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bioRxiv · 10.1101/2025.11.26.689062

Dynamic changes in mRNA isoform usage during human retinal development

Keuthan, C. J.·Parthiban, S.·Chang, Y.-Y.·Shan, X.·Chang, X.·Yan, E.·Cavalier, S.·Timp, W.·Hicks, S. C.·Zack, D. J.
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Abstract

BackgroundAlternative 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. ResultsWe 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 observed 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 gene expression analysis revealed extensive allelic imbalance in induced pluripotent stem cell-derived organoid cultures. ConclusionsBy combining direct long-read RNA sequencing with human stem cell retinal models we were able to develop a comprehensive database of isoform-level changes in differentiating human retinal cells during development. 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.

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Keuthan, C. J., Parthiban, S., Chang, Y.-Y., Shan, X., Chang, X., Yan, E., Cavalier, S., Timp, W., Hicks, S. C., Zack, D. J.. 2025-11-26. Dynamic changes in mRNA isoform usage during human retinal development. https://doi.org/10.1101/2025.11.26.689062

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