CDCA-seq resolve the different chromatin structure on integral circular DNAs

Although ecDNAs have been a subject of sustained research activity for some years, the underlying mechanism driving the ecDNAs tumorigenesis has begun to unfold recently. Overall, from the results presented in conventional research, the high throughput short reads sequencing largely ignores the epigenetic status on most ecDNA regions except the junctional areas. We developed a method named CDCA-seq by using methylase to label the open chromatin without fragmentation, and exonuclease to enrich the ecDNA sequencing depth, followed by the long-read nanopore sequencing. Using this technology, the significantly different patterns of nucleosome/regulator binding were observed in ecDNAs at single-molecule resolution. These results further the understanding of the different regulatory mechanism on ecDNAs.