DNA double-strand breaks (DSB), one of the most serious types of damage to the genome. Efforts have been made to explain the general patterns observed in DSBs. However, the contribution of 3D chromatin spatial conformation to DSB formation upon the genome remains poorly understood. Here, we introduce the 3D-Genome Damage Analysis Framework (3DDAS). Utilizing standardized DSB datasets, 3DDAS constructs a genome-wide DSB prediction model named Hi-DSB. From a three-dimensional perspective, we annotate key genomic features identified by Hi-DSB and measure the impact of 3D chromatin interaction density on DSB susceptibility. Additionally, we apply the critical genomic loci identified by 3DDAS to recognize oncogenes and tumor suppressor genes pertinent to breast cancer patient survival outcomes. This framework provides a novel paradigm for investigating the relationship between chromatin structure, genomic stability, and cancer progression.
 

DSB, 3D chromatin spatial conformation, Benchmark, AI