Global transcriptome profiling of single cells reveals key molecules involved in cellular function and development in <i>C. elegans</i>.

Abstract

The <i>C. elegans</i> 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 <i>C. elegans</i> genome. Our results show that about 75% of transcripts with detectable expression are differentially expressed among developmental stages and across cell types. Additionally, we used self-organizing maps to define groups of co-regulated 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. In a second project, I have identified an immunoglobulin-domain containing cell adhesion molecule that promotes synaptic-connectivity between the AVA command interneuron and A-class motor neurons in the <i>C. elegans</i> motor circuit. Animals carrying a mutation in <i>rig-3</i> show moderate backward locomotion defects. Additionally, <i>rig-3</i> mutants show minor AVA axon guidance defects and most synapses between AVA and A-class motor neurons are lost. These data suggest <i>rig-3</i> plays a critical role in synapse formation. It will be interesting to determine the involvement of <i>rig-3</i> function in connectivity between other neurons in the motor circuit and the entire nervous system.