Single-cell Circle-seq unveils diversity and cell specificity of circular DNA in single cells

Circular DNAs have been reported for decades and have been linked to tumorigenesis in humans. Previous sequencing-based genomic approaches capture circular DNA and average their readout over millions of cells, thereby losing insight into intercellular variation. Here, we introduce single-cell Circle-seq and show that the occurrence of most circular DNA species is stochastic, with some oncogene-containing large circular DNAs observed relatively frequently among different single cells. Despite this stochasticity, circular DNA is cell type-specific, which is concordant with H3K9me3 and H3K4me3 chromatin modification specificity of the corresponding cell lines. Moreover, we identify a cell type-specific circular DNA signature in cancer cells, which, we believe holds potential for early cancer diagnosis. In sum, our novel method single-cell Circle-seq dissects the randomness and cell type-specificity of circular DNAs at the single-cell level and uncovers the potential clinical application of circular DNA. Colo320DM, PC3, HeLa, K562 and HEK293T cells are mouth-pippeted into single tubes and subjected to scCircle-seq protocol.