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Updated: Jan 10, 2026
Visualizing and Quantifying Endonuclease-Based Site-Specific DNA Damage
Published on: August 21, 2021
Identification and Characterization of eccDNA in HepG2 Cells Under DOX-Induced DNA Damage
Jinyuan Zhang1, Yuguo Li1, Weijie Chen1
1School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
Abstract:
Extrachromosomal circular DNA (eccDNA) has been recognized as a key player in tumorigenesis and progression. However, eccDNA transcriptional regulatory mechanisms under DNA damage in cancer remain poorly characterized. Here, we used doxorubicin to induce DNA damage in the hepatocellular carcinoma cell line HepG2 and performed Circle-seq to profile eccDNAs before and after the damage. We observed a significant increase in the number, length, and chromosomal distribution density of eccDNAs following DNA damage. RNA-seq revealed that the expression of genes carried on eccDNA was positively correlated with eccDNA copy number under DNA damage. Further ATAC-seq profiling identified distinct chromatin characteristics at eccDNA breakpoint regions compared to other regions of eccDNA and linear genomic regions. Additionally, eccDNAs generated under DNA damage preferentially originated from linear genomic regions characterized by low GC content and hypomethylation. Finally, by integrating Hi-C and H3K27ac ChIP-seq, we uncovered that eccDNAs with mobile enhancer activity (ME-eccDNAs) display significantly enhanced chromatin interactions and H3K27ac enrichment after DNA damage. Overall, our findings systematically elucidate the DNA damage-driven mechanisms underlying eccDNA biogenesis, chromatin characteristics and transcriptional regulation in HCC HepG2 cells.
Insights
DNA damage increases extrachromosomal circular DNA (eccDNA) in liver cancer cells. These eccDNAs, particularly mobile enhancer eccDNAs (ME-eccDNAs), show altered chromatin and gene expression, impacting cancer progression.
Area of Science:
- Genomics
- Cancer Biology
- Epigenetics
Background:
- Extrachromosomal circular DNA (eccDNA) plays a role in cancer development.
- Mechanisms of eccDNA regulation under DNA damage in cancer are not well understood.
Purpose of the Study:
- To investigate eccDNA changes and transcriptional regulation following DNA damage in hepatocellular carcinoma (HCC) cells.
- To characterize the biogenesis and chromatin features of eccDNA under genotoxic stress.
Main Methods:
- Doxorubicin-induced DNA damage in HepG2 cells.
- Circle-seq for eccDNA profiling.
- RNA-seq and ATAC-seq for gene expression and chromatin accessibility.
- Hi-C and H3K27ac ChIP-seq for enhancer activity analysis.
Main Results:
- DNA damage significantly increased eccDNA number, length, and density.
- Gene expression on eccDNA correlated positively with eccDNA copy number post-damage.
- eccDNAs originated from hypomethylated, low GC content regions.
- Mobile enhancer eccDNAs (ME-eccDNAs) showed enhanced chromatin interactions and H3K27ac enrichment.
Conclusions:
- DNA damage drives eccDNA biogenesis and alters their transcriptional regulatory functions in HCC.
- ME-eccDNAs emerge as key players in DNA damage response and cancer progression.
- This study provides a systematic elucidation of DNA damage-induced eccDNA mechanisms in liver cancer.
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