2018
The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors
Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston R. The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics 2018, 208: 937-949. PMID: 29284660, PMCID: PMC5844342, DOI: 10.1534/genetics.117.300657.Peer-Reviewed Original ResearchConceptsIndividual transcription factorsTranscription factorsModel organismsGenome-wide binding profilesMajor model organismsKey model organismDifferent transcription factorsTissue-specific patternsFly genomeWorm genomeChromatin immunoprecipitationStock CenterRegulatory pathwaysRegulatory sitesCaenorhabditisDrosophilaOrganismsGenomeBinding profileGenesModENCODESitesGFPImmunoprecipitationVast number
2016
A novel small molecule that disrupts a key event during the oocyte-to-embryo transition in C. elegans
Weicksel SE, Mahadav A, Moyle M, Cipriani PG, Kudron M, Pincus Z, Bahmanyar S, Abriola L, Merkel J, Gutwein M, Fernandez AG, Piano F, Gunsalus KC, Reinke V. A novel small molecule that disrupts a key event during the oocyte-to-embryo transition in C. elegans. Development 2016, 143: 3540-3548. PMID: 27510972, PMCID: PMC5087616, DOI: 10.1242/dev.140046.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCaenorhabditis elegansCaenorhabditis elegans ProteinsEmbryo, NonmammalianEmbryonic DevelopmentOocytesTranscription FactorsConceptsEmbryo transitionProtein traffickingEarly embryonic eventsCandidate target genesComplex cellular eventsSmall-molecule screenCaenorhabditis elegansInviable embryosC. elegansEmbryonic lethalityMore key componentsEarly embryogenesisTranscription factorsEarly embryosEmbryonic eventsTarget genesCellular eventsSpecies specificityEggshell integrityNovel small moleculesElegansRemarkable specificityKey eventsOsmotic sensitivityDiverse aspects
2014
The C. elegans SNAPc Component SNPC-4 Coats piRNA Domains and Is Globally Required for piRNA Abundance
Kasper DM, Wang G, Gardner KE, Johnstone TG, Reinke V. The C. elegans SNAPc Component SNPC-4 Coats piRNA Domains and Is Globally Required for piRNA Abundance. Developmental Cell 2014, 31: 145-158. PMID: 25373775, PMCID: PMC4223638, DOI: 10.1016/j.devcel.2014.09.015.Peer-Reviewed Original ResearchConceptsRNA genesPIWI-interacting RNA (piRNA) pathwayTransfer RNA genesSmall RNA genesDiscrete genomic regionsDNA-binding subunitSmall nuclear RNAPiRNA abundanceRNA pathwaysPiRNA genesChromatin organizationPiRNA clustersPiRNA expressionProtein complexesGenomic regionsCoordinated expressionNuclear RNAExpression environmentForeign sequencesGenesExpressionDomainPiRNAsLocalizationTransposonRegulatory analysis of the C. elegans genome with spatiotemporal resolution
Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M. Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature 2014, 512: 400-405. PMID: 25164749, PMCID: PMC4530805, DOI: 10.1038/nature13497.Peer-Reviewed Original ResearchConceptsTranscription factorsRegulatory bindingMetazoan transcription factorsGlobal transcription factorTranscriptional regulatory eventsChIP-seq experimentsKey transcription factorFate specificationGenomic distributionC. elegansIndividual lineagesRegulatory circuitsGenomic coverageRegulatory eventsRegulatory underpinningsRegulatory proteinsBiological processesExpression dataCell typesShared patternRegulatory analysisBindingCaenorhabditisElegansGenomeComparative analysis of regulatory information and circuits across distant species
Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. Comparative analysis of regulatory information and circuits across distant species. Nature 2014, 512: 453-456. PMID: 25164757, PMCID: PMC4336544, DOI: 10.1038/nature13668.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesCaenorhabditis elegansChromatin ImmunoprecipitationConserved SequenceDrosophila melanogasterEvolution, MolecularGene Expression RegulationGene Expression Regulation, DevelopmentalGene Regulatory NetworksGenomeHumansMolecular Sequence AnnotationNucleotide MotifsOrgan SpecificityTranscription Factors
2010
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Research 2010, 21: 245-254. PMID: 21177963, PMCID: PMC3032928, DOI: 10.1101/gr.114587.110.Peer-Reviewed Original ResearchConceptsTranscription factorsTarget genesGenome-wide ChIP-seqDevelopmental processesSequence-specific transcription factorsNon-coding RNA genesHigh-throughput DNA sequencingSelect target genesSingle transcription factorDiverse developmental stagesTranscript start siteCandidate gene targetsEgl-5Hox factorsVulval differentiationLin-39Caenorhabditis elegansTranscriptional networksRNA genesModENCODE consortiumChIP-seqChromatin immunoprecipitationDevelopmental programMab-5Regulatory networksGenome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response
Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M. Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response. PLOS Genetics 2010, 6: e1000848. PMID: 20174564, PMCID: PMC2824807, DOI: 10.1371/journal.pgen.1000848.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesCaenorhabditis elegansCaenorhabditis elegans ProteinsChromatin ImmunoprecipitationEmbryo, NonmammalianEnvironmentGene Expression Regulation, DevelopmentalGenes, HelminthGenome, HelminthGreen Fluorescent ProteinsLarvaProtein BindingRecombinant Fusion ProteinsRNA Polymerase IIStarvationSurvival AnalysisTrans-ActivatorsTranscription FactorsConceptsTranscription factorsPHA-4PHA-4/FOXADiverse biological rolesDifferent biological processesBinding sitesWide IdentificationStarvation responseCellular processesChromatin immunoprecipitationRegulatory networksOrgan developmentDistinct functionsDeep sequencingBiological roleBiological processesEmbryonic pharynxEnvironmental responsesGlobal identificationEnvironmental stimuliDistinct rolesExperimental pipelineCaenorhabditisGenesCritical role
2009
DPL-1 (DP) acts in the germ line to coordinate ovulation and fertilization in C. elegans
Chi W, Reinke V. DPL-1 (DP) acts in the germ line to coordinate ovulation and fertilization in C. elegans. Cells And Development 2009, 126: 406-416. PMID: 19368797, PMCID: PMC2680456, DOI: 10.1016/j.mod.2009.01.008.Peer-Reviewed Original ResearchConceptsEFL-1/DPLDpl-1Germ lineTissue-specific rescue experimentsGonad armsItr-1RME-2Caenorhabditis elegansEfl-1C. elegansGene functionTranscriptional programsInositol triphosphate receptorGonad structureSuccessful reproductionSevere defectsRescue experimentsGerm cellsFunction mutationsSuccessful fertilizationLikely disruptsMutantsSpermathecaTriphosphate receptorElegans
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 viewHermaphrodites