2016
The time-resolved transcriptome of C. elegans
Boeck ME, Huynh C, Gevirtzman L, Thompson OA, Wang G, Kasper DM, Reinke V, Hillier LW, Waterston RH. The time-resolved transcriptome of C. elegans. Genome Research 2016, 26: 1441-1450. PMID: 27531719, PMCID: PMC5052054, DOI: 10.1101/gr.202663.115.Peer-Reviewed Original ResearchConceptsTime-resolved transcriptomeAlternative splice formsPost-embryonic stagesRNA-seq dataLife cycleC. elegansNematode CaenorhabditisHistone mRNATranscriptional programsLate embryogenesisRNA-seqSplice formsPromoter usageSplice junctionsDifferential usageDetailed annotationGenesExpression correlatesCaenorhabditisElegansTranscriptomeOperonWormBaseEmbryogenesisSL1
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 expression
2009
Massively 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
2003
Adaptation of the nematode Caenorhabditis elegans to extreme osmotic stress
Lamitina ST, Morrison R, Moeckel GW, Strange K. Adaptation of the nematode Caenorhabditis elegans to extreme osmotic stress. American Journal Of Physiology - Cell Physiology 2003, 286: c785-c791. PMID: 14644776, DOI: 10.1152/ajpcell.00381.2003.Peer-Reviewed Original ResearchConceptsExtreme osmotic stressOsmotic stressCell osmoregulationHypertonic stressFunctional genomic analysisNematode Caenorhabditis elegansOrganic osmolyte glycerolPowerful model systemNumerous experimental advantagesCellular osmotic homeostasisCaenorhabditis elegansC. elegansCellular lifeNematode CaenorhabditisOsmolyte glycerolGenomic analysisOsmotic homeostasisGenetic basisOsmotic adaptationTranscriptional expressionOsmotic balanceMolecular understandingAccumulation of glycerolGlycerol accumulationNaCl agar
1995
Caenorhabditis elegans embryos contain only one major species of Ro RNP.
Van Horn D, Eisenberg D, O'Brien C, Wolin S. Caenorhabditis elegans embryos contain only one major species of Ro RNP. RNA 1995, 1: 293-303. PMID: 7489501, PMCID: PMC1369082.Peer-Reviewed Original ResearchConceptsY RNAsRo proteinRo RNPsC. elegans proteinsRNA recognition motifHuman Y RNAsN-terminal extensionPyrimidine-rich internal loopRo autoantigenRNP functionVertebrate proteinsDiscard pathwayVertebrate cellsC. elegansInvertebrate speciesNematode CaenorhabditisVertebrate speciesProtein functionHuman proteinsRNA biosynthesisDefective precursorsRecognition motifRNA moleculesGenetic analysisRNA
1993
The Epithelial Sodium Channel: Recent Developments
Horisberger J, Canessa C, Rossier B. The Epithelial Sodium Channel: Recent Developments. Cellular Physiology And Biochemistry 1993, 3: 283-294. DOI: 10.1159/000154694.Peer-Reviewed Original ResearchApical membraneLarge protein complexesPutative transmembrane segmentsNew channel proteinsAmino acid sequenceSingle cDNA cloneProtein kinase CNematode CaenorhabditisProtein complexesTransmembrane segmentsCDNA clonesAcid sequenceEpithelial sodium channelPotential subunitsChannel proteinsKinase CG proteinsCell deathNeuronal cell deathSensory transductionIntracellular factorsCation channelsMembrane ionic permeabilityAmiloride-sensitive channelsGenes
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