下一代测序技术在表观遗传学研究中的重要应用及进展

doi:10.3724/SP.J.1005.2014.0256

遗传 ›› 2014, Vol. 36 ›› Issue (3): 256-275.doi: 10.3724/SP.J.1005.2014.0256

下一代测序技术在表观遗传学研究中的重要应用及进展

沈圣, 屈彦纯, 张军

美国德州理工大学医学中心神经科学研究中心, 德克萨斯州埃尔帕索 79905

收稿日期:2013-10-16 修回日期:2013-12-07 出版日期:2014-03-20 发布日期:2014-02-25
通讯作者: 张军, 博士, 教授, 研究方向：分子遗传。E-mail: jun.zhang2000@gmail.com E-mail:jun.zhang2000@gmail.com
作者简介:沈圣, 博士, 研究方向：分子遗传。E-mail: saint_ss@163.com
基金资助:
美国国立神经病与中风研究所/美国国立卫生院及Coldwell基金会项目资助

The application of next generation sequencing on epigenetic study

Sheng Shen, Yanchun Qu, Jun Zhang

COE for Neuroscience, Texas Tech University Health Sciences Center, El Paso, Texas 79905, USA

Received:2013-10-16 Revised:2013-12-07 Online:2014-03-20 Published:2014-02-25

摘要/Abstract

摘要：

下一代测序技术(Next generation sequencing, NGS)的出现, 极大地促进了表观遗传学的研究。将NGS技术引入表观遗传学, 便形成了以NGS为基础的各种表观遗传学测序及研究方法, 如：全基因组亚硫酸氢盐测序法(Whole genome bisulfite sequencing, WGBS)、简化代表性亚硫酸氢盐测序法(Reduced representation bisulfite sequencing, RRBS)、甲基化DNA免疫共沉淀测序(Methylated DNA immunoprecipitationsequencing, MeDIP-seq)、染色质免疫共沉淀测序(Chromatin immunoprecipitation-sequencing, ChIP-seq)、Tet辅助重亚硫酸盐测序法(Tet-assisted bisulfite sequencing, TAB-seq)、各种染色体构象捕获测序(Chromosome conformation capture se-quencing, 3C-seq)技术、DnaseⅠ-seq/MNase-seq/FAIRE-seq以及RNA测序(RNA sequencing, RNA-seq)。这些方法的应用和普及改变了人们对多种表观遗传现象的传统认识, 使研究人员能够更加全面地深入了解各种表观遗传标志在机体内的广泛分布, 以及如何在外界因素的影响下发生相应的动态变化。文章概述了当今主要商业NGS平台的原理和特点, 系统介绍了以NGS方法为基础衍生出来的各种表观遗传学测序及研究方法, 并在此基础上对近年来应用NGS技术在表观遗传学研究领域中取得的最新研究成果进行了综述。

关键词: 下一代测序技术, 表观遗传学, DNA甲基化, 组蛋白修饰, 染色质构象捕获

Abstract:

The application of next generation sequencing (NGS) technique has a great impact on epigenetic studies. Coupled with NGS, a number of sequencing-based methodologies have been developed and applied in epigenetic studies, such as Whole Genome Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS), Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq), Chromatin Immunoprecipitation-Sequencing (ChIP-seq), TAB-seq (Tet-assisted Bisulfite Sequencing), Chromosome Conformation Capture Sequencing (3C-seq) and various of 3C-seq de-rivatives, DNaseⅠ-seq/MNase-seq/FAIRE-seqand RNA Sequencing (RNA-seq). These new techniques were used to iden-tify DNA methylation patterns and a broad range of protein/nucleic acid interactions, and to analyze chromatin conforma-tion.With these new technologies, researchers have gained a broader view and better tools to investigate the distributions and dynamic changes of epigenetic markers affected by both internal and external factors. The principles and characteristics of major applications of NGS technologies on epigenetics were summarized; and the recent advances and the future direc-tions in NGS-based epigenetic studies were further discussed.

Key words: next generation sequencing, epigenetics, DNA methylation, histone modifications, chromosome con-formation capture

沈圣, 屈彦纯, 张军. 下一代测序技术在表观遗传学研究中的重要应用及进展[J]. 遗传, 2014, 36(3): 256-275.

Sheng Shen, Yanchun Qu, Jun Zhang. The application of next generation sequencing on epigenetic study[J]. HEREDITAS, 2014, 36(3): 256-275.

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下一代测序技术在表观遗传学研究中的重要应用及进展

The application of next generation sequencing on epigenetic study

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