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Updated: Jan 6, 2026
14:26
Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
25.8K
CircleBase V2: an eccDNA annotation platform across cancers and species.
Ling Wei1,2,3, Leisheng Shi1,2,3, Ning Wu4,5,6,7
1Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing100191, China.
Nucleic Acids Research
|November 22, 2025
Summary
CircleBase V2 significantly expands extrachromosomal circular DNA (eccDNA) data for human and mouse, incorporating millions of new entries and advanced analysis tools. This resource aids in understanding eccDNA roles in cancer, development, and disease.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Extrachromosomal circular DNA (eccDNA) are increasingly recognized for their roles in various biological processes, including cancer.
- Existing databases for eccDNA lack comprehensive data and advanced analytical functionalities for human and mouse genomes.
- Understanding the formation and function of eccDNA is crucial for advancing research in development and disease.
Purpose of the Study:
- To present CircleBase V2, a substantially updated and enhanced database for human and mouse eccDNA.
- To provide a resource with expanded data, new analytical modules, and improved usability for eccDNA research.
- To facilitate the discovery of biological roles and regulatory functions of eccDNA.
Main Methods:
- Expanded the database with over 7.4 million human and 3.6 million mouse eccDNA entries from diverse cell lines and tissues.
- Integrated a motif discovery module to identify sequence patterns associated with eccDNA formation.
- Developed an enhanced functional scoring framework using multi-omic data (chromatin accessibility, regulatory elements, variants, interactions).
Main Results:
- CircleBase V2 now contains over 11 million eccDNA entries, a 12-fold increase, covering >300 human cell lines/tissues and >20 mouse tissues.
- The motif discovery module identified junction-specific sequence patterns, offering insights into eccDNA biogenesis.
- The functional scoring framework successfully integrated multi-omic data to prioritize functionally relevant eccDNAs.
Conclusions:
- CircleBase V2 represents a significant advancement in eccDNA research resources, offering unprecedented data volume and analytical capabilities.
- The database serves as an indispensable platform for exploring the biological significance of eccDNA in human and mouse models.
- CircleBase V2 will accelerate discoveries related to eccDNA's roles in cancer, development, and other complex diseases.
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