Mechanism for local attenuation of DNA replication at double-strand breaks

DNA double-strand breaks (DSBs) destroy the continuity of our genome with consequences for malignant transformation. Massive DNA damage can elicit a cellular checkpoint response that prevents cell proliferation. However, how highly aggressive cancer cells, which can tolerate widespread DNA damage, respond to DSBs alongside continuous chromosome duplication is unknown. Here we show that DSBs induce a local, hitherto unreported genome maintenance mechanism that inhibits replication initiation in DSB-containing topologically associating domains (TADs) without affecting DNA synthesis at other genomic locations. This process is facilitated by Mediators of Replication and DSBs (MRDs). In normal and cancer cells, MRDs include the TIMELESS-TIPIN complex and the WEE1 kinase, which actively dislodges the TIMELESS-TIPIN complex from replication origins adjacent to DSBs and prevents initiation of DNA synthesis at DSB-containing TADs. Dysregulation of MRDs, or disruption of 3D chromatin architecture by dissolving TADs, results in inadvertent replication in damaged chromatin and increased DNA damage in cancer cells. We propose that the intact MRD cascade precedes DSB repair to prevent genomic instability, which is otherwise observed when replication is forced, or when genome architecture is challenged, in the presence of DSBs. These observations reveal a previously undiscovered vulnerability in the DNA replication machinery that may be exploited to therapeutically target cancer cells. Overall design: BrdU seq, ChIP seq, Nascent strand seq