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D. J. Zack, T. Masuda, Y. Yang, J. Qian; Identification and Characterization of Retina-Specific Alternative Splicing. Invest. Ophthalmol. Vis. Sci. 2008;49(13):1682.
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Alternative splicing is a critical mechanism in the regulation and modulation of tissue-specific gene expression. Disorders in splicing are associated with a variety of diseases. In the eye, retinal degeneration has been associated both with mutations in general splicing factors (PRPF 3, 8 and 31) and with mutations that affect splicing of individual retina expressed genes. We have begun an analysis of retina-specific alternative splicing patterns with the goal of understanding more about the mechanisms regulating retinal development and the pathogenesis of retinal disease.
Candidate retina-specific/predominant splice variants were identified by a bioinformatic approach. Individual cell layers in the retina were isolated by laser capture microdissection (LCM). Expression profiles in mouse and human tissues including retina were assessed by quantitative real-time PCR (qRT-PCR). Splice microarrays were performed using the ExonHit whole genome platform.
The bioinformatic analysis identified 77 candidate genes that were predicted to have eye specific/predominant splice variants. Among these were basigin (BSG) and pleckstrin homology domain containing, family B member 1 (PLEKHB1). For both genes, we confirmed the predictions, showing that the long form splice variant was preferentially expressed in the retina, whereas other tissues expressed predominantly the short (exon skipped) form. By qRT-PCR analysis of LCM samples, photoreceptors express mostly the long form of both genes, while the expression pattern observed in cells of the ganglion cell layer, inner nuclear layer, and retinal pigment epithelium resembled that seen in non-retinal tissues.
Based on a bioinformatic approach, we identified 77 candidate genes with a retina-specific/predominant alternative splicing pattern. qRT-PCR analysis demonstrated that 2 of these genes, BSG and PLEKHB1, demonstrate a splicing pattern that is not only retina-specific, but is also photoreceptor-specific. Further studies, including use of splice microarrays, are ongoing to more comprehensively characterize the unique aspects of the retina splicome. Studies are also underway to identify the splice signals and protein factors that regulate retina-specific splicing, with the goal of understanding how alterations in this process can lead to retinal disease.
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