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The embryonic muscle transcriptome of Caenorhabditis elegans

Rebecca M Fox14, Joseph D Watson12, Stephen E Von Stetina1, Joan McDermott3, Thomas M Brodigan3, Tetsunari Fukushige3, Michael Krause3 and David M Miller12*

Author Affiliations

1 Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Ave. S., Nashville, TN 37232-8240, USA

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

3 Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room B1-04, Bethesda, MD 20892, USA

4 Current address: Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA

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Genome Biology 2007, 8:R188  doi:10.1186/gb-2007-8-9-r188

Published: 12 September 2007



The force generating mechanism of muscle is evolutionarily ancient; the fundamental structural and functional components of the sarcomere are common to motile animals throughout phylogeny. Recent evidence suggests that the transcription factors that regulate muscle development are also conserved. Thus, a comprehensive description of muscle gene expression in a simple model organism should define a basic muscle transcriptome that is also found in animals with more complex body plans. To this end, we applied microarray profiling of Caenorhabtidis elegans cells (MAPCeL) to muscle cell populations extracted from developing C. elegans embryos.


We used fluorescence-activated cell sorting to isolate myo-3::green fluorescent protein (GFP) positive muscle cells, and their cultured derivatives, from dissociated early C. elegans embryos. Microarray analysis identified 7,070 expressed genes, 1,312 of which are enriched in the myo-3::GFP positive cell population relative to the average embryonic cell. The muscle enriched gene set was validated by comparisons with known muscle markers, independently derived expression data, and GFP reporters in transgenic strains. These results confirm the utility of MAPCeL for cell type specific expression profiling and reveal that 60% of these transcripts have human homologs.


This study provides a comprehensive description of gene expression in developing C. elegans embryonic muscle cells. The finding that more than half of these muscle enriched transcripts encode proteins with human homologs suggests that mutant analysis of these genes in C. elegans could reveal evolutionarily conserved models of muscle gene function, with ready application to human muscle pathologies.