The Control of Gene Expression Following Injury in the Rat Retina: QTL and PCA

Abstract

Abstract: : Purpose: This study brings two very powerful approaches together to identify regions of the mouse genome regulating changes in gene expression that occur following injury in the retina.Methods: The first aspect of the project used microarrray to define the changes in gene expression after an experimentally induced retinal tear in the rat. The retinae of adult Sprague-Dawley rats were injured by scraping a needle across the surface. Four groups of rats were analyzed: control, 7-day injury (moderate), 7-day injury (severe) and 30-day injury. RNA was isolated and used as targets for Affymetrix Rat Chip (RG_U34A). Specific levels of mRNA were also confirmed using real time PCR. Results: Principle component analysis (PCA) was used to cluster genes that changed in a similar manner following injury. These data were then compared to a data set in which variation in gene expression levels for forebrain were mapped as conventional quantitative traits using interval mapping methods were used to map quantitative traits loci (QTL) for the mouse forebrain. We show that specific PCA clusters are associated with identifiable QTL generated for the mouse forebrain. One PCA cluster contained genes associated with reactive gliosis and mapped to chromosome 6, at 125 Mb in the mouse. Some PCA clusters do not have tightly associated QTL clusters. For example, the crystallin family of proteins is dramatically upregulated following injury; however, members of this family of proteins map to multiple QTLs.Conclusions: In the present study, we show that the response of the retina to injury involves groups of genes some of which can be clustered by PCA. Selected groups of these clustered genes appear to be controlled by single QTLs suggesting that the response to injury may involve broad cascades of gene expression regulated in part by major effect QTLs.

Keywords: lesion study • gene/expression • gene microarray