ATAC-seq identifies thousands of extrachromosomal circular DNA in cancers and cell lines

Abstract

Extrachromosomal circular DNAs (eccDNAs) lack centromeres and are not passed equally into daughter cells and thus provide a source of cell-cell heterogeneity in normal and tumor cells. Previously we and other groups purified circular DNA and linearized them by rolling circle amplification for paired end high throughput sequencing to identify eccDNA in cells and tissues. We hypothesized that many eccDNA will have more open chromatin and so will be susceptible to linearization and sequencing by tagmentation. Indeed, we find that ATAC-seq on cell lines and cancers, without any enrichment of circular DNA, identifies thousands of eccDNAs. The identified eccDNAs in cell lines were validated by inverse PCR on DNA that survives exonuclease digestion of linear DNA and by metaphase FISH. We demonstrate that ATAC-seq data generated in Lower Grade Gliomas (LGG) and Glioblastomas (GBM) identify eccDNAs, including one containing the well-known EGFR gene amplicon from chr7. Many of the eccDNAs are identified even before amplification of the locus is detected by genotyping arrays. Thus, standard ATAC-seq is a sensitive method to detect segments of DNA that are present as eccDNA in a subset of the tumor cells, ready to be further amplified under appropriate selection, as during therapy.