Gene Expression Analysis of the Rat Retina during Maturation

Recently we reported that the rat inner retina undergoes significant functional changes during maturation. Aiming to gain knowledge on additional aspects of retinal development and maturation, we used the microarray system to monitor gene expression patterns in the rat retina at ages 5, 11, and 20 weeks. The analysis revealed the expression of many well-documented retinal genes as well as a high number of non–annotated genes. Quantitative realtime PCR analysis verified the microarray results in the majority of studied genes. A statistical analysis of the 4 microarray slides revealed 603 differentially expressed genes which were grouped into 6 expression clusters. A bioinformatic analysis of these clusters revealed sets of genes encoding proteins with functions that are likely to be relevant to inner retinal function (e.g. potassium, sodium, calcium, and chloride channels, synaptic vesicle transport, and axonogenesis). In addition, we performed a histological analysis of the maturing retina and studied different aspects of retinal structure. The analysis revealed a significant reduction of outer nuclear layer thickness between 11 and 19 weeks of age and a significant reduction of retinal ganglion cell number at 11 and 19 weeks comparing to 5 weeks. We identified in this study genes with differential expression pattern during retinal maturation. Some of the genes encode proteins that may be involved in the functional maturation of inner retinal cells. These data, taken together with our histological and electrophysiological data, contribute to our understanding of the developmental processes occurring in the retina of this widely-used animal model. Keywords: Dye-swap, Ganglion cells, Gene, Gene expression, Histology, Inner retina, Maturation, Microarray, Rat, Retina, Vision. Rat retinal samples at ages 5, 11, and 20 weeks were studied using 4 microarray slides in a dye-swap design: 5-11, 11-5, 5-20, and 20-5.