Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 27;24(1):47.
doi: 10.1186/s12864-023-09135-5.

TeCD: The eccDNA Collection Database for extrachromosomal circular DNA

Jing Guo #  1   2   3   4 , Ze Zhang #  1   2   5 , Qingcui Li  5 , Xiao Chang  6 , Xiaoping Liu  7   8   9
Affiliations

TeCD: The eccDNA Collection Database for extrachromosomal circular DNA

Jing Guo et al. BMC Genomics. .

Abstract

Background: Extrachromosomal circular DNA (eccDNA) is a kind of DNA that widely exists in eukaryotic cells. Studies in recent years have shown that eccDNA is often enriched during tumors and aging, and participates in the development of cell physiological activities in a special way, so people have paid more and more attention to the eccDNA, and it has also become a critical new topic in modern biological research.

Description: We built a database to collect eccDNA, including animals, plants and fungi, and provide researchers with an eccDNA retrieval platform. The collected eccDNAs were processed in a uniform format and classified according to the species to which it belongs and the chromosome of the source. Each eccDNA record contained sequence length, start and end sites on the corresponding chromosome, order of the bases, genomic elements such as genes and transposons, and other information in the respective sequencing experiment. All the data were stored into the TeCD (The eccDNA Collection Database) and the BLAST (Basic Local Alignment Search Tool) sequence alignment function was also added into the database for analyzing the potential eccDNA sequences.

Conclusion: We built TeCD, a platform for users to search and obtain eccDNA data, and analyzed the possible potential functions of eccDNA. These findings may provide a basis and direction for researchers to further explore the biological significance of eccDNA in the future.

Keywords: Circular DNA; Extrachromosomal DNA; eccDNA.

PubMed Disclaimer

Conflict of interest statement

Not applicable.

Figures

Fig. 1
Fig. 1
The flow chart of TeCD. The raw data were collected from published literature. The chromosome sequence corresponding to eccDNA was obtained according to the locus. The gene, locus information, number of reads variants, and other information were extracted from the data and stored in MySQL 8.0.26 database. The information could be browsed and retrieved according to organism and item. Finally, the TeCD website was built with Django web framework for users
Fig. 2
Fig. 2
Sample types for different tissues and cells. a Sample types for all organisms and the corresponding number of eccDNA. The 5 colors of the inner ring correspond to 5 organisms. The outer ring represents the sample type for each organism. b-f Sample types of Saccharomyces cerevisiae, Arabidopsis thaliana, Gallus gallus, homo sapiens, and Mus musculus. And the color of its inner ring corresponds to the inner ring of the (a). g The number of eccDNA shared by samples from different parts of Arabidopsis. The different colored circles represent samples of different parts of Arabidopsis. h The figure above shows the number of eccDNA from four samples of Arabidopsis. The figure below shows the number of eccDNA that belongs to 1–4 different samples in common
Fig. 3
Fig. 3
Data distribution plot. a-e The histogram shows the quantitative distribution of eccDNA of different organisms on chromosomes. These species are Homo sapiens, Gallus gallus, Saccharomyces cerevisiae, Arabidopsis thaliana and Mus musculus in turn. The line chart shows the ratio standardized with Z-score. And this ratio is the number of eccDNA in the chromosome divided by the length of the chromosome
Fig. 4
Fig. 4
Screenshot of search page from the TeCD. a Search and browse pages. Users can search by organization and item, and we also provide some examples. Selected entry information will be displayed at the bottom of the page for users to browse. b Details of an eccDNA. Here, we provide a lot of information about eccDNA, including complete sequence, contained genes, transposons, data sources, etc. All information categories can be queried and explained on the about page. c JBrowse style visualization of individual eccDNAs and their location on the host genome
Fig. 5
Fig. 5
Screenshot of BLAST and statistics page. a Screenshot of blast page from the TeCD. Users can use BLAST to search the database by sequence alignment. b Screenshot of statistics page from the TeCD
Fig. 6
Fig. 6
Screenshot of contribute and download page. a Screenshot of contribute page from the TeCD. b Screenshot of search results page from the TeCD. Users can export some data optionally. c Screenshot of download page from the TeCD. TeCD provides download links of all data by species, and the data formats are. csv and. fa
Fig. 7
Fig. 7
The number of eccDNA with and without DNA damaging. Taking Saccharomyces cerevisiae as an example, a bidirectional comparison of nucleic acid sequences was performed by BLAST
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggros M, Dorado Garcia H, et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet. 2020;52(1):29–34. doi: 10.1038/s41588-019-0547-z. - DOI - PMC - PubMed
    1. Yan Y, Guo G, Huang J, Gao M, Zhu Q, Zeng S, Gong Z, Xu Z. Current understanding of extrachromosomal circular DNA in cancer pathogenesis and therapeutic resistance. J Hematol Oncol. 2020;13(1):124. doi: 10.1186/s13045-020-00960-9. - DOI - PMC - PubMed
    1. Turner KM, Deshpande V, Beyter D, Koga T, Rusert J, Lee C, Li B, Arden K, Ren B, Nathanson DA, et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature. 2017;543(7643):122–125. doi: 10.1038/nature21356. - DOI - PMC - PubMed
    1. Mansisidor A, Molinar T, Srivastava P, Dartis DD, Delgado AP, Blitzblau HG, Klein H, Hochwagen A. Genomic Copy-Number Loss Is Rescued by Self-Limiting Production of DNA Circles. Mol Cell. 2018;72(3):583. doi: 10.1016/j.molcel.2018.08.036. - DOI - PMC - PubMed
    1. Hull RM, Houseley J. The adaptive potential of circular DNA accumulation in ageing cells. Curr Genet. 2020;66(5):889–894. doi: 10.1007/s00294-020-01069-9. - DOI - PMC - PubMed