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          Institute: MPI für Entwicklungsbiologie     Collection: Abteilung 6 - Molecular Biology (D. Weigel)     Display Documents

ID: 591493.0, MPI für Entwicklungsbiologie / Abteilung 6 - Molecular Biology (D. Weigel)
A spatial and temporal map of C. elegans gene expression
Authors:Spencer, W. C.; Zeller, G.; Watson, J. D.; Henz, S. R.; Watkins, K. L.; McWhirter, R. D.; Petersen, S.; Sreedharan, V. T.; Widmer, C.; Jo, J.; Reinke, V.; Petrella, L.; Strome, S.; Von Stetina, S. E.; Katz, M.; Shaham, S.; Ratsch, G.; Miller, D. M.
Date of Publication (YYYY-MM-DD):2011-02
Title of Journal:Genome Research
Issue / Number:2
Start Page:325
End Page:341
Review Status:not specified
Audience:Not Specified
Abstract / Description: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.
Free Keywords:Animals; Caenorhabditis elegans/*genetics; Computational Biology; Databases, Genetic; Gene Expression Profiling; *Gene Expression Regulation, Developmental/genetics; Male; Meiosis/genetics; Molecular Sequence Data; Oogenesis/genetics; Open Reading Frames/genetics; Transcription, Genetic; Untranslated Regions/genetics; X Chromosome Inactivation/genetics
External Publication Status:published
Document Type:Article
Version Comment:Automatic journal name synchronization
Affiliations:MPI für Entwicklungsbiologie/Abteilung 6 - Molekulare Biologie (Detlef Weigel)
External Affiliations:%G eng
Identifiers:ISSN:1549-5469 (Electronic) 1088-9051 (Linking) %R 10.1... [ID No:1]
URL:http://www.ncbi.nlm.nih.gov/pubmed/21177967 [ID No:2]
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