2010
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, Consortium M, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science 2010, 330: 1775-1787. PMID: 21177976, PMCID: PMC3142569, DOI: 10.1126/science.1196914.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCaenorhabditis elegansCaenorhabditis elegans ProteinsChromatinChromosomesComputational BiologyConserved SequenceEvolution, MolecularGene Expression ProfilingGene Expression RegulationGene Regulatory NetworksGenes, HelminthGenome, HelminthGenomicsHistonesModels, GeneticMolecular Sequence AnnotationRegulatory Sequences, Nucleic AcidRNA, HelminthRNA, UntranslatedTranscription FactorsConceptsAccurate gene modelsGenome-wide identificationTranscription factor-binding sitesKey model organismTranscription factor bindingAlternative splice formsFactor-binding sitesChromatin compositionModENCODE projectChromatin organizationHistone modificationsGenome annotationModel organismsNematode CaenorhabditisChromosomal locationPutative functionsGene modelsTranscriptome profilingChromosome armsTranscription factorsNoncoding RNAsFactor bindingSplice formsX chromosomeGene expressionThe Landscape of C. elegans 3′UTRs
Mangone M, Manoharan A, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak S, Mis E, Zegar C, Gutwein M, Khivansara V, Attie O, Chen K, Salehi-Ashtiani K, Vidal M, Harkins T, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus K, Kim J. The Landscape of C. elegans 3′UTRs. Science 2010, 329: 432-435. PMID: 20522740, PMCID: PMC3142571, DOI: 10.1126/science.1191244.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsAnimalsBinding SitesCaenorhabditis elegansComputational BiologyConserved SequenceDisorders of Sex DevelopmentGene Expression Regulation, DevelopmentalGene LibraryGenes, HelminthHelminth ProteinsHistonesMaleMicroRNAsOperonPoly APolyadenylationRNA, HelminthRNA, MessengerTrans-SplicingConceptsMetazoan messenger RNAsPolyadenylation signalComplementary DNAProtein-coding genesAmplification of complementary DNAMicroRNA target sitesVariant polyadenylation signalHistone genesGenome-widePolyadenylation sitesAlternative isoformsTrans-splicingGene modelsRNA-seqRegulatory elementsCaenorhabditis elegansLong 3'UTRUntranslated regionIsoform specificityPolyadenylationGenesMessenger RNATarget siteIsoformsAnimal ageGenome-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
MEG-1 and MEG-2 Are Embryo-Specific P-Granule Components Required for Germline Development in Caenorhabditis elegans
Leacock SW, Reinke V. MEG-1 and MEG-2 Are Embryo-Specific P-Granule Components Required for Germline Development in Caenorhabditis elegans. Genetics 2008, 178: 295-306. PMID: 18202375, PMCID: PMC2206079, DOI: 10.1534/genetics.107.080218.Peer-Reviewed Original ResearchConceptsP granulesMeg 1Germline developmentGerm lineageMEG 2Embryonic germ lineagesP-granule componentEmbryonic cell divisionGerm cell proliferationGLH-1Germ granulesSomatic lineagesCaenorhabditis elegansGermline segregationMis-segregationMaternal germlineCell divisionGerm cellsPhenotype increasesLineagesGermline defectsPGL-1MutantsProliferationGranules
2006
Regulation of developmental rate and germ cell proliferation in Caenorhabditis elegans by the p53 gene network
Derry W, Bierings R, van Iersel M, Satkunendran T, Reinke V, Rothman J. Regulation of developmental rate and germ cell proliferation in Caenorhabditis elegans by the p53 gene network. Cell Death & Differentiation 2006, 14: 662-670. PMID: 17186023, DOI: 10.1038/sj.cdd.4402075.Peer-Reviewed Original ResearchConceptsCEP-1Genotoxic stressP53 family membersComplex transcriptional regulatory networksDevelopmental rateTranscriptional regulatory networksCell proliferationP53-binding siteGerm cell proliferationTumor suppressor p53Absence of stressGermline apoptosisCaenorhabditis elegansTranscriptional networksC. elegansMammalian counterpartsCheckpoint responseGene networksRegulatory networksTranscriptional targetsP53 gene networkEmbryonic viabilityHuman p63Negative regulatorP53 family
2004
Genetic Analysis of RGS Protein Function in Caenorhabditis elegans
Chase DL, Koelle MR. Genetic Analysis of RGS Protein Function in Caenorhabditis elegans. Methods In Enzymology 2004, 389: 305-320. PMID: 15313573, DOI: 10.1016/s0076-6879(04)89018-9.Peer-Reviewed Original ResearchConceptsRGS proteinsC. elegansG proteinsRGS protein functionStructure/function studiesG protein geneCaenorhabditis elegansGalpha mutantsClose homologProtein functionGalpha proteinsElegansGenetic analysisDetailed protocolTransgenic expressionProteinMost mammaliansMutantsFunction studiesOrthologsCaenorhabditisHomologMammalianGenesOrganisms
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 viewHermaphroditesMutations in β-Spectrin Disrupt Axon Outgrowth and Sarcomere Structure
Hammarlund M, Davis W, Jorgensen E. Mutations in β-Spectrin Disrupt Axon Outgrowth and Sarcomere Structure. Journal Of Cell Biology 2000, 149: 931-942. PMID: 10811832, PMCID: PMC2174563, DOI: 10.1083/jcb.149.4.931.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsAxonsCaenorhabditis elegansCaenorhabditis elegans ProteinsCell MembraneCell PolarityDNA PrimersDNA, ComplementaryEpithelial CellsGenes, HelminthGenes, ReporterGreen Fluorescent ProteinsIntestinesIntracellular MembranesLuminescent ProteinsMolecular Sequence DataMutationSarcomeresSequence Homology, Amino AcidSpectrinSynaptic VesiclesConceptsCell polarityBeta spectrinMembrane skeletonCell membraneCaenorhabditis elegans homologueMost animal cellsSpecific membrane proteinsMembrane integrityAxon outgrowthNull mutantsMembrane proteinsAnimal cellsAbnormal axon outgrowthPlasma membraneSarcomere structureProteinDense bodiesMembraneOutgrowthMajor componentMyofilament latticeMutantsHomologuesGenesPolarity
1999
Ancylostoma secreted protein 2: cloning and characterization of a second member of a family of nematode secreted proteins from Ancylostoma caninum
Hawdon J, Narasimhan S, Hotez P. Ancylostoma secreted protein 2: cloning and characterization of a second member of a family of nematode secreted proteins from Ancylostoma caninum. Molecular And Biochemical Parasitology 1999, 99: 149-165. PMID: 10340481, DOI: 10.1016/s0166-6851(99)00011-0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAncylostomaAncylostomatoideaAnimalsAntibodies, HelminthAntibody SpecificityAspartic Acid EndopeptidasesBase SequenceBlotting, SouthernBlotting, WesternCloning, MolecularDNA, HelminthDogsGenes, HelminthHelminth ProteinsLarvaMolecular Sequence DataRecombinant ProteinsSequence AlignmentConceptsHost-specific signalsLife history stagesFamilies of nematodesEarly eventsNematode physiologyHistory stagesHookworm Ancylostoma caninumParasitic speciesCDNA encodesCDNA libraryParasitic nematodesGene productsDevelopmental eventsInfective third-stage larvaeDiverse familyNematodesAmino acidsExcretory/secretory productsProtein 2ProteinSpecific signalsDatabase searchingAncylostoma caninumThird-stage larvaeImportant functions
1996
Ancylostoma caninum anticoagulant peptide: cloning by PCR and expression of soluble, active protein in E. coli
Cappello M, Hawdon J, Jones B, Kennedy W, Hotez P. Ancylostoma caninum anticoagulant peptide: cloning by PCR and expression of soluble, active protein in E. coli. Molecular And Biochemical Parasitology 1996, 80: 113-117. PMID: 8885227, DOI: 10.1016/0166-6851(96)02658-8.Peer-Reviewed Original ResearchEGL-10 Regulates G Protein Signaling in the C. elegans Nervous System and Shares a Conserved Domain with Many Mammalian Proteins
Koelle M, Horvitz H. EGL-10 Regulates G Protein Signaling in the C. elegans Nervous System and Shares a Conserved Domain with Many Mammalian Proteins. Cell 1996, 84: 115-125. PMID: 8548815, DOI: 10.1016/s0092-8674(00)80998-8.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAmino Acid SequenceAnimalsBase SequenceCaenorhabditis elegansCaenorhabditis elegans ProteinsConserved SequenceFungal ProteinsGene DosageGenes, HelminthGTP-Binding ProteinsMammalsMolecular Sequence DataMusclesMutationNervous SystemNervous System Physiological PhenomenaOvumProteinsRatsRGS ProteinsSerotoninSignal TransductionYeastsConceptsEGL-10G proteinsNematode C. elegansG protein signalingMammalian genesGOA-1Mammalian proteinsC. elegansConserved domainProtein signalingNegative regulatorNeurotransmitter signalingProteinSignalingDose-dependent mannerPathwaySst2pElegansYeastGenesNervous systemDose-dependent fashionRegulatorCertain periodic behaviorsActivity
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