近日，美国纽约大学Gilad D. Evrony及其研究组报道单分子测序揭示的DNA错配和损伤模式。相关论文于2024年6月12日在线发表在《自然》杂志上。

研究人员开发了一种单分子长读数测序方法（发夹双链增强保真测序，HiDEF-seq），它能以单分子的保真度检测存在于一条或两条DNA链中的碱基置换。HiDEF-seq还能以单分子保真度检测胞嘧啶脱氨——一种常见的DNA损伤类型。研究人员分析了来自不同组织的134个样本，包括来自癌症易感综合征患者的样本，并从中得出了单链错配和损伤特征。研究人员发现这些单链特征与已知的双链突变特征之间存在对应关系，从而确定了起始病变的身份。与只缺乏聚合酶校对功能的样本相比，同时缺乏错配修复和复制聚合酶校对功能的肿瘤显示出不同的单链错配模式。

研究人员还确定了APOBEC3A的单链损伤特征。在线粒体基因组中，研究结果支持主要发生在复制过程中的突变机制。由于DNA双链突变只是突变过程的终点，研究人员以单分子分辨率检测单链启动事件的方法将有助于研究突变是如何在各种情况下产生的，尤其是在癌症和衰老过程中。

据介绍，在人的一生中，突变会在每个细胞的基因组中累积，导致癌症和其他疾病。大多数突变开始时是DNA双链中一条链上的核苷酸错配或损伤，如果未修复或修复不当，就会变成双链突变。然而，目前的DNA测序技术无法准确分辨这些最初的单链事件。

附：英文原文

Title: DNA mismatch and damage patterns revealed by single-molecule sequencing

Author: Liu, Mei Hong, Costa, Benjamin M., Bianchini, Emilia C., Choi, Una, Bandler, Rachel C., Lassen, Emilie, Groska-Pski, Marta, Schwing, Adam, Murphy, Zachary R., Rosenkjr, Daniel, Picciotto, Shany, Bianchi, Vanessa, Stengs, Lucie, Edwards, Melissa, Nunes, Nuno Miguel, Loh, Caitlin A., Truong, Tina K., Brand, Randall E., Pastinen, Tomi, Wagner, J. Richard, Skytte, Anne-Bine, Tabori, Uri, Shoag, Jonathan E., Evrony, Gilad D.

Issue&Volume: 2024-06-12

Abstract: Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other diseases1,2. Most mutations begin as nucleotide mismatches or damage in one of the two strands of the DNA before becoming double-strand mutations if unrepaired or misrepaired3,4. However, current DNA-sequencing technologies cannot accurately resolve these initial single-strand events. Here we develop a single-molecule, long-read sequencing method (Hairpin Duplex Enhanced Fidelity sequencing (HiDEF-seq)) that achieves single-molecule fidelity for base substitutions when present in either one or both DNA strands. HiDEF-seq also detects cytosine deamination—a common type of DNA damage—with single-molecule fidelity. We profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes, and derive from them single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumours deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples that are deficient in only polymerase proofreading. We also define a single-strand damage signature for APOBEC3A. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. As double-strand DNA mutations are only the end point of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable studies of how mutations arise in a variety of contexts, especially in cancer and ageing.

DOI: 10.1038/s41586-024-07532-8

Source: https://www.nature.com/articles/s41586-024-07532-8