Oncogene amplification on extrachromosomal DNA (ecDNA) is prevalent in human cancer and is associated with poor outcomes. Clonal, megabase-sized circular ecDNAs in cancer are distinct from nonclonal, small sub-kilobase-sized DNAs that may arise during normal tissue homeostasis. ecDNAs enable profound changes in gene regulation beyond copy-number gains. An emerging principle of ecDNA regulation is the formation of ecDNA hubs: micrometer-sized nuclear structures of numerous copies of ecDNAs tethered by proteins in spatial proximity. ecDNA hubs enable cooperative and intermolecular sharing of DNA regulatory elements for potent and combinatorial gene activation. The 3D context of ecDNA shapes its gene expression potential, selection for clonal heterogeneity among ecDNAs, distribution through cell division, and reintegration into chromosomes. Technologies for studying gene regulation and structure of ecDNA are starting to answer long-held questions on the distinct rules that govern cancer genes beyond chromosomes.

染色体外 DNA (ecDNA) 上的癌基因扩增在人类癌症中普遍存在，并且与不良预后相关。癌症中的克隆性、兆碱基大小的环状 ecDNA 与正常组织稳态过程中可能出现的非克隆、亚千碱基大小的小 DNA 不同。 ecDNA 能够使基因调控发生深刻的变化，而不仅仅是拷贝数的增加。 ecDNA 调控的一个新兴原理是 ecDNA 中心的形成：由空间邻近的蛋白质束缚的许多 ecDNA 拷贝的微米大小的核结构。 ecDNA 中心能够实现 DNA 调控元件的合作和分子间共享，从而实现有效的组合基因激活。 ecDNA 的 3D 背景决定了其基因表达潜力、ecDNA 之间克隆异质性的选择、通过细胞分裂的分布以及重新整合到染色体中。研究基因调控和 ecDNA 结构的技术开始回答长期以来关于控制染色体以外癌症基因的独特规则的问题。