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 the multi-layer perceptron model, a series of imaging strategies in human cancer cells, and clinical chip verification, we demonstrate that ecDNA biogenesis depends on transcription factor Yin Yang 1 (YY1)-mediated DNA looping coupled with religation catalyzed 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-targeted strategies in cancer therapy.