ArticleJournal of visualized experiments : JoVE2016
Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.
Article in Journal of visualized experiments : JoVE, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
45 citing papers in PubMed, 57 citations in OpenAlex.
- Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.Genome research · 2026Article
- Extrachromosomal DNA Amplification as a Prognostic Factor for Cancer.Journal of personalized medicine · 2026Review
- Targeting extrachromosomal DNA in human cancers.Nature reviews. Drug discovery · 2026Review
- Article
- Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination.GigaScience · 2026Article
- Machine learning identified extrachromosomal DNA-related 12 gene signatures to predict cancer immunotherapy response.Cancer cell international · 2025Article
- EccDNA Analysis Provides Novel Insights Into the Molecular Mechanism of Firmness of Fish Fillet.Food science & nutrition · 2025Article
- Molecular mechanisms of extrachromosomal circular DNA formation.Nucleic acids research · 2025Review
- Plasma cell-free extrachromosomal circular DNA is a molecular hallmark of preeclampsia.Computational and structural biotechnology journal · 2025Article
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- Comprehensive profiling of extrachromosomal circular DNAs in colorectal cancer progression.Scientific reports · 2024Article
- Identification and Characterization of Extrachromosomal Circular DNA in Slimming Grass Carp.Biomolecules · 2024Article
- Extrachromosomal DNA in cancer.Nature reviews. Cancer · 2024Review
- Genome-wide sequencing identified extrachromosomal circular DNA as a transcription factor-binding motif of the senescence genes that govern replicative senescence in human mesenchymal stem cells.Frontiers in cellular neuroscience · 2024Article
- Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation.Microbial cell (Graz, Austria) · 2023Article
- Identification and characterization of extrachromosomal circular DNA in patients with high myopia and cataract.Epigenetics · 2023Article
- MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing.Genome biology · 2023Article
- FLED: a full-length eccDNA detector for long-reads sequencing data.Briefings in bioinformatics · 2023Article
- The characteristics of extrachromosomal circular DNA in patients with end-stage renal disease.European journal of medical research · 2023Article
- TeCD: The eccDNA Collection Database for extrachromosomal circular DNA.BMC genomics · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 10(10) cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.