RT Journal
A1 Spencer, W. Clay
A1 Zeller, Georg
A1 Watson, Joseph D.
A1 Henz, Stefan R.
A1 Watkins, Kathie L.
A1 McWhirter, Rebecca D.
A1 Petersen, Sarah
A1 Sreedharan, Vipin T.
A1 Widmer, Christian
A1 Jo, Jeanyoung
A1 Reinke, Valerie
A1 Petrella, Lisa
A1 Strome, Susan
A1 Von Stetina, Stephen E.
A1 Katz, Menachem
A1 Shaham, Shai
A1 Rätsch, Gunnar
A1 Miller, David M.
T1 A spatial and temporal map of C. elegans gene expression
JF Genome Research 
JO Genome Research 
YR 2011 
FD February 01 
VO 21 
IS 2 
SP 325 
OP 341 
DO 10.1101/gr.114595.110 
UL http://genome.cshlp.org/content/21/2/325.abstract 
AB 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.