Fig. 2.

Schematic comparison of the RPE65 promoter among vertebrates. The vertebrate RPE65 upstream promoter regions (2.8 kb from ATG start codon) were analyzed by MEME pattern motif recognition and TRANSFAC 6.0 software. All vertebrates contained at least one MITF response site, a critical factor for RPE development. The consensus sequences for the motifs described herein are shown in Tables S 2–6 Online Resource. In most higher vertebrates, motif boxes 1, 2, and 3 have a conserved distribution proximal to the ATG codon. Motif boxes 1 and 2 contain nuclear factor 1 (NF-1) and activating enhancer binding protein 4 (AP-4); both are derived from mammalian promoters. Motif 2 was found to be rich in CRX elements. Motif 3 contains the 5′ UTR. NF-1, AP-4, and the 5′ UTR have been shown to be key elements for driving a luciferase reporter gene in mouse and human promoters (Boulanger et al. 2000; Nicoletti et al. 1998). Sequence sites for motif boxes 4 and 5 have not been previously characterized in mammalian promoters (Boulanger et al. 2000; Nicoletti et al. 1998). A TOMTOM motif scan revealed that motif 4 contains tentative elements with sequence similarity values of p < 0.01 for the neural retina leucine zipper (NRL), the sex-determining region Y box (SRY) and FOXO1. Motif 5 shares sequence similarity with LHX2 (p < 0.005). Double underlining denotes an annotated mRNA site upstream of the RPE65 promoter. The accession numbers corresponding to the above species are shown in Table S1 Online Resource. RPE65b is the fish (D. rerio) RPE65 ortholog previously described by Schonthaler et al. (2007)