Identification of differentially expressed genes in carp rods and cones

PURPOSE: Rods and cones differ in their photoresponse characteristics, morphology, and susceptibilities to certain diseases. To contribute to the studies at the molecular level of these differences, we tried to identify genes expressed preferentially in rods or cones. METHODS: From purified carp rods and cones, we extracted their RNA and obtained corresponding cDNA pools (rod cDNA and cone cDNA). We employed the suppression subtractive hybridization method to identify the genes expressed preferentially in rods or cones. Cone cDNA was subtracted from rod cDNA to obtain cDNA, which ideally contained cDNA expressed preferentially in rods (R/c cDNA). Similarly, rod cDNA was subtracted from cone cDNA to obtain C/r cDNA. With differential array screening, we screened candidate genes that were expressed mainly or exclusively in rods or cones. The nucleotide sequences of the positive genes were determined. In some of them, their mRNA localizations were confirmed by in situ hybridization. RESULTS: R/c cDNA contained genes already known to code rod specific proteins, such as cGMP gated channel, transducin β1, and rhodopsin. In sharp contrast, C/r cDNA contained genes that code proteins of which functions are mostly unknown. Among them, N-myc downregulated gene 1-like (NDRG1L) and aryl hydrocarbon receptor 2 (AhR2) were most abundant, and by in situ hybridization, they were proven to be expressed specifically in cones. CONCLUSIONS: Using purified rods and cones, we identified mRNAs expressed preferentially in rods or cones. Of particular interest is the specific expression of NDRG1L and AhR2 in cones.