2025
SLC25A38 is required for mitochondrial pyridoxal 5’-phosphate (PLP) accumulation
Pena I, Shi J, Chang S, Yang J, Block S, Adelmann C, Keys H, Ge P, Bathla S, Witham I, Sienski G, Nairn A, Sabatini D, Lewis C, Kory N, Vander Heiden M, Heiman M. SLC25A38 is required for mitochondrial pyridoxal 5’-phosphate (PLP) accumulation. Nature Communications 2025, 16: 978. PMID: 39856062, PMCID: PMC11760969, DOI: 10.1038/s41467-025-56130-3.Peer-Reviewed Original ResearchConceptsPyridoxal 5'-phosphateGenome-wide CRISPR interference screenPyridoxal 5'-phosphate-dependent enzymeCRISPR interference screenSerine hydroxymethyltransferase-2Active form of vitamin B6One-carbon unitsImpaired cellular proliferationAmino acid metabolismOne-carbon metabolismInterference screenEssential proteinsMolecular machineryNucleotide synthesisCongenital sideroblastic anemiaProliferation defectSLC25A38Acid metabolismErythroleukemia cellsOrnithine aminotransferaseActive formK562 cellsEnzymatic reactionsCellular proliferationPolyamine synthesis
2022
ACTR5 controls CDKN2A and tumor progression in an INO80-independent manner
Xu X, Chan A, Li M, Liu Q, Mattson N, Pokharel S, Chang W, Yuan Y, Wang J, Moore R, Pirrotte P, Wu J, Su R, Müschen M, Rosen S, Chen J, Yang L, Chen C. ACTR5 controls CDKN2A and tumor progression in an INO80-independent manner. Science Advances 2022, 8: eadc8911. PMID: 36563143, PMCID: PMC9788768, DOI: 10.1126/sciadv.adc8911.Peer-Reviewed Original ResearchCell cycle signalingCRISPR interference screenCell cycle machineryHallmark of tumorigenesisINO80 chromatinInterference screenEpigenetic regulatorsTumor progressionEpigenetic mechanismsCycle machineryEpigenetic dysregulationComplex membersTumor suppressorCell cycleCRISPR geneHCC tumor growthIes6CDKN2A expressionPharmacological inhibitionSignalingMultiple cancersHCC proliferationNovel opportunitiesTumor growthDynamic interplayReovirus infection is regulated by NPC1 and endosomal cholesterol homeostasis
Ortega-Gonzalez P, Taylor G, Jangra RK, Tenorio R, Fernandez de Castro I, Mainou BA, Orchard RC, Wilen CB, Brigleb PH, Sojati J, Chandran K, Sachse M, Risco C, Dermody TS. Reovirus infection is regulated by NPC1 and endosomal cholesterol homeostasis. PLOS Pathogens 2022, 18: e1010322. PMID: 35263388, PMCID: PMC8906592, DOI: 10.1371/journal.ppat.1010322.Peer-Reviewed Original ResearchConceptsNiemann-Pick C1Cholesterol homeostasisActive reovirus core particlesRNA interference screenReovirus outer capsidInfectious subvirion particlesPutative host factorsReovirus infectionTreatment of cellsInterference screenMembrane proteinsEndocytic pathwayMammalian orthoreovirusGenome replicationLate endosomesEndosomal membranesPlasma membraneReovirus attachmentEndoplasmic reticulumOuter capsidViral transcriptionTransport activityEndosomesHomeostasisHuman immunodeficiency virus-1
2019
Spz/Toll-6 signal guides organotropic metastasis in Drosophila
Mishra-Gorur K, Li D, Ma X, Yarman Y, Xue L, Xu T. Spz/Toll-6 signal guides organotropic metastasis in Drosophila. Disease Models & Mechanisms 2019, 12: dmm039727. PMID: 31477571, PMCID: PMC6826028, DOI: 10.1242/dmm.039727.Peer-Reviewed Original ResearchConceptsToll-6Cell migrationRNA interference screenToll family receptorsNovel signaling mechanismReceptive organsInterference screenDevelopmental biologyToll ligandToll receptorWing discGenetic analysisJNK signalingKey regulatorSignaling mechanismCancer biologyOrgan-specific metastasisExhibit traitsHuman cancersOrganotropic metastasisGuidance moleculesPromotes metastasisPowerful modelInnate immunityNF-κB pathwayProximity labeling reveals novel interactomes in live Drosophila tissue
Mannix KM, Starble RM, Kaufman RS, Cooley L. Proximity labeling reveals novel interactomes in live Drosophila tissue. Development 2019, 146: dev176644. PMID: 31208963, PMCID: PMC6679357, DOI: 10.1242/dev.176644.Peer-Reviewed Original ResearchMeSH KeywordsActin CytoskeletonActinsAnimalsAnimals, Genetically ModifiedCell CommunicationCell DifferentiationCytological TechniquesCytoskeletonDNA-(Apurinic or Apyrimidinic Site) LyaseDrosophila melanogasterFemaleGenes, ReporterGerm CellsIntercellular JunctionsMolecular ImagingOocytesOogenesisProtein BindingProtein Interaction MapsStaining and LabelingConceptsProximity labelingIntercellular bridgesProximity-dependent biotinylationStable intercellular bridgesRC proteinDynamic actin cytoskeletonProtein interactome analysisRNA interference screenNovel interactomePrey genesUncharacterized proteinsDistinct interactomesDrosophila tissuesActin cytoskeletonInterference screenInteractome analysisLive tissueMultiple proteinsProximity ligationInteractomeGerm cellsIntercellular communicationRespective preyFunctional roleProtein
2015
Chapter 7 RNAi screens of lysosomal trafficking
Garg S, Brenner M. Chapter 7 RNAi screens of lysosomal trafficking. Methods In Cell Biology 2015, 126: 119-138. PMID: 25665444, DOI: 10.1016/bs.mcb.2014.10.030.Peer-Reviewed Original ResearchConceptsShort hairpin RNA screenRNA interference screenStudy lysosome functionCargo traffickingInterference screenTrafficking proteinsGene candidatesMammalian cellsArray screeningRNA screeningLysosomal functionMicrobial killingAssay developmentLysosomesScreening systemPresentation to T cellsAntigen presentation to T cellsRNATraffickingProteinVesiclesScreeningT cellsBiologyCentral position
2014
Application of the Proximity-Dependent Assay and Fluorescence Imaging Approaches to Study Viral Entry Pathways
Lipovsky A, Zhang W, Iwasaki A, DiMaio D. Application of the Proximity-Dependent Assay and Fluorescence Imaging Approaches to Study Viral Entry Pathways. Methods In Molecular Biology 2014, 1270: 437-451. PMID: 25702134, DOI: 10.1007/978-1-4939-2309-0_30.Peer-Reviewed Original ResearchConceptsGenome-wide RNA interference screenEnriched gene categoriesConfirmation of phenotypesGenome-wide lossRNA interference screenVirus entryFunction genetic screenRNA interference studiesFluorescence imaging approachesProximity ligation assayGenetic screenGene categoriesInterference screenMembrane compartmentsIndividual genesBiochemical approachesCellular compartmentsMolecular intricaciesMicroscopy-based methodBioinformatics analysisProtein locationRNA interferenceCellular organellesViral entry pathwayCellular factors
2009
A role for Lin28 in primordial germ-cell development and germ-cell malignancy
West JA, Viswanathan SR, Yabuuchi A, Cunniff K, Takeuchi A, Park IH, Sero JE, Zhu H, Perez-Atayde A, Frazier AL, Surani MA, Daley GQ. A role for Lin28 in primordial germ-cell development and germ-cell malignancy. Nature 2009, 460: 909-913. PMID: 19578360, PMCID: PMC2729657, DOI: 10.1038/nature08210.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell DifferentiationCell LineChromosomal Proteins, Non-HistoneEmbryonic Stem CellsFemaleGene Expression Regulation, NeoplasticGerm CellsHumansMiceMice, Inbred C57BLNeoplasms, Germ Cell and EmbryonalPositive Regulatory Domain I-Binding Factor 1Repressor ProteinsRNA-Binding ProteinsTranscription FactorsTransgenes
2008
RNA interference screen for human genes associated with West Nile virus infection
Krishnan MN, Ng A, Sukumaran B, Gilfoy FD, Uchil PD, Sultana H, Brass AL, Adametz R, Tsui M, Qian F, Montgomery RR, Lev S, Mason PW, Koski RA, Elledge SJ, Xavier RJ, Agaisse H, Fikrig E. RNA interference screen for human genes associated with West Nile virus infection. Nature 2008, 455: 242-245. PMID: 18690214, PMCID: PMC3136529, DOI: 10.1038/nature07207.Peer-Reviewed Original ResearchMeSH KeywordsComputational BiologyDengue VirusEndoplasmic ReticulumGene Expression ProfilingGenome, HumanHeLa CellsHIVHumansImmunityMonocarboxylic Acid TransportersMuscle ProteinsProtein BindingRNA InterferenceUbiquitin-Protein LigasesUbiquitinationVesiculovirusVirus ReplicationWest Nile FeverWest Nile virus
2005
Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences
Robert VJ, Sijen T, van Wolfswinkel J, Plasterk RH. Chromatin and RNAi factors protect the C. elegans germline against repetitive sequences. Genes & Development 2005, 19: 782-787. PMID: 15774721, PMCID: PMC1074315, DOI: 10.1101/gad.332305.Peer-Reviewed Original ResearchConceptsRepetitive sequencesRepetitive transgenesCaenorhabditis elegans germlineC. elegans germlineProtection of genomeRNA interference screenChromatin factorsRNAi factorsTranscriptional geneChromatin remodelingEndogenous genesInterference screenMolecular dataCatalog genesSelective silencingPutative roleGenesRNAiGermlineSequenceTransgeneTrans effectCosuppressionChromatinGenome
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