eccDNA biogenesis and its role in innate immunity

Extrachromosomal circular DNA elements (EccDNAs) have been described in the literature for several decades and are known for their wide existence across species as well as their high heterogeneity in genomic origins. Due to their scarcity and lack of validation tools, their biogenesis as well as their functions are largely unknown. Here, by using a newly developed circular DNA enrichment method, we purified eccDNAs from different cells and mapped their genomic location using both Illumine and Nanopore sequencing. We found that eccDNAs are mapped to genome in a largely random fashion, suggesting a biogenesis mechanism of random ligation of genomic DNA fragments. Consistently, we found that apoptosis inducers can increase the eccDNA generation, which is dependent on DNase 1/3 and DNA ligase 3. Importantly, we demonstrate that eccDNAs function as potent innate immunostimulants in a sequence-independent, but circularization-dependent fashion. Overall design: We developed a new three-step eccDNA enrichment method that allows the purification of eccDNA. We used eccDNAs purified from mESCs because the genetic integrity of ESCs is believed to be maintained during culture. To get the full-length sequence of eccDNA, we employed rolling-circle amplification of the purified eccDNA followed by Oxford Nanopore single-molecular long read sequencing. In addition, we sequenced the purified eccDNA from mESCs using Tn5 transposase tagmentation followed by Illumina paired-end sequencing, without rolling-circle amplification.