasePPARγ agonist rosiglitazoneCrypt base cellsEnvironmental risk factorsPaneth cellsGenesSelective downregulationCigarette smokingCrohn's diseasePhenotypeRelevant environmental exposuresCD subjectsTranscriptional analysis of immune genes in Epstein-Barr virus-associated gastric cancer and association with clinical outcomes.
Sundar R, Qamra A, Tan A, Zhang S, Ng C, Teh B, Lee J, Kim K, Tan P. Transcriptional analysis of immune genes in Epstein-Barr virus-associated gastric cancer and association with clinical outcomes. Journal Of Clinical Oncology 2018, 36: e16024-e16024. DOI: 10.1200/jco.2018.36.15_suppl.e16024.Peer-Reviewed Original ResearchEpstein-Barr virus-associated gastric cancerClinical outcomesGastric cancerImmune genesTranscriptional analysis
2017
Multiparameter Single Cell Profiling of Airway Inflammatory Cells
Yao Y, Welp T, Liu Q, Niu N, Wang X, Britto CJ, Krishnaswamy S, Chupp G, Montgomery RR. Multiparameter Single Cell Profiling of Airway Inflammatory Cells. Cytometry Part B Clinical Cytometry 2017, 92: 12-20. PMID: 27807928, PMCID: PMC5250532, DOI: 10.1002/cyto.b.21491.Peer-Reviewed Original ResearchConceptsSingle-cell methodsComplex trait diseasesSubgroup of asthmaticsSingle-cell analysisMultiparameter single cell analysisMillions of patientsTranscriptional analysisImmunologic underpinningsInduced sputumAirway diseaseAsthmatic patientsAirway samplesCell subsetsImmune statusFunctional statusClinical severityDistinct biologic mechanismsTreatment successPhysiologic manifestationsBiologic mechanismsCystic fibrosisCellular analysisPatientsCytometry studiesU.S. population
2012
Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology
Sikhakolli UR, López-Giráldez F, Li N, Common R, Townsend JP, Trail F. Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology. Fungal Genetics And Biology 2012, 49: 663-673. PMID: 22705880, DOI: 10.1016/j.fgb.2012.05.009.Peer-Reviewed Original ResearchConceptsF. graminearumOrthologous genesLife historyFusarium graminearumF. verticillioidesGene expressionSexual developmentStage-specific gene expressionSpecies' life historyDifferent life historiesPrevious morphological analysesMorphological developmentLife cycleSexual sporesCereal pathogensUnclassified proteinsFunctional assignmentTranscriptional programsTranscriptome analysisTranscriptional analysisType genesEcological characteristicsApoptotic processFusarium speciesGraminearumInsight into the Transmission Biology and Species-Specific Functional Capabilities of Tsetse (Diptera: Glossinidae) Obligate Symbiont Wigglesworthia
Rio RV, Symula RE, Wang J, Lohs C, Wu YN, Snyder AK, Bjornson RD, Oshima K, Biehl BS, Perna NT, Hattori M, Aksoy S. Insight into the Transmission Biology and Species-Specific Functional Capabilities of Tsetse (Diptera: Glossinidae) Obligate Symbiont Wigglesworthia. MBio 2012, 3: 10.1128/mbio.00240-11. PMID: 22334516, PMCID: PMC3280448, DOI: 10.1128/mbio.00240-11.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsChorismic AcidDNA, BacterialEvolution, MolecularFlagellaFolic AcidGene Expression Regulation, BacterialGenome, BacterialGenome, InsectImmunohistochemistryInheritance PatternsMolecular Sequence DataPhenylalaninePlasmidsSpecies SpecificitySymbiosisSyntenyTranscription, GeneticTsetse FliesWigglesworthiaConceptsSister speciesObligate endosymbiontsTranscriptional regulationHost speciesDevelopment-specific gene expressionTissue-specific functional rolesRobust transcriptional regulationTsetse fliesHigher parasite susceptibilityRole of flagellaAncient endosymbiontGenomic stasisSymbiont genomesSymbiont transmissionGene inventoryHigh syntenySister genomesSmall genomesExtensive conservationUnique genesReproductive biologyFunctional biologyTranscriptional analysisHost developmentLarge inversions
2011
FGF-dependent regulation of VEGF receptor 2 expression in mice
Murakami M, Nguyen LT, Hatanaka K, Schachterle W, Chen PY, Zhuang ZW, Black BL, Simons M. FGF-dependent regulation of VEGF receptor 2 expression in mice. Journal Of Clinical Investigation 2011, 121: 2668-2678. PMID: 21633168, PMCID: PMC3223828, DOI: 10.1172/jci44762.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCells, CulturedEndothelial CellsEnzyme ActivationFibroblast Growth FactorsHindlimbHumansIschemiaMiceMice, Inbred C57BLMitogen-Activated Protein Kinase 1Mitogen-Activated Protein Kinase 3Neovascularization, PhysiologicProto-Oncogene Proteins c-etsSignal TransductionVascular Endothelial Growth Factor Receptor-2Vascular Endothelial Growth FactorsConceptsFGF-dependent regulationETS transcription factorsERK1/2-dependent mannerVEGF receptor-2 expressionActivation of ERK1/2Enhancer activationTranscriptional analysisTranscription factorsVEGFR2 expressionVascular morphogenesisFGF stimulationVEGF stimulationFGFVascular formationExpressionVascular integrityReceptor 2 expressionActivationMorphogenesisVEGFERK1/2Numerous studiesPathwayRegulationDownregulation
1998
Physical and transcriptional analysis of the Trypanosoma brucei genome reveals a typical eukaryotic arrangement with close interspersionof RNA polymerase II- and III-transcribed genes
Marchetti M, Tschudi C, Silva E, Ullu E. Physical and transcriptional analysis of the Trypanosoma brucei genome reveals a typical eukaryotic arrangement with close interspersionof RNA polymerase II- and III-transcribed genes. Nucleic Acids Research 1998, 26: 3591-3598. PMID: 9671824, PMCID: PMC147737, DOI: 10.1093/nar/26.15.3591.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceChloramphenicol O-AcetyltransferaseDNA, ProtozoanEukaryotic CellsGene DosageGenome, ProtozoanMolecular Sequence DataPromoter Regions, GeneticProtozoan ProteinsRibonucleoprotein, U2 Small NuclearRibonucleoproteins, Small NuclearRNA Polymerase IIRNA Polymerase IIIRNA, MessengerTranscription, GeneticTrypanosoma brucei bruceiConceptsPol II transcription unitsPol III genesSmall nuclear RNAU3 small nuclear RNACAT gene cassettePol IITranscription unitRNA genesTranscriptional domainsPol IIICAT mRNAU2 small nuclear RNARNA gene lociPol II genesRNA polymerase IIGene cassettesMRNA processing signalsPolymerase IITranscriptional mapTranscriptional analysisCosmid clonesNuclear RNADistinct initiation sitesCAT geneGene locus
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