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TeCD: The eccDNA Collection Database for extrachromosomal circular DNA.

Jing Guo^1,2,3,4, Ze Zhang^1,2,5, Qingcui Li⁵

¹Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013, China.

|January 28, 2023

Summary

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.

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DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

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This summary is machine-generated.

Researchers developed The eccDNA Collection Database (TeCD), a new platform for accessing and analyzing extrachromosomal circular DNA (eccDNA) data. This resource aids in understanding eccDNA

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Extrachromosomal circular DNA (eccDNA) is prevalent in eukaryotic cells.
eccDNA is increasingly recognized for its role in tumors and aging.
eccDNA is a significant area of modern biological research.

Purpose of the Study:

To create a centralized database for eccDNA data.
To provide a retrieval platform for researchers studying eccDNA.
To facilitate the analysis of eccDNA functions.

Main Methods:

Compiled eccDNA data from animals, plants, and fungi.
Standardized data format and classified by species and chromosome.
Integrated Basic Local Alignment Search Tool (BLAST) for sequence analysis.

Keywords:

Circular DNA Extrachromosomal DNA eccDNA

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Main Results:

Developed The eccDNA Collection Database (TeCD).
Stored comprehensive eccDNA information including sequence, genomic elements, and experimental data.
Enabled sequence alignment for potential eccDNA identification.

Conclusions:

TeCD serves as a valuable resource for eccDNA data retrieval and analysis.
The database supports further investigation into the biological significance of eccDNA.
Findings provide a foundation for future eccDNA research.