Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells

SUMMARY Whereas chromosomal translocations are common pathogenetic events in cancer, mechanisms that promote them are poorly understood. To elucidate translocation mechanisms in mammalian cells, we developed high-throughput, genome-wide translocation sequencing (HTGTS). We employed HTGTS to identify tens of thousands of independent translocationjunctionsinvolvingfixedI-SceImeganucleasegenerated DNA double-strand breaks (DSBs) within the c-myc oncogene or IgH locus of B lymphocytes induced for activation-induced cytidine deaminase (AID)-dependent IgH class switching. DSBs translocated widely across the genome but were preferentially targeted to transcribed chromosomal regions. Additionally, numerous AID-dependent and AIDindependent hot spots were targeted, with the latter comprisingmainlycrypticI-SceItargets.Comparison of translocation junctions with genome-wide nuclear run-onsrevealedamarkedassociationbetweentranscription start sites and translocation targeting. The majority of translocation junctions were formed via end-joiningwithshortmicrohomologies.Ourfindings have implications for diverse fields, including gene therapy and cancer genomics.