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Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
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Deciphering extrachromosomal circular DNA in Arabidopsis
Keyi Wang1, Hui Tian2, Lequn Wang1
1Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China.
Computational and Structural Biotechnology Journal
|March 8, 2021
Summary
Extrachromosomal circular DNAs (eccDNAs) in plants were identified, revealing their association with transposon activity and tRNA genes. These findings offer new insights into the function and origin of plant eccDNA.
Area of Science:
- Plant molecular biology
- Genomics
- Epigenetics
Background:
- Extrachromosomal circular DNA (eccDNA) exists in eukaryotes but its nature and origin in plants are poorly understood.
- eccDNA plays roles in various biological processes, including stress response and genome instability.
Purpose of the Study:
- To investigate the characteristics and potential origins of eccDNA in plants.
- To explore the relationship between eccDNA, transposon activity, and tRNA genes in plant tissues.
Main Methods:
- Whole-genome sequencing of 12 plant samples across four tissues (leaf, flower, stem, root) with three biological replicates.
- Bioinformatic analysis to identify and characterize eccDNA sequences and their genomic context.
Main Results:
- Identification of 743 eccDNAs present in at least two samples.
- Most identified eccDNAs feature inverted repeats (4-12 bp) at their boundaries.
- eccDNA presence is linked to transposon activity and the hosting of tRNA genes, suggesting a role in regulating protein synthesis under stress.
Conclusions:
- This study provides a comprehensive view of plant eccDNA, revealing novel insights into their structure and potential functions.
- Plant eccDNAs are associated with mobile genetic elements and tRNA genes, hinting at their involvement in stress adaptation and gene regulation.
