Recent advances in the detection of base modifications using the Nanopore sequencer
Recent advances in the detection of base modifications using the Nanopore sequencer
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DOI：
10.1038/s10038-019-0679-0
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发表时间：
2019-09
影响因子：
3.5
通讯作者：
Liu Xu;Masahide Seki
中科院分区：
文献类型：
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作者：
Liu Xu;Masahide Seki
DNA和RNA修饰具有重要的功能，包括调节基因表达。现有的基于短读段测序的修饰检测方法难以确定单个染色体或整个转录物序列的修饰模式。此外，检测方法可用的修改种类非常有限。Nanopore测序仪是一种单分子、长读取测序仪，可以直接对RNA和DNA进行测序。此外，Nanopore测序仪检测长DNA和RNA分子上的修饰。在这篇综述中，我们主要集中在使用纳米孔测序仪检测哺乳动物的DNA和RNA中的碱基修饰。我们总结了目前使用纳米孔测序仪，使用统计测试或机器学习的检测工具，以及该技术的应用，如开放染色质，DNA复制和RNA代谢分析的修改研究。
DNA and RNA modifications have important functions, including the regulation of gene expression. Existing methods based on short-read sequencing for the detection of modifications show difficulty in determining the modification patterns of single chromosomes or an entire transcript sequence. Furthermore, the kinds of modifications for which detection methods are available are very limited. The Nanopore sequencer is a single-molecule, long-read sequencer that can directly sequence RNA as well as DNA. Moreover, the Nanopore sequencer detects modifications on long DNA and RNA molecules. In this review, we mainly focus on base modification detection in the DNA and RNA of mammals using the Nanopore sequencer. We summarize current studies of modifications using the Nanopore sequencer, detection tools using statistical tests or machine learning, and applications of this technology, such as analyses of open chromatin, DNA replication, and RNA metabolism.