ABSTRACT
Caenorhabditis elegans males undergo sex-specific tail tip morphogenesis (TTM) under the control of the DM-domain transcription factor DMD-3. To find genes regulated by DMD-3, we performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males versus dmd-3(-) males and hermaphrodites. The transcription profile of dmd-3(-) tail tips is similar to that in hermaphrodites. For validation, we analyzed transcriptional reporters for 49 genes and found male-specific or male-biased expression for 26 genes. Only 11 DE genes overlapped with genes found in a previous RNAi screen for defective TTM. GO enrichment analysis of DE genes finds upregulation of genes within the unfolded protein response pathway and downregulation of genes involved in cuticle maintenance. Of the DE genes, 40 are transcription factors, indicating that the gene network downstream of DMD-3 is complex and potentially modular. We propose modules of genes that act together in TTM and are co-regulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response.
Footnotes
Author contributions
Conceptualization: K.C.K., R.A.H., D.A.M., D.H.A.F.; Methodology: K.C.K., R.A.H., D.A.M., D.H.A.F.; Software: Y.P.; Validation: K.C.K., D.A.M.; Formal analysis: A.W.; Investigation: K.C.K., D.A.M., S.V.; Resources: K.C.K., D.A.M.; Data curation: A.W.; Writing - original draft: K.C.K.; Writing - review & editing: R.A.H., D.A.M., D.H.A.F.; Visualization: K.C.K., D.A.M., Y.P., A.W.; Supervision: K.C.K., D.A.M., D.H.A.F.; Project administration: D.A.M., D.H.A.F.; Funding acquisition: D.A.M., D.H.A.F.
Funding
This work was supported by the National Institutes of Health (R01GM141395 to D.H.A.F.) and by the National Science Foundation (1656736 to D.H.A.F. and IOS-1255877 to D.A.M.). Deposited in PMC for release after 12 months.
Data availability
The sequencing reads have been deposited in the SRA database under BioProject ID PRJNA1046486.
