Identification and Characterization of eccDNA in Hepatocellular Carcinoma during DNA damage

Extrachromosomal circular DNA (eccDNA) has been recognized as a key player in tumorigenesis and progression. However, the mechanisms that eccDNA transcriptional regulatory mechanism under DNA damage in cancer remain poorly characterized. Here, we observed a significant increase in eccDNA number, length, and chromosomal distribution density after DNA damage in hepatocellular carcinoma (HCC). RNAseq revealed that the expression of genes carried on eccDNA were positively correlated with eccDNA copy number under DNA damage. Further ATACseq 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 HiC and H3K27ac ChIPseq, 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.