2024
Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships.
Kudron M, Gevirtzman L, Victorsen A, Lear B, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Huynh C, Vafeados D, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker S, Reinke V, Waterston R. Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships. Genome Research 2024 PMID: 39438113, DOI: 10.1101/gr.279037.124.Peer-Reviewed Original ResearchHigh-occupancy targetC. elegans transcription factorsSingle cell RNA-seq dataRegulatory relationshipsTranscription factor (TFChromatin immunoprecipitation sequencing dataTF-target relationshipsChIP-seq dataConsensus sequence motifRNA-seq dataDrosophila melanogaster</i>Promote target gene expressionTarget gene expressionChIP-seqSequence motifsSequence dataRegulatory networksEvents in vivoStock CenterModel organismsTranscription factorsTF functionGene expressionBinding sitesCell types
2023
Characterization of the distribution and dynamics of chromatin states in the C. elegans germ line reveals substantial H3K4me3 remodeling during oogenesis
Mazzetto M, Gonzalez L, Sanchez N, Reinke V. Characterization of the distribution and dynamics of chromatin states in the C. elegans germ line reveals substantial H3K4me3 remodeling during oogenesis. Genome Research 2023, 34: gr.278247.123. PMID: 38164610, PMCID: PMC10903938, DOI: 10.1101/gr.278247.123.Peer-Reviewed Original ResearchEpigenetic regulatory mechanismsGerm lineChromatin stateGerm cellsC. elegans germ lineGene expressionRegulatory mechanismsDevelopmental transitionsActive histone modification H3K4me3Most genomic studiesZygotic genome activationSmall RNA pathwaysSpatio-temporal expression patternsHistone modifications H3K4me3Chromatin accessibility dataGerm cell differentiationOverall transcript abundanceUndifferentiated germ cellsGenome activationRNA pathwaysChromatin landscapeChromatin organizationChromatin structureEssential genesHistone modifications
2019
Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression
Han M, Wei G, McManus CE, Hillier LW, Reinke V. Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression. BMC Genomics 2019, 20: 500. PMID: 31208332, PMCID: PMC6580472, DOI: 10.1186/s12864-019-5893-9.Peer-Reviewed Original ResearchConceptsHistone modificationsGerm cellsC. elegansC. elegans germ cellsGene expressionDevelopmental gene expressionGene expression mechanismsIsolation of nucleiGene regulationTranscriptome analysisChromatin immunoprecipitationGerm lineGenomic analysisDistinct genomic profilesRegulatory mechanismsRepressive mechanismsExpression mechanismElegansPure populationsGenomic profilesConsequent discoveriesCellsExpressionGenomeNucleus
2013
Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs
Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology 2013, 14: r5. PMID: 23347407, PMCID: PMC4053757, DOI: 10.1186/gb-2013-14-1-r5.Peer-Reviewed Original ResearchConceptsRb/E2FLin-35Target genesGenome-wide binding profilesGene expressionTissue-specific gene regulationLin-35 mutantsDistinct cell fatesSmall RNA pathwaysEffector target genesDirect target geneBinding profileGermline programHPL-2Chromatin associationH3K36 methylationRNA pathwaysCSR-1Germline transformationC. elegansGene regulationCell fateE2FDirect targetMultiple tissues
2006
Promotion of oogenesis and embryogenesis in the C. elegans gonad by EFL-1/DPL-1 (E2F) does not require LIN-35 (pRB)
Chi W, Reinke V. Promotion of oogenesis and embryogenesis in the C. elegans gonad by EFL-1/DPL-1 (E2F) does not require LIN-35 (pRB). Development 2006, 133: 3147-3157. PMID: 16854972, DOI: 10.1242/dev.02490.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesCaenorhabditis elegansCaenorhabditis elegans ProteinsE2F Transcription FactorsEmbryonic DevelopmentFertilityGene Expression Regulation, DevelopmentalGonadsOligonucleotide Array Sequence AnalysisOogenesisReceptors, LDLRepressor ProteinsRNA-Binding ProteinsTranscription FactorsTranscriptional ActivationConceptsEFL-1/DPLLin-35 mutantsLin-35Dpl-1Efl-1Target genesC. elegansTissue-specific transcriptional programsEctopic cell divisionE2F-binding sitesCell cycle componentsCaenorhabditis elegansTranscriptional programsEarly embryogenesisResponsive genesCell divisionCause defectsRegulatory regionsSomatic tissuesExpression profilingGene expressionReduced broodsOogenesisElegansFunction mutations
2000
Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans
Jiang M, Ryu J, Kiraly M, Duke K, Reinke V, Kim S. Genome-wide analysis of developmental and sex-regulated gene expression profiles in Caenorhabditis elegans. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 98: 218-223. PMID: 11134517, PMCID: PMC14571, DOI: 10.1073/pnas.98.1.218.Peer-Reviewed Original ResearchMeSH KeywordsAgingAnimalsCaenorhabditis elegansCyclinsDisorders of Sex DevelopmentFemaleGene Expression ProfilingGene Expression Regulation, DevelopmentalGenes, HelminthGenes, RetinoblastomaGenomeGenomicsMaleOligonucleotide Array Sequence AnalysisProto-Oncogene ProteinsSex CharacteristicsSex DifferentiationSignal TransductionTranscription FactorsWnt ProteinsZebrafish ProteinsConceptsDNA microarraysCaenorhabditis elegansFull-genome DNA microarraysGene expressionSex-specific differentiationGenome-wide analysisGene expression profilesDifferent developmental stagesComplete molecular profileGene expression levelsExpression profilesExpression dataGenesDevelopmental stagesMolecular levelWorm strainsElegansExpression levelsMicroarrayGrowth conditionsRelative levelsMolecular profileExpressionGlobal viewHermaphroditesA Global Profile of Germline Gene Expression in C. elegans
Reinke V, Smith H, Nance J, Wang J, Van Doren C, Begley R, Jones S, Davis E, Scherer S, Ward S, Kim S. A Global Profile of Germline Gene Expression in C. elegans. Molecular Cell 2000, 6: 605-616. PMID: 11030340, DOI: 10.1016/s1097-2765(00)00059-9.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsCaenorhabditis elegansCaenorhabditis elegans ProteinsCell Cycle ProteinsCytoskeletal ProteinsDrosophila ProteinsGene Expression ProfilingGene Expression Regulation, DevelopmentalHelminth ProteinsMaleMembrane ProteinsOocytesProteinsReceptors, NotchRNA, MessengerRNA-Induced Silencing ComplexSpermatogenesisSpermatozoaX ChromosomeConceptsC. elegans germlineGermline gene expressionEmbryonic signaling pathwaysGene expression patternsStem cell proliferationChromosomal locationProtein kinaseX chromosomeDNA microarraysExpression patternsGene expressionSignaling pathwaysGermline transcriptsGenesCell proliferationGermlineGlobal profileTranscriptsChromosomesNew componentsKinaseMicroarrayPhosphatasePathwayOocytes