Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system

Stephen E Von Stetina^*¹ , Joseph D Watson^*² , Rebecca M Fox¹^,3 , Kellen L Olszewski¹^,4 , W Clay Spencer¹ , Peter J Roy⁵ and David M Miller III¹^,2

¹Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232-8240, USA

²Graduate Program in Neuroscience, Center for Molecular Neuroscience, Vanderbilt University, Nashville, TN 37232-8548, USA

³Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA

⁴Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University 246 Carl Icahn Laboratory, Princeton NJ 08544, USA

⁵Department of Medical Genetics and Microbiology, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 1A, Canada

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R135doi:10.1186/gb-2007-8-7-r135


Published:	5 July 2007

Subject areas: Neurobiology, Development, Genome studies

Abstract

Background

With its fully sequenced genome and simple, well-defined nervous system, the nematode Caenorhabditis elegans offers a unique opportunity to correlate gene expression with neuronal differentiation. The lineal origin, cellular morphology and synaptic connectivity of each of the 302 neurons are known. In many instances, specific behaviors can be attributed to particular neurons or circuits. Here we describe microarray-based methods that monitor gene expression in C. elegans neurons and, thereby, link comprehensive profiles of neuronal transcription to key developmental and functional properties of the nervous system.

Results

We employed complementary microarray-based strategies to profile gene expression in the embryonic and larval nervous systems. In the MAPCeL (Microarray Profiling C. elegans cells) method, we used fluorescence activated cell sorting (FACS) to isolate GFP-tagged embryonic neurons for microarray analysis. To profile the larval nervous system, we used the mRNA-tagging technique in which an epitope-labeled mRNA binding protein (FLAG-PAB-1) was transgenically expressed in neurons for immunoprecipitation of cell-specific transcripts. These combined approaches identified approximately 2,500 mRNAs that are highly enriched in either the embryonic or larval C. elegans nervous system. These data are validated in part by the detection of gene classes (for example, transcription factors, ion channels, synaptic vesicle components) with established roles in neuronal development or function. Of particular interest are 19 conserved transcripts of unknown function that are also expressed in the mammalian brain. In addition to utilizing these profiling approaches to define stage-specific gene expression, we also applied the mRNA-tagging method to fingerprint a specific neuron type, the A-class group of cholinergic motor neurons, during early larval development. A comparison of these data to a MAPCeL profile of embryonic A-class motor neurons identified genes with common functions in both types of A-class motor neurons as well as transcripts with roles specific to each motor neuron type.

Conclusion

We describe microarray-based strategies for generating expression profiles of embryonic and larval C. elegans neurons. These methods can be applied to particular neurons at specific developmental stages and, therefore, provide an unprecedented opportunity to obtain spatially and temporally defined snapshots of gene expression in a simple model nervous system.