scCircle-seq unveils the diversity and complexity of circular DNAs in single cells

Abstract We describe scCircle-seq, a method for genomically profiling extrachromosomal circular DNAs (circDNAs) in single cells. We implemented and validated scCircle-seq in normal and cancer cell lines, demonstrating that most circDNA species vary between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. circDNAs are preferentially produced from chromatin regions enriched in H3K9me3 histone mark and are induced during replication stress conditions. Concomitant sequencing of circDNA and RNA from the same cell uncovered the absence of correlation between circDNA copy number and gene expression levels, except for few oncogenes contained within large circDNAs in colorectal cancer cells, including MYC. scCircle-seq can be used to dissect the complexity of circDNAs across different cell types and further expands the potential of circDNAs for cancer diagnostics.