ArticleComputational and structural biotechnology journal2022
Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas9.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 20 citations in OpenAlex.
- Extrachromosomal DNA in urothelial carcinoma: mechanisms and clinical applications.Nature reviews. Urology · 2026Review
- Functional role of small extrachromosomal circular DNA in colorectal cancer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- An enhancement of extrachromosomal circular DNA enrichment and amplification to address the extremely low overlap between replicates.The Journal of biological chemistry · 2026Article
- A novel CRISPR-Cas9 nickase-mediated rolling circle amplification (CRIRCA) technique for gene identification and quantitative analysis of extrachromosomal DNA.Journal of advanced research · 2026Article
- EccDNA atlas in male mice reveals features protecting genes against transcription-induced eccDNA formation.Nature communications · 2025Article
- Characterization and identification of extrachromosomal circular DNA in cholangiocarcinoma.PloS one · 2025Article
- Insights into the human cDNA: A descriptive study using library screening in yeast.Journal, genetic engineering & biotechnology · 2024Article
- Identification and Characterization of Extrachromosomal Circular DNA in Slimming Grass Carp.Biomolecules · 2024Article
- Gene amplifications and extrachromosomal circular DNAs: function and biogenesis.Molecular biology reports · 2023Review
- Review
- Integrative profiling of extrachromosomal circular DNA in placenta and maternal plasma provides insights into the biology of fetal growth restriction and reveals potential biomarkers.Frontiers in genetics · 2023Article
- Variation of extrachromosomal circular DNA in cancer cell lines.Computational and structural biotechnology journal · 2023Article
- Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis.Computational and structural biotechnology journal · 2023Review
- CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences.Briefings in bioinformatics · 2022Article
- Review
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is common in eukaryotic cells. Amplification of oncogenes on large eccDNA (ecDNA) can drive biological processes such as tumorigenesis, and identification of eccDNA by sequencing after removal of chromosomal DNA is therefore important for understanding their impact on the expressed phenotype. However, the circular mitochondrial DNA (mtDNA) might challenge the detection of eccDNA because the average somatic cell has hundreds of copies of mtDNA. Here we show that 61.2-99.5% of reads from eccDNA-enriched samples correspond to mtDNA in mouse tissues. We have developed a method to selectively remove mtDNA from total circular DNA by CRISPR/Cas9 guided cleavage of mtDNA with one single-guide RNA (sgRNA) or two sgRNAs followed by exonuclease degradation of the linearized mtDNA. Sequencing revealed that mtDNA reads were 85.9% ± 12.6% removed from eccDNA of 9 investigated mouse tissues. CRISPR/Cas9 cleavage also efficiently removed mtDNA from a human HeLa cell line and colorectal cancer samples. We identified up to 14 times more, and also larger eccDNA in CRISPR/Cas9 treated colorectal cancer samples than in untreated samples. We foresee that the method can be applied to effectively remove mtDNA from any eukaryotic species to obtain higher eccDNA yields.
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