Analysis of gene expression in the developing mouse retina

Abstract

In the visual system, differential gene expression underlies development of the anterior-posterior and dorsal-ventral axes. Here we present the results of a microarray screen to identify genes differentially expressed in the developing retina. We assayed gene expression in nasal (anterior), temporal (posterior), dorsal, and ventral embryonic mouse retina. We used a statistical method to estimate gene expression between different retina regions. Genes were clustered according to their expression pattern and were ranked within each cluster. We identified groups of genes expressed in gradients or with restricted patterns of expression as verified by in situ hybridization. A common theme for the identified genes is the differential expression in the dorsal-ventral axis. By analyzing gene expression patterns, we provide insight into the molecular organization of the developing retina.A fundamental aspect of nervous system development is the spatial and temporal regulation of gene expression that underlies cell fate specification and connectivity. In the visual system, generation of the anterior-posterior (A-P) and dorsalventral (D-V) axes underlies positional specificity within the retina. The best example is the formation of a topographic map on the retinal axon output target, the superior colliculus (SC). Axons from D and V retina project to V and D SC, respectively, while A (also defined as nasal, N) and P (also defined as temporal, T) retinal axons project to P and A SC, respectively (1-4). Map formation depends upon complementary gradients of positional labels in the retina and the SC (5), specifically retinal EphA receptors and collicular ephrin-A ligands. In chick, EphA3 is expressed in a high-T to low-N gradient in the retina (6), whereas ephrin-A2 and ephrin-A5 are expressed in corresponding P-A gradients across the target (6, 7). Current models suggest that retinocollicular mapping is independent of the absolute level of EphA receptor signaling in retinal ganglion cells (RGCs), but, rather, is dependent on relative differences between neighboring RGCs (8).Other molecules are differentially expressed in the visual system. Two EphB receptors and A and B type ephrins are expressed in gradients in the retina (9-12). The early eye can also be subdivided by expression of retinoic acid-generating enzymes along the D-V axis (13-15). Transcription factors and signaling components are expressed in gradients in the retina during development (16)(17)(18)(19). To gain a broader view of gene expression patterns in the retina, we applied a microarray-based approach to identify new genes with restricted patterns of expression during development. Our results provide insight into the organization of the retina structure as well as identify candidate genes with potential roles in positional identity. Materials and MethodsMicroarray Hybridizations. Embryonic day 14.5 (E14.5) CD-1 mouse retinas were divided into N, T, D, and V portions for RNA isolation with TRIzol (Invitrogen) and RNeasy columns (Qiagen, Valencia, CA). RNA amp...

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