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Jun Wang, Rachayata Dharmat, Yumei Li, Leah Owen, Margaret M DeAngelis, Rui Chen; An integrative approach to identify transcript isoforms essential for retina function. Invest. Ophthalmol. Vis. Sci. 2018;59(9):2350. doi: https://doi.org/.
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© ARVO (1962-2015); The Authors (2016-present)
It is known that vast majority of the genes in the human genome undergo alternative splicing during gene expression with many of the transcript isoforms showing developmental stage or tissue specificity. Due to its complexity, interpreting the function of these vast number of transcript isoforms and their relevance to diseases is a major challenging. By integrating both short-read and long-read mRNA-sequencing data from human retina tissue with population and patient exome sequencing data, we have designed a novel approach to systematically assess the functional importance of each transcript isoform in human retina and their relevance to inherited retinal diseases.
Long-read and short-read deep mRNA-sequencing were performed on rapidly autopsied, well characterized human donor retina on PacBio and Illumina platform respectively. To assess the evolution selection pressure on each transcript isoform, a matrix of genomic variant frequencies was computed for each coding exon based on human population variant database. To measure the functional importance of each exon/isoform, functional constraint score was calculated by integrating the mRNA-Sequencing data with the genomic variant data. The prediction was evaluated by performing mutation screens in a cohort of about 5,000 patients with inherited retinal diseases (IRD) as well as functional tests in animal models.
By integrating long-read and short-read deep mRNA-sequencing data, we have identified and quantified the abundance of each transcript isoform in human retina. As expected, evolution selection pressure analysis indicates that alternative exons in abundant isoforms are under stronger functional constraint than those in minor isoforms. To further test our approach, major transcript isoforms that are under strong functional constraint are identified for all known genes associated with IRD. Screening of our IRD patient cohort leads to the identification of isoform specific mutations.
Our study established a novel integrative approach to systematically assess the functional importance of alternative transcript isoforms in retina and relevant diseases. This approach could potentially be adapted to other tissues and diseases in general.
This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.
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