Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis inC. elegans

Abstract

Caenorhabditis elegansmales undergo sex-specific tail tip morphogenesis (TTM) under the control of the 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 vs.dmd-3(-)males and hermaphrodites. The transcription profile ofdmd-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 (UPR) 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 coregulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response.

Morphologically defined substages of tail morphogenesis inC. elegansmales

“…Instead, we speculate that a meshwork of intermediate filaments (IF) could support the retracting tail tip cells similar to that in the terminal web under the luminal membrane of the excretory canal (Buechner et al, 2020) until the aECM is laid down. Consistent with this idea, the genes for the IF IFC-2, and the IF regulators BBLN-1 (Remmelzwaal et al, 2021) and SMA-5 (MAPKinase) (Geisler et al, 2023) are differentially expressed in tail tips undergoing TTM (Kiontke et al, 2024). Visualization of IFC-2 in the tail tip during TTM can be used to test this hypothesis.…”

“…DMD-3 is the master-regulator for TTM, and, together with its paralog MAB-3 required for morphogenesis of all male tail structures (Mason et al, 2008). Reporters for GRL-26 and BLI-1, which are under the control of DMD-3 (Kiontke et al, 2024), are not expressed yet. The BM in the tail tip forms a “roof” over hyp8, hyp9 and the anterior part of hyp10.…”

“…Abundance of UNC-52 is controlled by CRT-1/Calreticulin (Zahreddine et al, 2010). The tail tip-specific RNA-seq analysis (Kiontke et al, 2024) showed that mup-4 and vab-19 are repressed and crt-1 is activated in tails undergoing TTM. This suggests that fibrous organelles play a role in attaching the cuticle to the tail tip epidermis even in the absence of muscle cells in this part of the body.…”

“…RNA-seq of tail tip-specific transcriptomes (Kiontke et al, 2024) identified several genes that are specifically expressed in the tail tip cells. We made translational reporters for two of these genes, grl-26 and bli-1 to follow the fate of the tail tip cells throughout TTM in the context of reporters for other cellular components like AJs and the BM, and redescribe the process of TTM.…”