Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA.
Laboratory of Biology and Modelling of the Cell (UMR5239), Ecole Normale Supérieure de Lyon, 69007 Lyon, France.
Genes Dev. 2023 Jul 1;37(13-14):621-639. doi: 10.1101/gad.350618.123. Epub 2023 Aug 4.
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/Pol-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.
结构基因组变异 (SV) 的间歇性爆发已在各种生物体中被描述，但它们的病因仍不完全清楚。同源重组 (HR) 是一种模板指导的 DNA 双链断裂和停滞或崩溃的复制叉的修复机制。我们最近发现了一种源自 HR 过程中形成的多入侵 (MI) DNA 连接分子的末端内切酶处理的 DNA 断裂扩增和基因组重排途径。全基因组方法证实，多入侵诱导的重排 (MIR) 经常导致几种重复介导的 SV 和非整倍体。使用分子和遗传分析以及一种新颖的、基于高度敏感的邻近连接的染色体重排定量检测方法，我们进一步描绘了两种 MIR 亚途径。MIR1 是一种在任何序列背景下发生的普遍途径，它产生次级断裂，并经常导致额外的 SV。MIR2 仅在重组供体表现出大量同源性时发生，并且不会导致额外的断裂或 SV，而是导致序列插入。最具危害性的 MIR1 途径以 PCNA/Pol 独立的方式在一小部分持续存在的 DNA 连接分子上发生，这与重组 DNA 合成不同。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 可以在没有置换 DNA 合成的情况下发生。还提出了从长读数据推断 MIR1 的序列特征。
