3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression.

Cancer genomes are composed of many complex structural alterations on chromosomes and extrachromosomal DNA (ecDNA), making it difficult to identify non-coding enhancer regions that are hijacked to activate oncogene expression. Here, we describe a 3D genomics-based analysis called HAPI (Highly Active Promoter Interactions) to characterize enhancer hijacking. HAPI analysis of HiChIP data from 34 cancer cell lines identified enhancer hijacking events that activate both known and potentially novel oncogenes such as , , , and . Furthermore, we found enhancer hijacking among multiple oncogenes from different chromosomes, often including , on the same complex amplicons such as ecDNA. We characterized a - chimeric ecDNA, in which heavily hijacks 's enhancers. Notably, CRISPRi of the promoter led to increased interaction of with enhancers and elevated expression. Our HAPI analysis tool provides a robust strategy to detect enhancer hijacking and reveals novel insights into oncogene activation.