Identification Of Regulatory Elements In The Mammalian Eye

Abstract

Purpose: : Identification novel regulatory elements in the mammalian eye.

Methods: : Two inbred rat strains (SHR/SP and SR/JR/HSD) were crossed, and the resulting F1 animals were then intercrossed to generate 120 F2 progeny. The F2 animals were euthanized at 12 weeks of age, and RNA was collected from whole eye, and DNA was collected from the liver. Gene expression analysis was performed on the F2 animals using Affymetrix GeneChip Rat Genome 230 2.0 arrays. The F2 animals were also genotyped at 399 informative genetic markers.

Results: : More than 1262 distinct regulatory relationships have been identified, correlating gene expression with the genotype of a specific locus. The majority of these gene–marker linkages have the marker at the same locus as the gene (contiguous). However, a sizeable number are at different loci (non–contiguous). Particularly interesting are the 269 genes for which multiple regulating loci have been identified. From these sets of multiple regulatory relationships, we have identified three in which mutations are known to cause retinal degeneration. These include ABCA4, OPN1SW, and TIMM8A. Similarly, the marker linked to the most genes is D20Mgh3, which is linked to 32 distinct probes. Many of these linkages belong to the RT1 family of immune genes, which are part of the MHC class II family of immune genes in the rat. These genes are all near each other and D20Mgh3, so the mechanism may be the up–regulation of a transcribed gene that then regulates the expression of the RT1 family members, or there may be a locus control region (enhancer) nearby that regulates the expression multiple RT1 genes over a multi–megabase region.

Conclusions: : This research identified numerous elements that regulate the expression of genes in the mammalian visual system. Further study should enable the identification of these factors, which will impact our ability to further manipulate the profiles of gene expression within the visual system.

Keywords: genetics • gene microarray • gene modifiers