Extrachromosomal DNA biogenesis is dependent on DNA looping and religation by YY1-Lig3-PARylation complex

The link between extrachromosomal DNA (ecDNA) and tumors has been well established, and its role in cancer is of increasing interest. While ecDNA is thought to originate from genomic instability, the molecular mechanisms driving DNA end ligation during ecDNA formation and the regulatory factors controlling its selective gene packaging remain unresolved. Here, using machine learning, bioinformatics, cellular assays, and clinical validation, we demonstrate that ecDNA biogenesis depends on YY1-mediated DNA looping coupled with ligation executed by DNA ligase 3 (Lig3), a mechanism that extends existing models. Notably, PARylation-dependent acidic microenvironments mediated by the Lig3-YY1 complex play a critical role in the formation of Z-DNA, which potentially facilitates the fusion-religation process to drive ecDNA biogenesis. Furthermore, our findings establish PARP inhibitors as specific agents for ecDNA-targeting strategies in cancer therapy.