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CASA: a comprehensive database resource for the COVID-19 Alternative Splicing Atlas
Yaxin Chen1, Gang Wang1, Jingyi Li2
1Frontiers Science Center for Disease-Related Molecular Network, Precision Medicine Research Center, West China Hospital, Department of Respiratory and Critical Care Medicine, Sichuan University, Chengdu, Sichuan, China.
Journal of Translational Medicine
|October 21, 2022
Summary
The COVID-19 Alternative Splicing Atlas (CASA) provides a platform to study alternative splicing (AS) in infectious diseases. It visualizes AS events and potential regulators, aiding research into viral manipulation of host cell splicing.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Alternative splicing (AS) is vital for RNA and protein diversity.
- AS plays a key role in immune responses to infectious diseases, including COVID-19.
- Understanding AS profiles in infected cells is crucial for COVID-19 research.
Purpose of the Study:
- To create a comprehensive database for studying alternative splicing in COVID-19 and related infectious diseases.
- To provide a user-friendly computing platform for analyzing AS data.
- To facilitate the understanding of viral manipulation of host cell splicing.
Main Methods:
- Reanalyzed thousands of RNA-seq datasets from diverse human tissues, organoids, and cell lines.
- Systematically quantified alternative splicing events across various infectious disease conditions.
- Performed functional annotation and drug-target interaction analyses for dynamic AS events.
Main Results:
- Detected and visualized 262,994 alternative splicing events from multiple infectious diseases.
- Identified microbe-induced alterations in the host cell splicing landscape.
- Provided data on RNA-binding proteins (RBPs) that may regulate dynamic AS events.
Conclusions:
- CASA offers a valuable resource for exploring AS profiles in virus-infected cells.
- The database aids in identifying condition-specific splicing patterns and regulators.
- CASA facilitates research into novel mechanisms of viral manipulation of host cell splicing.
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