A 
Spatial 
and 
Temporal 
Map 
of 
C.
 elegans 
Gene 
Expression

The C. elegans genome has been completely sequenced and the developmental anatomy of this model organism is defined at the resolution of the single cell. Here we describe a strategy that exploits this precisely defined architecture to link gene expression to cell type. We have isolated 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 >30 different cells and developmental stages using tiling arrays. A machine‐learning‐based analysis detects transcripts from established gene models as well as from novel transcriptionally active regions (TARs) in intergenic and intronic domains comprising at least 10% of the total C. elegans genome. Our results show that ~75% of transcripts with detectable expression are differentially expressed among developmental stages and across cell‐types. Biased detection of known tissue and cell‐ specific transcripts validates these data sets and suggests that newly identified differentially expressed TARs may exercise cell‐specific functions. Additionally, regulatory element analysis identifies known transcription factor and miRNA binding sites and predicts novel motifs that likely function to control gene expression. 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.

Published online before print December 22, 2010