title: A spatial and temporal map of C. elegans gene expression.
abstract: The C. elegans genome has been completely sequenced, and the developmental anatomy of this model organism is described at single-cell resolution. Here we utilize strategies that exploit this precisely defined architecture to link gene expression to cell type. We obtained RNAs from specific cells and from each developmental stage using tissue-specific promoters to mark cells for isolation by FACS or for mRNA extraction by the mRNA-tagging method. We then generated gene expression profiles of more than 30 different cells and developmental stages using tiling arrays. Machine-learning-based analysis detected transcripts corresponding to established gene models and revealed novel transcriptionally active regions (TARs) in noncoding domains that comprise at least 10% of the total C. elegans genome. Our results show that about 75% of transcripts with detectable expression are differentially expressed among developmental stages and across cell types. Examination of known tissue- and cell-specific transcripts validates these data sets and suggests that newly identified TARs may exercise cell-specific functions. Additionally, we used self-organizing maps to define groups of coregulated transcripts and applied regulatory element analysis to identify known transcription factor- and miRNA-binding sites, as well as novel motifs that likely function to control subsets of these genes. By using cell-specific, whole-genome profiling strategies, we have detected a large number of novel transcripts and produced high-resolution gene expression maps that provide a basis for establishing the roles of individual genes in cellular differentiation.
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: W Clay
authors.initials: WC
authors.lastname: Spencer
authors.forename: Georg
authors.initials: G
authors.lastname: Zeller
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Watson
authors.forename: Stefan R
authors.initials: SR
authors.lastname: Henz
authors.forename: Kathie L
authors.initials: KL
authors.lastname: Watkins
authors.forename: Rebecca D
authors.initials: RD
authors.lastname: McWhirter
authors.forename: Sarah
authors.initials: S
authors.lastname: Petersen
authors.forename: Vipin T
authors.initials: VT
authors.lastname: Sreedharan
authors.forename: Christian
authors.initials: C
authors.lastname: Widmer
authors.forename: Jeanyoung
authors.initials: J
authors.lastname: Jo
authors.forename: Valerie
authors.initials: V
authors.lastname: Reinke
authors.forename: Lisa
authors.initials: L
authors.lastname: Petrella
authors.forename: Susan
authors.initials: S
authors.lastname: Strome
authors.forename: Stephen E
authors.initials: SE
authors.lastname: Von Stetina
authors.forename: Menachem
authors.initials: M
authors.lastname: Katz
authors.forename: Shai
authors.initials: S
authors.lastname: Shaham
authors.forename: Gunnar
authors.initials: G
authors.lastname: Rätsch
authors.forename: David M
authors.initials: DM
authors.lastname: Miller
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics; D008297:Male; D008540:Meiosis / Q000235:genetics; D008969:Molecular Sequence Data; D009866:Oogenesis / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D014158:Transcription, Genetic; D020506:Untranslated Regions / Q000235:genetics; D049951:X Chromosome Inactivation / Q000235:genetics
chemical_list: D020506:Untranslated Regions