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Updated: Jan 15, 2026
08:35
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
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Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods
Carlos Alfonso-Gonzalez1,2, Valérie Hilgers3,4
1Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
Nature Reviews. Molecular Cell Biology
|October 6, 2025
Summary
New sequencing technologies reveal how alternative RNA processing impacts gene regulation and diseases like cancer. Understanding transcript variations is key to advancing molecular biology and medicine.
Area of Science:
- Molecular Biology
- Genomics
- Transcriptomics
Background:
- mRNA maturation is vital for gene regulation and proteome diversity.
- Eukaryotic gene processing involves complex, co-transcriptional mechanisms.
- Alternative RNA processing, including TSS, splicing, and polyadenylation, adds complexity.
Purpose of the Study:
- To review advances in sequencing technologies for studying RNA processing.
- To integrate findings on the functional links between alternative TSS, splicing, and polyadenylation.
- To discuss implications for diseases and insights from CRISPR tools.
Main Methods:
- Short-read RNA sequencing for measuring alternative TSS, splicing, and polyadenylation.
- Long-read sequencing (LRS) for characterizing co-transcriptional RNA processing.
- CRISPR tools for investigating the coordination of RNA processing events.
Main Results:
- Advances in short-read and LRS enable detailed analysis of nascent and mature transcripts.
- LRS provides whole-molecule read lengths and single-cell resolution.
- Functional links between alternative TSS, splicing, and polyadenylation are increasingly understood.
Conclusions:
- New sequencing technologies offer unprecedented insights into RNA processing.
- Alternative RNA processing plays a significant role in diseases like cancer and neurological disorders.
- Understanding RNA processing coordination is crucial for future therapeutic strategies.
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