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 typesThe Upstream Sequence Transcription Complex dictates nucleosome positioning and promoter accessibility at piRNA genes in the C. elegans germ line
Paniagua N, Roberts C, Gonzalez L, Monedero-Alonso D, Reinke V. The Upstream Sequence Transcription Complex dictates nucleosome positioning and promoter accessibility at piRNA genes in the C. elegans germ line. PLOS Genetics 2024, 20: e1011345. PMID: 38985845, PMCID: PMC11262695, DOI: 10.1371/journal.pgen.1011345.Peer-Reviewed Original ResearchPiRNA genesPiRNA clustersGenomic domainsC. elegans germ lineUpstream sequence transcription complexSmall RNA pathwaysGermline-specific expressionGlobal genome organizationPiRNA precursorsPiRNA pathwayChromosome IVGenome organizationRNA pathwaysChromatin stateTranscribed genesNucleosome positioningNucleosome densityGenome integrityTranscriptional regulationTranscription complexC. elegansPiRNAsGerm lineISW-1Nucleosomal environment
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
2021
The zinc-finger protein OEF-1 stabilizes histone modification patterns and promotes efficient splicing in the Caenorhabditis elegans germline
McManus CE, Mazzetto M, Wei G, Han M, Reinke V. The zinc-finger protein OEF-1 stabilizes histone modification patterns and promotes efficient splicing in the Caenorhabditis elegans germline. G3: Genes, Genomes, Genetics 2021, 11: jkab329. PMID: 34519784, PMCID: PMC8664474, DOI: 10.1093/g3journal/jkab329.Peer-Reviewed Original ResearchConceptsH3K36me3 levelsAutosomal lociC. elegans germ lineGerm cellsC. elegans germlineActive chromatin stateHistone modification patternsMES-4Chromatin stateEpigenetic balanceMutant phenotypeCaenorhabditis elegansSex chromosomesGenomic domainsGerm lineEfficient splicingDifferentiation programX chromosomeGenetic informationModification patternsTranscript integrityEfficient mRNANovel modifierH3K36me3Downstream effects
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
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 numberThe Germline-Specific Factor OEF-1 Facilitates Coordinated Progression Through Germ Cell Development in Caenorhabditis elegans
McManus CE, Reinke V. The Germline-Specific Factor OEF-1 Facilitates Coordinated Progression Through Germ Cell Development in Caenorhabditis elegans. Genetics 2018, 208: 549-563. PMID: 29167199, PMCID: PMC5788521, DOI: 10.1534/genetics.117.1123.Peer-Reviewed Original ResearchConceptsGerm cell developmentGerm cellsCell developmentGermline-expressed genesNovel nuclear proteinCell cycle checkpointsGermline expressionGenomic integrityUnique fateOocyte differentiationFaithful transmissionCycle checkpointsNuclear proteinsMature gametesX chromosomeDevelopmental eventsLarval stagesMaturation eventsGenetic materialCaenorhabditisFactor 1Developmental progressionSubtle defectsCellsExpression
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 ResearchConceptsEmbryo 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
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
2011
C. elegans meg‐1 and meg‐2 differentially interact with nanos family members to either promote or inhibit germ cell proliferation and survival
Kapelle WS, Reinke V. C. elegans meg‐1 and meg‐2 differentially interact with nanos family members to either promote or inhibit germ cell proliferation and survival. Genesis 2011, 49: 380-391. PMID: 21305687, DOI: 10.1002/dvg.20726.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, Genetically ModifiedCaenorhabditis elegansCaenorhabditis elegans ProteinsCell ProliferationCell SurvivalDisorders of Sex DevelopmentEmbryo, NonmammalianEpistasis, GeneticFemaleGene Expression Regulation, DevelopmentalGerm CellsLuminescent ProteinsMaleRNA InterferenceRNA-Binding ProteinsTime FactorsConceptsGerm cell proliferationMeg 1Germ cellsEmbryonic primordial germ cellsTargeted RNAi screenPrimordial germ cellsCell proliferationGerm cell survivalGerm lineageP granulesRNAi screenLarval stagesMEG 2Cell survivalFamily membersMultiple pathwaysGerm cell degenerationPhenotypeSterilityProliferationOptimal proliferationCellsCell degenerationEmbryogenesisLineagesThe kinase VRK1 is required for normal meiotic progression in mammalian oogenesis
Schober CS, Aydiner F, Booth CJ, Seli E, Reinke V. The kinase VRK1 is required for normal meiotic progression in mammalian oogenesis. Cells And Development 2011, 128: 178-190. PMID: 21277975, DOI: 10.1016/j.mod.2011.01.004.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromosomes, MammalianFemaleHistonesInfertility, FemaleInfertility, MaleMaleMeiosisMiceMice, Inbred C57BLMice, Mutant StrainsMutagenesis, InsertionalOocytesOogenesisOrgan SizeOrgan SpecificityOvaryPhenotypePhosphorylationProtein Serine-Threonine KinasesSeminiferous EpitheliumSpermatogenesisTestisTumor Suppressor Protein p53ConceptsMeiotic progressionNormal meiotic progressionGene trap insertionConserved roleDrosophila oogenesisMammalian gametogenesisMammalian oogenesisVRK1 activityPhosphorylation substratesFemale meiosisInvertebrate speciesProliferation defectMale spermatogoniaChromosomal configurationsMetaphase plateVRK1OogenesisVRK1 expressionFailure of oocytesMouse strainsDrosophilaMeiosisGametogenesisChromosomesLoci
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 analysis of germ cell proliferation in C . elegans identifies VRK-1 as a key regulator of CEP-1/p53
Waters K, Yang AZ, Reinke V. Genome-wide analysis of germ cell proliferation in C . elegans identifies VRK-1 as a key regulator of CEP-1/p53. Developmental Biology 2010, 344: 1011-1025. PMID: 20599896, PMCID: PMC3375680, DOI: 10.1016/j.ydbio.2010.06.022.Peer-Reviewed Original ResearchConceptsGerm cell proliferationVRK-1Germ cellsCEP-1CEP-1/p53Cell proliferationImportant regulatory relationshipsGenome-wide analysisGene expression profilingGermline proliferationCell cycle arrestUseful model systemC. elegansProliferation defectFunctional characterizationNegative regulationExpression profilingRegulatory relationshipsKey regulatorP53 activityCycle arrestUnsuspected mechanismElegansModel systemProliferationGenome-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 receptorElegansMassively parallel sequencing of the polyadenylated transcriptome of C. elegans
Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Research 2009, 19: 657-666. PMID: 19181841, PMCID: PMC2665784, DOI: 10.1101/gr.088112.108.Peer-Reviewed Original ResearchConceptsTrans-spliced leader sequenceSplice junctionsParallel sequencingProtein-coding genesProtein-coding transcriptsPolyadenylated transcriptomeNoncoding transcriptsPutative genesNematode CaenorhabditisSomatic nucleiIntergenic regionGene setsLeader sequenceX chromosomeUnprecedented depthMost sequencesTranscriptsGenesMRNA levelsSequencingNotable regionNovel statistical approachAnnotationQuantitative natureSequence
2008
C. elegans Nucleostemin Is Required for Larval Growth and Germline Stem Cell Division
Kudron MM, Reinke V. C. elegans Nucleostemin Is Required for Larval Growth and Germline Stem Cell Division. PLOS Genetics 2008, 4: e1000181. PMID: 18725931, PMCID: PMC2515194, DOI: 10.1371/journal.pgen.1000181.Peer-Reviewed Original ResearchConceptsRibosome biogenesisGermline stem cell divisionLarval arrest phenotypeGerm line functionGermline stem cellsStem cell divisionCell growthNematode C. elegansN-terminal domainStem cellsExhibit reduced levelsCell cycle arrestArrest phenotypeNucleolar factorsC. elegansRRNA transcriptionGrowth defectNucleolar functionGerm lineCell divisionLarval growthTransgenic studiesBiogenesisStable expressionProliferative state