S1-END-seq reveals DNA secondary structures in human cells.
S1-END-seq reveals DNA secondary structures in human cells.
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DOI：
10.1016/j.molcel.2022.08.007
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发表时间：
2022-10-06
期刊：
影响因子：
16
通讯作者：
Nussenzweig, Andre
中科院分区：
文献类型：
--
作者：
Matos-Rodrigues, Gabriel;van Wietmarschen, Niek;Wu, Wei;Tripathi, Veenu;Koussa, Natasha C.;Pavani, Raphael;Nathan, William J.;Callen, Elsa;Belinky, Frida;Mohammed, Ashraf;Napierala, Marek;Usdin, Karen;Ansari, Aseem Z.;Mirkin, Sergei M.;Nussenzweig, Andre
DNA在复制、转录和修复过程中变成单链（ssDNA）。瞬时形成的ssDNA区段可以采用替代构象，包括十字形、三链体和四链体。为了确定人类基因组中是否存在ssDNA的稳定区域，我们利用S1-END-seq将ssDNA区域转化为DNA双链断裂，然后进行高通量测序。这种方法揭示了两种主要的非B DNA结构：由在微卫星不稳定的人类癌细胞系中积累的扩展的（TA）n重复序列形成的十字形DNA和由在各种细胞系中常见的同型嘌呤/同型嘧啶镜像重复序列形成的DNA三链体（H-DNA）。我们表明，H-DNA是丰富的复制过程中，它的基因组位置是高度保守的，和H-DNA形成的（GAA）n重复可以被破坏的（GAA）n-结合聚酰胺治疗。最后，我们表明，三链体形成的重复序列是突变的热点。我们的研究结果确定动态DNA二级结构在体内，有助于提高基因组的不稳定性。Matos-Rodrigues等人使用S1-END-seq揭示了非B DNA二级结构，包括体内形成的十字形和三链体。DNA三链体在DNA复制过程中形成，在癌细胞中增强，并且是诱变的热点。该研究为非B DNA结构的生物学研究提供了基础。
DNA becomes single-stranded (ssDNA) during replication, transcription, and repair. Transiently formed ssDNA segments can adopt alternative conformations, including cruciforms, triplexes, and quadruplexes. To determine whether there are stable regions of ssDNA in the human genome, we utilized S1-END-seq to convert ssDNA regions to DNA double-strand breaks, which were then processed for high-throughput sequencing. This approach revealed two predominant non-B DNA structures: cruciform DNA formed by expanded (TA)n repeats that accumulate in microsatellite unstable human cancer cell lines and DNA triplexes (H-DNA) formed by homopurine/homopyrimidine mirror repeats common across a variety of cell lines. We show that H-DNA is enriched during replication, that its genomic location is highly conserved, and that H-DNA formed by (GAA)n repeats can be disrupted by treatment with a (GAA)n-binding polyamide. Finally, we show that triplex forming repeats are hotpots for mutagenesis. Our results identify dynamic DNA secondary structures in vivo that contribute to elevated genome instability. Matos-Rodrigues et al. use S1-END-seq to reveal non-B DNA secondary structures including cruciforms and triplexes formed in vivo. DNA triplexes form during DNA replication, are enhanced in cancer cells, and are hotspots for mutagenesis. This study provides a foundation for research into the biology of non-B DNA structures.
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