2024
Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships.
Kudron M, Gewirtzman L, Victorsen A, Lear B, Vafeados D, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Hyunh C, 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, gr.279037.124. 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 types
2010
Genome-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