2024
Hepatic GDP-fucose transporter SLC35C1 attenuates cholestatic liver injury and inflammation by inducing CEACAM1 N153 fucosylation
Zhang L, Xie P, Li M, Zhang X, Fei S, Zhao N, Li L, Xie Q, Xu Z, Tang W, Zhu G, Zhu Z, Xu Z, Li J, Zhang C, Boyer J, Chen W, Cai S, Pan Q, Chai J. Hepatic GDP-fucose transporter SLC35C1 attenuates cholestatic liver injury and inflammation by inducing CEACAM1 N153 fucosylation. Hepatology 2024, 81: 774-790. PMID: 38985995, PMCID: PMC11825483, DOI: 10.1097/hep.0000000000001003.Peer-Reviewed Original ResearchMouse model of cholestasisModel of cholestasisCholestatic liver injuryLiver injuryMouse modelCXCL2 expressionSolute carrier familyTandem mass spectrometry analysisPrimary mouse hepatocytesLiver-specific ablationMass spectrometry analysisProtein glycosylationSLC35C1Attenuate cholestatic liver injurySTAT3 SignalingBile ductular proliferationBile duct ligationCarrier familyLevels of serumCholic acid feedingMolecular mechanismsIncreased liver necrosisMRNA transcriptsFucosylationCXCL2 mRNA expression
2022
Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
Griffin KN, Walters BW, Li H, Wang H, Biancon G, Tebaldi T, Kaya CB, Kanyo J, Lam TT, Cox AL, Halene S, Chung JJ, Lesch BJ. Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction. Genome Research 2022, 32: 1655-1668. PMID: 36109149, PMCID: PMC9528986, DOI: 10.1101/gr.276578.122.Peer-Reviewed Original ResearchMammalian male reproductionArgonaute 2Distinct nuclear functionsConditional knockoutMale reproductionProtein Argonaute 2Abnormal sperm head morphologyMeiotic chromatinAnimal developmentCytoplasmic roleNuclear functionsMale meiosisNuclear roleMRNA translationAgo2 proteinImportant genesNuclear compartmentMRNA transcriptsBiological relevanceSperm head morphologyHead morphologySpermatogenic cellsWidespread associationChromatinProtein
2021
m6A mRNA methylation-directed myeloid cell activation controls progression of NAFLD and obesity
Qin Y, Li B, Arumugam S, Lu Q, Mankash SM, Li J, Sun B, Li J, Flavell RA, Li HB, Ouyang X. m6A mRNA methylation-directed myeloid cell activation controls progression of NAFLD and obesity. Cell Reports 2021, 37: 109968. PMID: 34758326, PMCID: PMC8667589, DOI: 10.1016/j.celrep.2021.109968.Peer-Reviewed Original ResearchConceptsNon-alcoholic fatty liver diseaseProgression of NAFLDLineage-restricted deletionFatty liver diseaseMultiple mRNA transcriptsMyeloid cell activationDiet-induced developmentMethyladenosine (m<sup>6</sup>A) RNA modificationMRNA metabolismProtein methyltransferaseLiver diseaseRNA modificationsCellular stressMetabolic reprogrammingDDIT4 mRNACell activationObesityDifferential expressionMammalian targetMRNA transcriptsSignificant downregulationCytokine stimulationPathway activityMetabolic phenotypeMRNA levels
2020
tRFtarget: a database for transfer RNA-derived fragment targets
Li N, Shan N, Lu L, Wang Z. tRFtarget: a database for transfer RNA-derived fragment targets. Nucleic Acids Research 2020, 49: d254-d260. PMID: 33035346, PMCID: PMC7779015, DOI: 10.1093/nar/gkaa831.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase PairingBase SequenceCaenorhabditis elegansDatabases, Nucleic AcidDrosophila melanogasterGene OntologyHumansMiceMolecular Sequence AnnotationNucleic Acid ConformationNucleic Acid HybridizationRhodobacter sphaeroidesRNA, MessengerRNA, Small UntranslatedRNA, TransferSchizosaccharomycesThermodynamicsXenopusZebrafishConceptsTarget genesTransfer RNASmall non-coding RNAsGene Ontology annotationsNon-coding RNAsFunctional pathway analysisAccessible web-based databaseMolecular functionsOntology annotationsBiological functionsPathway analysisMolecular mechanismsPhysiological processesTarget predictionHuman diseasesGenesMRNA transcriptsRNAWeb-based databaseConvenient linkTRFImportant roleRNAhybridTargetIntaRNAA psychiatric disease-related circular RNA controls synaptic gene expression and cognition
Zimmerman AJ, Hafez AK, Amoah SK, Rodriguez BA, Dell’Orco M, Lozano E, Hartley BJ, Alural B, Lalonde J, Chander P, Webster MJ, Perlis RH, Brennand KJ, Haggarty SJ, Weick J, Perrone-Bizzozero N, Brigman JL, Mellios N. A psychiatric disease-related circular RNA controls synaptic gene expression and cognition. Molecular Psychiatry 2020, 25: 2712-2727. PMID: 31988434, PMCID: PMC7577899, DOI: 10.1038/s41380-020-0653-4.Peer-Reviewed Original ResearchConceptsSynaptic gene expressionCircular RNAsGene expressionAlternative mRNA transcriptsDisease-associated circRNAsHomolog 1Neuronal RNAMRNA transcriptsRNASynaptic expressionAge of onsetMammalian brainCircRNAsPotential involvementDorsolateral prefrontal cortexOrbitofrontal cortexBipolar disorderPrefrontal cortexKnockdownExpressionFrontal cortexSynaptic plasticityNeuronal culturesPsychiatric diseasesMouse orbitofrontal cortex
2019
Aberrant splicing contributes to severe α-spectrin-linked congenital hemolytic anemia
Gallagher PG, Maksimova Y, Lezon-Geyda K, Newburger PE, Medeiros D, Hanson RD, Rothman J, Israels S, Wall DA, Sidonio RF, Sieff C, Gowans LK, Mittal N, Rivera-Santiago R, Speicher DW, Baserga SJ, Schulz VP. Aberrant splicing contributes to severe α-spectrin-linked congenital hemolytic anemia. Journal Of Clinical Investigation 2019, 129: 2878-2887. PMID: 31038472, PMCID: PMC6597203, DOI: 10.1172/jci127195.Peer-Reviewed Original ResearchConceptsRecessive hereditary spherocytosisSplice acceptor siteHuman genetic diseasesMRNA stability studiesAberrant splicing contributesSplicing contributesWhole-genome sequencingSplicing analysisHereditary pyropoikilocytosisTermination codonNull allelesGenome sequencingWhole-exome sequencingBranch pointsNumerous mutationsGenetic diseasesLinkage disequilibriumMRNA transcriptsΑ-spectrinMinigene studiesAcceptor sitesMutationsExome sequencingNew targets
2018
Altered Splicing from a Mutated Alternate Branch Point Is Common in Severe Alpha-Spectrin Linked Inherited Anemia
Lezon-Geyda K, Schulz V, Maksimova Y, Gallagher P. Altered Splicing from a Mutated Alternate Branch Point Is Common in Severe Alpha-Spectrin Linked Inherited Anemia. Blood 2018, 132: 503. DOI: 10.1182/blood-2018-99-117752.Peer-Reviewed Original ResearchMRNA transcriptsTermination codonK562 cellsMinigene assayIntron 30Precise genetic basisAcceptor sitesInsertion/deletion mutationsHereditary pyropoikilocytosisWhole-genome sequencingNMD inhibitorsAcceptor splice siteDiagnostic gene panelsGenome databaseMRNA splicingWild-type minigeneConsensus sitesAltered splicingExon 31Genetic basisTranscript productionErythroid cellsGene manipulationGenetic analysisWT backgroundSpatial distribution of marker gene activity in the mouse lung during alveolarization
Ljungberg MC, Sadi M, Wang Y, Aronow BJ, Xu Y, Kao RJ, Liu Y, Gaddis N, Ardini-Poleske ME, Umrod T, Ambalavanan N, Nicola T, Kaminski N, Ahangari F, Sontag R, Corley RA, Ansong C, Carson JP. Spatial distribution of marker gene activity in the mouse lung during alveolarization. Data In Brief 2018, 22: 365-372. PMID: 30596133, PMCID: PMC6307338, DOI: 10.1016/j.dib.2018.10.150.Peer-Reviewed Original ResearchRNA-seq expression profilesMarker gene activityGene expression patternsLung developmentLung Development ProgramGene activityRNA-seqMolecular atlasCellular differentiationDifferent genesExpression patternsExpression profilesNormal lung developmentMouse lungMRNA transcriptsMammalian lungMRNA probesProbe sequencesAbnormal lung developmentCurated CollectionGenesSpatial distributionTranscriptsE16.5E18.5
2014
High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing
Cho H, Davis J, Li X, Smith K, Battle A, Montgomery S. High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing. PLOS ONE 2014, 9: e108095. PMID: 25251678, PMCID: PMC4176000, DOI: 10.1371/journal.pone.0108095.Peer-Reviewed Original ResearchConceptsAllele-specific expressionTranscriptome analysisRNA sequencingAlternative splicing patternsCell line GM12878RNA-seq protocolsSequencing of cDNARNA-seq datasetsIndividual transcriptomesGenomic elementsAlternative splicingSplicing patternsAllelic expressionTranscript quantificationRead lengthMRNA transcriptsMapping biasSequencingExpressionTranscriptomeGM12878SplicingTechnical hurdlesCDNAGenes
2013
mRNA-Binding Protein ZFP36 Is Expressed in Atherosclerotic Lesions and Reduces Inflammation in Aortic Endothelial Cells
Zhang H, Taylor WR, Joseph G, Caracciolo V, Gonzales DM, Sidell N, Seli E, Blackshear PJ, Kallen CB. mRNA-Binding Protein ZFP36 Is Expressed in Atherosclerotic Lesions and Reduces Inflammation in Aortic Endothelial Cells. Arteriosclerosis Thrombosis And Vascular Biology 2013, 33: 1212-1220. PMID: 23559629, PMCID: PMC3844532, DOI: 10.1161/atvbaha.113.301496.Peer-Reviewed Original ResearchConceptsVascular endothelial cellsEndothelial cellsAortic endothelial cellsAtherosclerotic lesionsFoam cellsAnti-inflammatory effectsHuman aortic endothelial cellsNuclear factor-κB transcriptional activationLow-density lipoproteinMacrophage foam cellsZinc finger protein 36Vascular inflammationAngiotensin IIInflammatory cytokinesCytokine mRNAZFP36 expressionBacterial lipopolysaccharideHealthy aortaInflammationTarget cellsLesionsZFP36Protein 36CellsMRNA transcripts
2011
In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma
Karreth FA, Tay Y, Perna D, Ala U, Tan SM, Rust AG, DeNicola G, Webster KA, Weiss D, Perez-Mancera PA, Krauthammer M, Halaban R, Provero P, Adams DJ, Tuveson DA, Pandolfi PP. In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma. Cell 2011, 147: 382-395. PMID: 22000016, PMCID: PMC3236086, DOI: 10.1016/j.cell.2011.09.032.Peer-Reviewed Original ResearchConceptsMicroRNA recognition elementsLow PTEN levelsPTEN protein levelsZEB2 expressionBeauty insertional mutagenesisMicroRNA decoysPI3K/Akt pathwayLoss of PTENCeRNA activityInsertional mutagenesisZeb2 transcriptTumor suppressorCell transformationCeRNAsPTEN levelsAkt pathwayFunctional roleMRNA transcriptsSignificant enrichmentZEB2 mRNAProtein levelsMouse modelCeRNATranscriptsPTEN
2010
Proliferative arrest of neural cells induces prion protein synthesis, nanotube formation, and cell‐to‐cell contacts
Miyazawa K, Emmerling K, Manuelidis L. Proliferative arrest of neural cells induces prion protein synthesis, nanotube formation, and cell‐to‐cell contacts. Journal Of Cellular Biochemistry 2010, 111: 239-247. PMID: 20518071, PMCID: PMC2930104, DOI: 10.1002/jcb.22723.Peer-Reviewed Original ResearchConceptsProliferative arrestTerminal differentiationCell division arrestT antigenStationary cellsNeuronal precursor cellsDivision arrestHost prion proteinKey developmental timesSV-40 T antigenAdherent junctionsDevelopmental timeProtein synthesisLiving cellsMRNA transcriptsPrion proteinNeural cellsPrecursor cellsCell contactGrowth conesDNA-synthesizing cellsCellsReduced serumNeuritic processesDifferentiation
2009
Metastatic gene signatures and emerging novel prognostic tests in the management of early stage breast cancer
Tordai A, Liedtke C, Pusztai L. Metastatic gene signatures and emerging novel prognostic tests in the management of early stage breast cancer. Clinical & Experimental Metastasis 2009, 26: 625-632. PMID: 19381845, DOI: 10.1007/s10585-009-9261-z.Peer-Reviewed Original ResearchConceptsMetastatic gene signatureGene expression studiesGene expression profilingDistinct neoplastic diseasesExpression profilingDNA microarraysExpression studiesGene expressionMRNA transcriptsGene signatureSingle experimentNovel diagnostic assaysTranscriptsDiagnostic assaysNovel prognostic testsMicroarrayProfilingExpression
2007
Impaired microRNA processing enhances cellular transformation and tumorigenesis
Kumar MS, Lu J, Mercer KL, Golub TR, Jacks T. Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nature Genetics 2007, 39: 673-677. PMID: 17401365, DOI: 10.1038/ng2003.Peer-Reviewed Original ResearchConceptsTarget mRNA transcriptsShort hairpin RNAGlobal repressionCellular transformationMRNA transcriptsMiRNA processing machinerySmall noncoding RNAsMature miRNA expressionMiRNA lossMiRNA maturationMiRNA processingMicroRNA processingNoncoding RNAsUndifferentiated stateProcessing machineryMiRNA expressionHairpin RNAConditional deletionTumorigenesisMiRNA levelsCancer cellsTumor developmentRepressionTranscriptsRNA1,25-Dihydroxyvitamin D3 induces expression of the Wnt signaling co-regulator LRP5 via regulatory elements located significantly downstream of the gene's transcriptional start site
Fretz JA, Zella LA, Kim S, Shevde NK, Pike JW. 1,25-Dihydroxyvitamin D3 induces expression of the Wnt signaling co-regulator LRP5 via regulatory elements located significantly downstream of the gene's transcriptional start site. The Journal Of Steroid Biochemistry And Molecular Biology 2007, 103: 440-445. PMID: 17229572, PMCID: PMC1868540, DOI: 10.1016/j.jsbmb.2006.11.018.Peer-Reviewed Original ResearchConceptsTranscriptional start siteGene transcriptional start siteChIP-chip analysisLRP5/LRP6Chromatin structureHuman genomeRegulatory regionsStart siteRegulatory elementsWnt familyHeterologous promoterCanonical WntMembrane receptorsMRNA transcriptsWntSecreted memberOsteoblastic cellsLRP5GenesVDRELRP5 geneBone formationProteinLrp5 locusOsteoblast number
2006
The Challenge of Viral snRNPs
CONRAD NK, FOK V, CAZALLA D, BORAH S, STEITZ JA. The Challenge of Viral snRNPs. Cold Spring Harbor Symposia On Quantitative Biology 2006, 71: 377-384. PMID: 17381320, DOI: 10.1101/sqb.2006.71.057.Peer-Reviewed Original ResearchConceptsNuclear noncoding RNAsHSURs 1Sarcoma-associated herpesvirusRibosomal protein L22Aggressive T-cell leukemiaT cell signalingViral gene expressionKaposi's sarcoma-associated herpesvirusHeterokaryon assayU RNADependent RNA degradationMammalian cellsNoncoding RNAsProtein L22Nuclear surveillanceRNA degradationHost mRNAsHost proteinsGene expressionMRNA transcriptsMutant virusHerpesvirus saimiriRNAImportant functionsRNAs
2005
Integrating mRNA Decay Information into Co-Regulation Study
Chen L, Zhao H. Integrating mRNA Decay Information into Co-Regulation Study. Journal Of Computer Science And Technology 2005, 20: 434-438. DOI: 10.1007/s11390-005-0434-1.Peer-Reviewed Original ResearchMRNA decay ratesTranscript amountsTranscription rateBioinformatics analysisTranscriptional regulatory networksCo-regulated genesRelative transcript amountsMRNA degradation ratesHigh-throughput technologiesGene regulationGenomic signalsRegulatory networksDifferent genesGene clusteringMRNA synthesisMRNA transcriptsDownstream analysisGenesDNAMotifSimilarity analysisTranscriptsRegulationIdentification
2002
Integrin‐dependent regulation of gene expression in leukocytes
Rossetti G, Collinge M, Molteni R, Bender J, Pardi R. Integrin‐dependent regulation of gene expression in leukocytes. Immunological Reviews 2002, 186: 189-207. PMID: 12234372, DOI: 10.1034/j.1600-065x.2002.18616.x.Peer-Reviewed Original ResearchConceptsIntegrin engagementGene expression regulationIntegrin-dependent regulationCell cycle restriction pointExpression regulationNumerous genesTransduce signalsMatrix degrading proteinsTranscriptional activationGenetic programTranscription modulatorsIntegrin-dependent mechanismJAK-STATsGene expressionIntercellular adhesionDegrading proteinsCell differentiationAlphaLbeta2 integrinJab-1Restriction pointMRNA transcriptsT cell differentiationEnvironmental stimuliPotent signalCell phenotypeIdentification and characterization of genes differentially expressed in the testis/vas deferens of the fed male tick, Amblyomma hebraeum
Weiss BL, Stepczynski JM, Wong P, Kaufman WR. Identification and characterization of genes differentially expressed in the testis/vas deferens of the fed male tick, Amblyomma hebraeum. Insect Biochemistry And Molecular Biology 2002, 32: 785-793. PMID: 12044495, DOI: 10.1016/s0965-1748(01)00161-8.Peer-Reviewed Original ResearchConceptsTestis/vas deferensMature male gonadsCharacterization of genesNorthern blot analysisSequence similarityCDNA libraryMale developmentGonad maturationGenomic DNAMale gonadsMolecular phenotypesMRNA transcriptsGenesBlot analysisTissues of fedUnfed malesClonesUnfed animalsFed ticksPhysiological changesAmblyomma hebraeumVas deferensTicksHomologyAcylphosphatase
1998
Detection of thyroglobulin, thyroid peroxidase, and RET/PTC1 mRNA transcripts in the peripheral blood of patients with thyroid disease.
Tallini G, Ghossein RA, Emanuel J, Gill J, Kinder B, Dimich AB, Costa J, Robbins R, Burrow GN, Rosai J. Detection of thyroglobulin, thyroid peroxidase, and RET/PTC1 mRNA transcripts in the peripheral blood of patients with thyroid disease. Journal Of Clinical Oncology 1998, 16: 1158-66. PMID: 9508203, DOI: 10.1200/jco.1998.16.3.1158.Peer-Reviewed Original ResearchConceptsReverse transcription-polymerase chain reactionPeripheral bloodThyroid diseaseThyroid carcinomaBenign thyroid nodulesThyroid peroxidaseThyroid nodulesRT-PCR positivityPeripheral blood samplesDiagnosis of carcinomaTranscription-polymerase chain reactionPapillary thyroid carcinomaBenign thyroid lesionsRET/PTC1Cervical lymphInitial surgeryClinical evidenceExtrathyroid extensionNodular hyperplasiaBenign lesionsPatientsCarcinomaBlood collectionMRNA transcriptsThyroid lesions
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