Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR subpathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology and results in sequence insertion without additional breaks or SVs. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.

中文翻译：

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描述对基因组稳定性有不同影响的两种多重入侵诱导的重排途径

结构基因组变异（SV）的间断爆发已在多种生物体中得到描述，但其病因学仍不完全清楚。同源重组 (HR) 是一种模板引导的 DNA 双链断裂和停滞或折叠复制叉修复机制。我们最近发现了一条 DNA 断裂扩增和基因组重排途径，该途径源自 HR 过程中形成的多侵入 (MI) DNA 联合分子的核酸内切加工。全基因组方法证实，多重入侵诱导重排 (MIR) 经常导致多个重复介导的 SV 和非整倍体。使用分子和遗传分析以及一种新颖的、高灵敏度的基于邻位连接的染色体重排定量测定，我们进一步描绘了两种 MIR 子通路。MIR1 是在任何序列环境中发生的通用途径，它会产生二次断裂并经常导致额外的 SV。仅当重组供体表现出显着的同源性并导致序列插入而没有额外的断裂或SV时，MIR2才会发生。与重组 DNA 合成不同，最有害的 MIR1 途径以 PCNA/Pol δ独立的方式发生在持久性 DNA 联合分子的子集上。这项工作提供了对这些基于 HR 的 SV 形成途径的精细机制理解，并表明复杂的重复介导的 SV 可以在不置换 DNA 合成的情况下发生。提出了从长读数据推断 MIR1 的序列签名。