Cell-free DNA in plasma has been used for noninvasive prenatal testing and cancer liquid biopsy. The physical properties of cell-free DNA fragments in plasma, such as fragment sizes and ends, have attracted much recent interest, leading to the emerging field of cell-free DNA fragmentomics. However, one aspect of plasma DNA fragmentomics as to whether double-stranded plasma molecules might carry single-stranded ends, termed a jagged end in this study, remains underexplored. We have developed two approaches for investigating the presence of jagged ends in a plasma DNA pool. These approaches utilized DNA end repair to introduce differential methylation signals between the original sequence and the jagged ends, depending on whether unmethylated or methylated cytosines were used in the DNA end-repair procedure. The majority of plasma DNA molecules (87.8%) were found to bear jagged ends. The jaggedness varied according to plasma DNA fragment sizes and appeared to be in association with nucleosomal patterns. In the plasma of pregnant women, the jaggedness of fetal DNA molecules was higher than that of the maternal counterparts. The jaggedness of plasma DNA correlated with the fetal DNA fraction. Similarly, in the plasma of cancer patients, tumor-derived DNA molecules in patients with hepatocellular carcinoma showed an elevated jaggedness compared with nontumoral DNA. In mouse models, knocking out of the Dnase1 gene reduced jaggedness, whereas knocking out of the Dnase1l3 gene enhanced jaggedness. Hence, plasma DNA jagged ends represent an intrinsic property of plasma DNA and provide a link between nuclease activities and the fragmentation of plasma DNA.

中文翻译：

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血浆中双链 DNA 锯齿状末端的检测和表征。

血浆中的无细胞 DNA 已被用于无创产前检测和癌症液体活检。血浆中无细胞 DNA 片段的物理特性，如片段大小和末端，最近引起了很多兴趣，从而导致了无细胞 DNA 片段组学的新兴领域。然而，血浆 DNA 片段组学的一个方面关于双链血浆分子是否可能携带单链末端，在本研究中称为锯齿状末端，仍未得到充分探索。我们开发了两种方法来研究血浆 DNA 池中锯齿状末端的存在。这些方法利用 DNA 末端修复在原始序列和锯齿状末端之间引入差异甲基化信号，具体取决于 DNA 末端修复过程中使用的是未甲基化还是甲基化胞嘧啶。大多数血浆 DNA 分子 (87. 8%）被发现带有锯齿状的末端。锯齿状因血浆 DNA 片段大小而异，似乎与核小体模式有关。在孕妇血浆中，胎儿DNA分子的锯齿状比母体高。血浆 DNA 的锯齿状与胎儿 DNA 分数相关。同样，在癌症患者的血浆中，与非肿瘤 DNA 相比，肝细胞癌患者的肿瘤衍生 DNA 分子呈锯齿状。在小鼠模型中，敲除 血浆 DNA 的锯齿状与胎儿 DNA 分数相关。同样，在癌症患者的血浆中，与非肿瘤 DNA 相比，肝细胞癌患者的肿瘤衍生 DNA 分子呈锯齿状。在小鼠模型中，敲除 血浆 DNA 的锯齿状与胎儿 DNA 分数相关。同样，在癌症患者的血浆中，与非肿瘤 DNA 相比，肝细胞癌患者的肿瘤衍生 DNA 分子呈锯齿状。在小鼠模型中，敲除Dnase1基因减少了锯齿状，而敲除Dnase1l3基因增强了锯齿状。因此，血浆 DNA 锯齿状末端代表了血浆 DNA 的固有特性，并提供了核酸酶活性与血浆 DNA 片段化之间的联系。