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
2014
Comparative 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 FactorsRegulatory 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 analysisBindingCaenorhabditisElegansGenome
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
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