EccDNAs are apoptotic products with high innate immunostimulatory activity

Extrachromosomal circular DNA elements (EccDNAs) have been described in the literature for several decades, and are known for their broad existence across different species(1,2). However, their biogenesis, and functions are largely unknown. By developing a new circular DNA enrichment method, here we purified, and sequenced full-length eccDNAs with Nanopore sequencing. We found that eccDNAs are mapped across the entire genome in a close to random fashion, suggesting a biogenesis mechanism of random ligation of genomic DNA fragments. Consistently, we found that apoptosis inducers can increase eccDNA generation, which is dependent on apoptotic DNA fragmentation followed by ligation by the DNA ligase 3. Importantly, we demonstrated that eccDNAs can function as potent innate immunostimulants in a sequence-independent, but circularity, and cytosolic DNA sensing Sting-dependent fashion. Collectively, our study not only revealed the origin, biogenesis, and immunostimulant function of eccDNAs, but also uncovered their sensing pathway and potential clinical implications in immune response.