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The signaling molecule retinoic acid (RA) regulates rod and cone photoreceptor fate, differentiation, and survival. Here we elucidate the role of RA in differential regulation of the tandemly-duplicated  long wavelength-sensitive  ( LWS ) cone opsin genes. Zebrafish embryos were treated with RA from 48 hours post-fertilization (hpf) to 75 hpf, and RNA was isolated from eyes for microarray analysis. ~170 genes showed significantly altered expression, including several transcription factors and components of cellular signaling pathways. Of interest, the  LWS1  opsin gene was strongly upregulated by RA.  LWS1  is the upstream member of the tandemly duplicated  LWS  opsin array and is normally not expressed embryonically. Embryos treated with RA 48 hpf to 100 hpf or beyond showed significant reductions in  LWS2 -expressing cones in favor of  LWS1 -expressing cones. The  LWS  reporter line,  LWS-PAC(H)  provided evidence that individual LWS cones switched from  LWS2  to  LWS1  expression in response to RA. The RA signaling reporter line,  RARE : YFP  indicated that increased RA signaling in cones was associated with this opsin switch, and experimental reduction of RA signaling in larvae at the normal time of onset of  LWS1  expression significantly inhibited  LWS1  expression. A role for endogenous RA signaling in regulating differential expression of the  LWS  genes in postmitotic cones was further supported by the presence of an RA signaling domain in ventral retina of juvenile zebrafish that coincided with a ventral zone of  LWS1  expression. This is the first evidence that an extracellular signal may regulate differential expression of opsin genes in a tandemly duplicated array.

Retinoic Acid Signaling Regulates Differential Expression of the Tandemly-Duplicated Long Wavelength-Sensitive Cone Opsin Genes in Zebrafish