Transcriptional control of <i>C. elegans</i> male tail tip morphogenesis by DMD-3

Sexually dimorphic morphogenesis is governed by DM-domain transcription factors (TFs) in many animals, but how this transcriptional control links to the morphogenetic mechanisms is insufficiently known. The DM-domain TF DMD-3 in Caenorhabditis elegans is the master regulator of a male-specific morphogenetic event that changes the shape of the tail tip from long and pointed in larvae to short and round in adults. This tail tip morphogenesis (TTM) involves cell-shape changes, cell migration, and fusion. To understand how transcriptional regulation by DMD-3 governs TTM, we used male-specific ChIP-seq to identify its direct targets. We found 1,755 DMD-3-bound sites. We identify a DMD-3-associated binding motif and validate its function in TTM. This motif is similar to the binding motif of EOR-1, and eor-1 mutations affect TTM at a penetrance of 13%. This suggests that DMD-3 may act cooperatively with EOR-1 and possibly other TFs. DMD-3 targets 273 genes that play a role in TTM. These genes include other TFs as well as effectors and components of morphogenetic mechanisms. By deleting DMD-3-bound sites endogenously and observing changes in reporter expression and tail tip phenotypes, we identify tissue-specific enhancers in the cis-regulatory regions of fos-1, pan-1, nmy-2, and hmr-1 that play a role in TTM. For fos-1, we propose that a feed-forward loop is responsible for the tail-tip-specific increase in gene expression. Our study suggests that the gene regulatory network for TTM downstream of DMD-3 involves an unexpectedly large hierarchical cascade of TFs, but DMD-3 directly targets some non-TF genes as well.