Break-induced replication (BIR) repairs one-ended double-strand breaks in DNA similar to those formed by replication collapse or telomere erosion, and it has been implicated in the initiation of genome instability in cancer and other human diseases^1,2. Previous studies have defined the enzymes that are required for BIR^1,2,3,4,5; however, understanding of initial and extended BIR synthesis, and of how the migrating D-loop proceeds through known replication roadblocks, has been precluded by technical limitations. Here we use a newly developed assay to show that BIR synthesis initiates soon after strand invasion and proceeds more slowly than S-phase replication. Without primase, leading strand synthesis is initiated efficiently, but is unable to proceed beyond 30 kilobases, suggesting that primase is needed for stabilization of the nascent leading strand. DNA synthesis can initiate in the absence of Pif1 or Pol32, but does not proceed efficiently. Interstitial telomeric DNA disrupts and terminates BIR progression, and BIR initiation is suppressed by transcription proportionally to the transcription level. Collisions between BIR and transcription lead to mutagenesis and chromosome rearrangements at levels that exceed instabilities induced by transcription during normal replication. Together, these results provide fundamental insights into the mechanism of BIR and how BIR contributes to genome instability.

断裂诱导复制 (BIR) 修复 DNA 中的单端双链断裂，类似于复制崩溃或端粒侵蚀形成的断裂，并且它与癌症和其他人类疾病^1,2中基因组不稳定性的启动有关。^{以前的研究已经定义了 BIR 1、2、3、4、5}所需的酶; 然而，对初始和扩展 BIR 合成的理解，以及迁移 D-loop 如何通过已知的复制障碍进行，已被技术限制排除在外。在这里，我们使用一种新开发的检测方法来表明 BIR 合成在链入侵后很快开始，并且比 S 期复制进行得更慢。如果没有引物酶，前导链合成会有效启动，但不能进行超过 30 kb，这表明需要引物酶来稳定新生前导链。DNA 合成可以在没有 Pif1 或 Pol32 的情况下启动，但不能有效地进行。间质端粒 DNA 破坏和终止 BIR 进程，并且 BIR 起始被转录抑制，与转录水平成比例。BIR 和转录之间的碰撞导致突变和染色体重排的水平超过了正常复制期间转录诱导的不稳定性。总之，这些结果提供了对 BIR 机制以及 BIR 如何导致基因组不稳定性的基本见解。