Genome-wide analysis of sex-enriched gene expression during C. elegans larval development

Kara Thoemke, Woelsung Yi, Jennifer M. Ross, Shinseog Kim, Valerie Reinke, David A Zarkower

Research output: Contribution to journalArticlepeer-review

33 Scopus citations


Sex determination in C. elegans is controlled by the TRA-1 zinc finger protein, a Ci/GLI homolog that promotes female cell fates throughout the body. The regulatory hierarchy that controls TRA-1 is well established, but the downstream effectors that establish sexual dimorphism during larval development remain largely unknown. Here, we describe the use of cDNA microarrays to identify sex-enriched transcripts expressed during three stages of C. elegans larval development. By excluding previously identified germline-enriched transcripts, we focused on somatic sexual development. This approach identified a large number of sex-enriched transcripts that are good candidates to encode regulators of somatic sexual development. We found little overlap between genes with sex-enriched expression in early versus late larval development, indicating that distinct sexual regulatory programs operate at these times. Genes with sex-enriched expression are found throughout the genome, with no strong bias between autosomes and X chromosomes. Reporter gene analysis revealed that these genes are expressed in highly specific patterns in a variety of sexually dimorphic cells. We searched for TRA-1 consensus DNA binding sites near genes with sex-enriched expression, and found that most strongly sex-enriched mRNAs are likely to be regulated indirectly by TRA-1. These results suggest that TRA-1 controls sexual dimorphism through a small number of intermediary regulators rather than by acting directly on the full constellation of genes involved in sex-specific differentiation.

Original languageEnglish (US)
Pages (from-to)500-508
Number of pages9
JournalDevelopmental Biology
Issue number2
StatePublished - Aug 15 2005

Bibliographical note

Funding Information:
The authors thank Jonathan Hodgkin for advice and nematode strains, Marc Sohrmann for DNA binding site searches, and members of the Zarkower lab for advice and assistance. This work was supported by a grant from the NIH to DZ (GM53099), NIH Pre-doctoral Training Grant HD07480 (K.T.). J.R. was supported by a Graduate School Fellowship from the University of Minnesota and an NIH pre-doctoral NRSA award.


  • C. elegans
  • Sex determination
  • Sex-enriched
  • Sexual dimorphism
  • tra-1


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