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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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Updated: Jan 8, 2026

MicroRNA Expression Profiles of Human iPS Cells, Retinal Pigment Epithelium Derived From iPS, and Fetal Retinal Pigment Epithelium
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Dynamic changes in mRNA isoform usage during human retinal development.

Casey J Keuthan1, Sowmya Parthiban2, Yen-Yu Chang1

  • 1Department of Ophthalmology, Wilmer Eye Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.

Biorxiv : the Preprint Server for Biology
|December 15, 2025
PubMed
Summary
This summary is machine-generated.

Alternative mRNA splicing drives diversity in eukaryotic cells. This study reveals dynamic isoform usage shifts during human retinal organoid development, uncovering neuron-specific splicing patterns and allelic imbalance.

Keywords:
RNAisoformslong-read sequencingnanoporeneurodevelopmentorganoidsretinasplicingstem cellstranscriptomics

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Area of Science:

  • Molecular Biology
  • Developmental Biology
  • Genomics

Background:

  • Alternative mRNA splicing generates crucial isoform diversity in eukaryotes.
  • The full scope of splicing changes during neurodevelopment remains largely uncharacterized.

Purpose of the Study:

  • To investigate temporal patterns of mRNA isoform usage during human retinal organoid differentiation.
  • To identify neuron-specific splicing signatures and allele-specific expression in developing retinal cells.

Main Methods:

  • Long-read RNA sequencing using nanopore technology on differentiating human stem cell-derived retinal organoids.
  • Analysis of isoform usage, gene expression, and allele-specific expression across developmental stages.
  • Focus on human stem cell-derived retinal ganglion cells.

Main Results:

  • Dynamic shifts in mRNA isoform usage were observed throughout retinal organoid differentiation, often independent of overall gene expression changes.
  • Specific splicing signatures unique to retinal neurons were identified.
  • Extensive allelic imbalance was detected in induced pluripotent stem cell-derived organoid cultures.

Conclusions:

  • Direct long-read RNA sequencing of human stem cell retinal models provides unprecedented detail on isoform-level changes during differentiation.
  • The study elucidates dynamic transcript usage shifts in retinal development, enhancing understanding of post-transcriptional regulation in the central nervous system and in vitro systems.