Single-cell characterization of transcript isoforms with long-read RNA sequencing

Abstract

The retina, a complex neuronal tissue with over 100 distinct cell types, has not been fully explored in terms of mRNA alternative splicing at the single-cell level. Addressing this, we employed single-cell RNA sequencing using both short-read and long-read high-throughput methodologies. We profiled approximately 30,000 mouse retina cells, yielding 1.54 billion Illumina short-reads and 1.4 billion long nanopore sequencing reads. Our analysis identified 44,325 transcript isoforms, of which 55% are novel and 17% exhibit cell-class-specific expression. Notably, while many isoforms were found across different cell types, their distribution varied significantly among them. This study substantially enriches our understanding of the retinal transcriptome isoform diversity, paving the way for deeper investigations into alternative splicing's role in retinal biology and associated diseases.

Biography

Dr. Chen, a professor in the Department of Molecular and Human Genetics, Baylor College of Medicine, USA, directs both the Center for Single Cell Omics and the ATC Single Cell Genomics Core. His research utilizes genetics, genomics, model systems, and bioinformatics to unravel the genetic basis of human retinal diseases. Additionally, Dr. Chen is leading the effort of creating the human eye's single-cell atlas for the Human Cell Atlas project, employing cutting-edge single-cell omics and spatial transcriptomics technologies.