Individual C. elegans cells can be easily visualized in vivo with GFP reporters but, owing to their small size, they are generally inaccessible for molecular analysis. We have now developed new methods for the isolation and gene expression profiling of GFP marked C. elegans cells (MAPCeL Microarray Profiling C. elegans Cells). In this strategy, GFP cells are isolated by FACS from in vitro cultures and RNA extracted for application to the C. elegans Affymetrix array. To demonstrate the utility of our approach, we have profiled cells in the embryonic motor circuit; we have identified genes that are differentially expressed in body muscle cells and in each of the three classes of embryonic ventral cord motor neurons (DA, DB, DD). Microarray data in each case were validated by strong correlation with genes known to be expressed in these cells as well as with GFP reporters that we constructed (~80%). For example, our MAPCeL data from inhibitory DD motor neurons confirms enrichment of transcripts required for the GABA phenotype (i.e.
unc-25,
unc-30,
unc-47,
snf-11). Conversely, the excitatory DA and DB motor neurons express cholinergic genes (
unc-17,
cha-1) as well as specific transcription factors that regulate cholinergic signaling (
unc-3,
unc-4). These data can now be used to identify novel genes with key roles in the locomotory circuit. For example, we have shown that DA motor neurons express a surprisingly diverse array of G-protein coupled receptors with the potential to modulate excitatory activity in response to neuropeptides as well as classical neurotransmitters. MAPCeL data from body muscle cells lead to the discovery that ACR-16 is a component of the levamisole-insensitive nicotinic ACh receptor (See Touroutine et al., this meeting). Finally, by identifying cohorts of genes with common expression patterns we can now search for cis-regulatory elements necessary for cell-specific expression. For example, we have identified enhancer element candidate motifs in the body wall muscle and DA motor neuron datasets (see Olszewski et al, this meeting). We conclude that MAPCeL can be used to generate reliable profiles of cell specific gene expression in the motor circuit and that these data will be valuable resources for correlating gene expression with function.1.Fox, RM, Von Stetina, SE, Barlow, SJ, Shaffer, C, Olszewski, KL, Moore, JH, Dupuy, D, Vidal, M, Miller, DM III. A gene expression fingerprint of C. elegans Embryonic motor neurons. BMC Genomics 2005, 6:42.