Genes encoding cell-surface proteins control nervous system development and are implicated in neurological disorders. These genes produce alternative mRNA isoforms which remain poorly characterized, impeding understanding of how disease-associated mutations cause pathology. Here we introduce a strategy to define complete portfolios of full-length isoforms encoded by individual genes. Applying this approach to neural cell-surface molecules, we identify thousands of unannotated isoforms expressed in retina and brain. By mass spectrometry we confirm expression of newly-discovered proteins on the cell surface in vivo. Remarkably, we discover that the major isoform of a retinal degeneration gene, CRB1, was previously overlooked. This CRB1 isoform is the only one expressed by photoreceptors, the affected cells in CRB1 disease. Using mouse mutants, we identify a function for this isoform at photoreceptor-glial junctions and demonstrate that loss of this isoform accelerates photoreceptor death. Therefore, our isoform identification strategy enables discovery of new gene functions relevant to disease.

编码细胞表面蛋白的基因控制神经系统发育，并与神经系统疾病有关。这些基因产生替代性的mRNA亚型，这些亚型的特征仍然很差，妨碍了人们对与疾病相关的突变如何引起病理学的理解。在这里，我们介绍一种策略来定义单个基因编码的全长同工型的完整组合。将这种方法应用于神经细胞表面分子，我们可以识别在视网膜和大脑中表达的数千种未注释的亚型。通过质谱法，我们证实了体内新发现的蛋白在细胞表面的表达。值得注意的是，我们发现视网膜退化基因CRB1的主要同种型以前被忽略了。这个CRB1异构体是由感光细胞表达的唯一一种，CRB1疾病中的受影响细胞。使用小鼠突变体，我们在感光细胞-神经胶质交界处确定此同工型的功能，并证明该同工型的丧失加速了感光细胞的死亡。因此，我们的同工型鉴定策略能够发现与疾病相关的新基因功能。