Shen Sheng, Qu Yanchun, Zhang Jun
COE for Neuroscience, Texas Tech University Health Sciences Center, El Paso, Texas 79905, USA.
Yi Chuan. 2014 Mar;36(3):256-75.
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, DNase1-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.
下一代测序(NGS)技术的应用对表观遗传学研究产生了巨大影响。与NGS相结合,已开发出多种基于测序的方法并应用于表观遗传学研究,如全基因组亚硫酸氢盐测序(WGBS)、简化代表性亚硫酸氢盐测序(RRBS)、甲基化DNA免疫沉淀测序(MeDIP-seq)、染色质免疫沉淀测序(ChIP-seq)、TAB-seq(Tet辅助亚硫酸氢盐测序)、染色体构象捕获测序(3C-seq)以及各种3C-seq衍生物、DNase1-seq/MNase-seq/FAIRE-seq和RNA测序(RNA-seq)。这些新技术用于识别DNA甲基化模式和广泛的蛋白质/核酸相互作用,并分析染色质构象。借助这些新技术,研究人员获得了更广阔的视野和更好的工具来研究受内部和外部因素影响的表观遗传标记的分布和动态变化。总结了NGS技术在表观遗传学主要应用的原理和特点;并进一步讨论了基于NGS的表观遗传学研究的最新进展和未来方向。