Extrachromosomal Circular DNA from TCGA Tumors Is Generated from Common Genomic Loci, Is Characterized by Self-Homology and DNA Motifs near Circle Breakpoints

SIMPLE SUMMARY: Extrachromosomal circular DNA is ubiquitous in eukaryotic cells. In tumors, highly amplified oncogenes exist in circular DNA, and circular DNA correlates with poor prognosis in multiple tumor types. Despite the emerging importance of extrachromosomal circular DNA, little is known about the origin or biological function of circular DNA. We investigated publicly available circular DNA from 355 TCGA tumors from 22 tumor types. We identify several locations frequently circularized irrespective of the type of cancer. Analysis of the genes present on circles revealed they are expressed, and at a higher level. These genes were enriched in cancer related functions regardless of tumor type. Analysis of circle breakpoints identified strong presence of homology and microhomology with an enrichment of specific DNA binding transcription factor motifs. Our results provide a framework for addressing key questions in the biogenesis and functional importance of extrachromosomal circular DNA. ABSTRACT: Extrachromosomal circular DNA has emerged as a frequent genomic alteration in tumors. High numbers of circular DNAs correspond to poor prognosis suggesting an important function in tumor biology. However, despite mounting evidence supporting the importance of circular DNA, little is known about their production, maintenance, or selection. To provide insight into these processes, we analyzed circular DNA elements computationally identified in 355 TCGA tumors spanning 22 tumor types. Circular DNAs originated from common genomic loci irrespective of cancer type. Genes found in circularized genomic regions were more likely to be expressed and were enriched in cancer-related pathways. Finally, in support of a model for circle generation through either a homology or microhomology-mediated process, circles exhibit homology near their breakpoint. These breakpoints are also enriched in specific DNA motifs. Our analysis supports a model where gene-containing circles emerge from common, highly transcribed regions through a homology-mediated process.