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Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing
Giovanni Quinones-Valdez1, Kofi Amoah2, Xinshu Xiao3,4
1Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA.
Nature Communications
|October 31, 2025
Summary
New RNA sequencing methods distinguish cis- and trans-regulated splicing events. This reveals individual-specific genetic links to splicing, aiding disease mechanism studies.
Area of Science:
- Genetics
- Molecular Biology
- Bioinformatics
Background:
- Alternative splicing is crucial for gene expression and disease.
- Splicing is regulated by cis-acting elements and trans-acting factors.
- Distinguishing these regulatory mechanisms is key to understanding genetic disease bases.
Purpose of the Study:
- To develop a method for segregating cis- and trans-directed splicing events.
- To investigate the individual-specific genetic regulation of splicing.
- To identify genetic variations impacting splicing in disease-relevant genes.
Main Methods:
- Utilized long-read RNA sequencing (RNA-seq).
- Developed and applied the isoLASER computational method.
- Analyzed RNA-seq data from human and mouse samples.
Main Results:
- Successfully segregated cis- and trans-directed splicing events per sample.
- Discovered that splicing's genetic linkage is largely individual-specific.
- Identified thousands of cis-directed splicing events influenced by genetic regulation, including in HLA, MAPT, and BIN1 genes.
Conclusions:
- Long-read RNA-seq with isoLASER clearly differentiates cis- and trans-splicing.
- Individual-specific splicing regulation offers new insights into genetic disease.
- This approach facilitates future research into the genetic underpinnings of diseases.
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