C. J. Keuthan, S. Parthiban, Y.-Y. Chang, X. Shan, X. Chang, E. Yan, S. Cavalier, W. Timp, S. C. Hicks, D. J. Zack
Background: Alternative mRNA splicing is a key mechanism for generating isoform diversity in eukaryotic cells. However, the extent of the splicing changes that occur during complex regulatory processes like neurodevelopment are still incompletely characterized. Results: We performed nanopore-based long-read RNA sequencing on differentiating human stem cell-derived retinal organoids to identify temporal patterns of isoform usage across developmental stages. We found that retinal organoids undergo dynamic shifts in isoform usage throughout differentiation, which were not necessarily accompanied with changes in overall gene expression, as was the case for many genes involved in the regulation of mRNA splicing itself. Further analysis of human stem cell-derived retinal ganglion cells uncovered neuron-specific splicing signatures. Additionally, allele-specific expression analysis revealed extensive allelic imbalance in induced pluripotent stem cell-derived organoid cultures. Conclusions: By combining direct long-read RNA sequencing with human stem cell retinal models we could explore isoform-level changes in differentiating human cells at unprecedented detail. These results uncovered dynamic shifts in transcript usage during retinal differentiation, adding to our knowledge base of post-transcriptional RNA processing in the developing central nervous system and human in vitro culture systems.