Enhancer evolution as a driving force for lineage-specific paralog usage in the central nervous system

Expression patterns of paralogous genes in the functionally homologous cells sometimes show differences across species. However, no reasonable explanation for the mechanism underlying such phenomena has been discovered. To understand this mechanism, the present study focused on the hypophysiotropic GnRH neurons in vertebrates as a model. These neurons express either gnrh1 or gnrh3 paralogs depending on species, and apparent switching of the expressed paralogs in them occurred at least four times in vertebrate evolution. First, we found redundant expressions of gnrh1 and gnrh3 in a single neuron in piranha and hypothesized that this situation may indicate an ancestral condition. We tested this hypothesis by examining the activity of piranha gnrh1/gnrh3 enhancers in zebrafish and medaka, in which the two gnrh paralogs are not co-expressed. Here, the gnrh1/gnrh3 enhancer of piranha induced reporter RFP/GFP co-expressions in a single hypophysiotropic GnRH neuron in both zebrafish and medaka. From these results, we propose that long-lasting (∼550 My) redundancy after gnrh1/3 duplication in 1R/2R WGD may be the key to apparent switching of the paralog usage among the present-day species. Moreover, interspecies analyses of enhancers indicated that the loss of enhancers rather than changes in trans-regulatory elements drove the role-division of these paralogs.