Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease

• Published in: Nature communications Vol. 11; no. 1; p. 3328
• Main Authors: Ray, Thomas A., Cochran, Kelly, Kozlowski, Chris, Wang, Jingjing, Alexander, Graham, Cady, Martha A., Spencer, William J., Ruzycki, Philip A., Clark, Brian S., Laeremans, Annelies, He, Ming-Xiao, Wang, Xiaoming, Park, Emily, Hao, Ying, Iannaccone, Alessandro, Hu, Gary, Fedrigo, Olivier, Skiba, Nikolai P., Arshavsky, Vadim Y., Kay, Jeremy N.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03-07-2020; Nature Publishing Group; Nature Portfolio
• Subjects: 38/32; 38/91; 45/41; 631/208/1792; 631/378/1689/364; 631/378/2571/1696; 631/378/2583; 64/60; 82/58; Amino Acid Sequence; Animals; Base Sequence; Cell junctions; Cell surface; Degeneration; Gene Expression Profiling - methods; Gene Expression Regulation, Developmental; Genes; Genetic Variation; Humanities and Social Sciences; Humans; Isoforms; Mass spectrometry; Mass spectroscopy; Membrane Proteins - genetics; Membrane Proteins - metabolism; Mice, Inbred C57BL; Mice, Inbred Strains; Mice, Knockout; mRNA; multidisciplinary; Mutation; Nerve Tissue Proteins - genetics; Nerve Tissue Proteins - metabolism; Nervous system; Neurodegeneration; Neurological diseases; Photoreceptor Cells, Vertebrate - metabolism; Photoreceptors; Proteins; Retina; Retina - cytology; Retina - growth & development; Retina - metabolism; Retinal degeneration; Retinal Degeneration - genetics; Retinal Degeneration - metabolism; RNA Isoforms - genetics; RNA Isoforms - metabolism; Science; Science (multidisciplinary); Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-17009-7

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.
Here the authors present an approach that can reveal the full complement of mRNA isoforms encoded by individual genes, and they identify a major isoform of the retinal degeneration gene
CRB1
which functions at the cell-cell junctions of the outer limiting membrane to promote photoreceptor survival.