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Open Access Highly Accessed Research article

Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE

Xin Wang1, Yongjun Zhao2, Kim Wong2, Peter Ehlers3, Yuji Kohara4, Steven J Jones2, Marco A Marra2, Robert A Holt2, Donald G Moerman5 and Dave Hansen1*

Author Affiliations

1 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada

2 Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4S6, Canada

3 Department of Mathematics and Statistics, University of Calgary, Calgary, Alberta T2N 1N4, Canada

4 National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japan

5 Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada

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BMC Genomics 2009, 10:213  doi:10.1186/1471-2164-10-213

Published: 9 May 2009



Germ cells must progress through elaborate developmental stages from an undifferentiated germ cell to a fully differentiated gamete. Some of these stages include exiting mitosis and entering meiosis, progressing through the various stages of meiotic prophase, adopting either a male (sperm) or female (oocyte) fate, and completing meiosis. Additionally, many of the factors needed to drive embryogenesis are synthesized in the germ line. To increase our understanding of the genes that might be necessary for the formation and function of the germ line, we have constructed a SAGE library from hand dissected C. elegans hermaphrodite gonads.


We found that 4699 genes, roughly 21% of all known C. elegans genes, are expressed in the adult hermaphrodite germ line. Ribosomal genes are highly expressed in the germ line; roughly four fold above their expression levels in the soma. We further found that 1063 of the germline-expressed genes have enriched expression in the germ line as compared to the soma. A comparison of these 1063 germline-enriched genes with a similar list of genes prepared using microarrays revealed an overlap of 460 genes, mutually reinforcing the two lists. Additionally, we identified 603 germline-enriched genes, supported by in situ expression data, which were not previously identified. We also found >4 fold enrichment for RNA binding proteins in the germ line as compared to the soma.


Using multiple technological platforms provides a more complete picture of global gene expression patterns. Genes involved in RNA metabolism are expressed at a significantly higher level in the germ line than the soma, suggesting a stronger reliance on RNA metabolism for control of the expression of genes in the germ line. Additionally, the number and expression level of germ line expressed genes on the X chromosome is lower than expected based on a random distribution.