Abstract
Variation in fin shape and size contributes to the outstanding morphological diversity of teleost fishes, but the regulation of fin growth has not yet been studied extensively outside the zebrafish model. A previous gene expression study addressing the ornamental elongations of unpaired fins in the African cichlid fish Neolamprologus brichardi identified three genes (cx43, mmp9 and sema3d) with strong and consistent expression differences between short and elongated fin regions. Remarkably, the expression patterns of these genes were not consistent with inferences on their regulatory interactions in zebrafish. Here, we identify a gene expression network (GRN) comprising cx43, mmp9, and possibly also sema3d by a stepwise approach of identifying co-expression modules and predicting their upstream regulators. Among the transcription factors (TFs) predicted as potential upstream regulators of 11 co-expressed genes, six TFs (foxc1, foxp1, foxd3, myc, egr2, irf8) showed expression patterns consistent with their cooperative transcriptional regulation of the gene network. Some of these TFs have already been implicated in teleost fish fin regeneration and formation. We particularly discuss the potential function of foxd3 as driver of the network and its role in the unexpected gene expression correlations observed in N. brichardi.
Highlights
The developmental mechanisms underlying fin formation in fish display remarkable similarities with those involved in appendage development in other vertebrates[1,2,3]
In N. brichardi, we found no correlation between cx[43] and sema3d expression, whereas the expression of cx[43] was positively correlated with mmp[9] expression in each of the unpaired fins[15]
After analysing the expression levels of the 13 most significantly enriched transcription factors (TFs) predicted by two different algorithms in the fins of N. brichardi, we found six TFs displaying L/S differential expression (Fig. 5; Supplementary data 2)
Summary
The developmental mechanisms underlying fin formation in fish display remarkable similarities with those involved in appendage development in other vertebrates[1,2,3]. A recent study, suggests diverse functions of cx[43] during zebrafish skeletal growth and different mutants of cx[43] can confer distinct bone phenotypes in fin and vertebrae[23], though the underlying gene regulatory networks have yet to be elucidated. The lack of an expression correlation between sema3d and cx[43] suggests their regulatory decoupling and the potential involvement of a distinct upstream effector for sema3d during fin morphogenesis in N. brichardi, in contrast to evidence from zebrafish[18]. Candidate genes were identified from co-expression data available for zebrafish and tested for co-expression with mmp[9], cx and sema3d in the intact and regenerating fin tissue of N. brichardi. We provide the first evidence for a potential GRN comprising cx[43], mmp[9] and sema3d, as well as several other genes with unknown roles in fin formation, and provide a basis for further functional investigations in model and non-model organisms
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