Comparative gene expression analysis of murine retina and brain

Abstract

Abstract: : Purpose: The retina is often used as a model system for investigating mechanisms of CNS development and function. In this study, we compared retina and brain gene expression using microarray analyses. Methods: RNA was extracted from mouse retina, brain and liver, and hybridized to a custom–made 5,376 gene cDNA microarray. Data normalization and statistical analyses were performed using Bioconductor and SAM. The cellular distribution of retina–enriched genes was determined by immunohistochemistry. Results: Microarray comparisons identified 733 genes preferentially expressed in retina and 427 in brain. Many genes important to neuronal activity were differentially expressed, including ion channels and cytoskeletal proteins. An additional 837 retina–enriched genes were identified by retina–liver comparisons. The non–vision related retina genes identified on the microarray had limited overlap with those found by analyses of published SAGE and EST library databases. Quantitative PCR confirmed preferential retinal expression of genes identified by microarray. To begin to characterize the retina–enriched transcripts, we determined the expression pattern of genes that had not previously been reported in the retina. EWS and PCPB1, two RNA binding proteins, were localized primarily to the inner nuclear layer. Conclusions: The differences in the gene groups identified by various profiling methodologies supports the use of multiple approaches to obtain a more complete description of retinal gene expression. Characterization of gene expression of retina and brain may facilitate the understanding of the processes that underlie differences between the retina and other parts of the central nervous system.

Keywords: gene microarray • transcription