遗传 ›› 2017, Vol. 39 ›› Issue (8): 717-725.doi: 10.16288/j.yczz.16-390

• 综述 • 上一篇    下一篇

下一代测序技术在干细胞转录调控研究中的应用

刘亚军(),张峰(),刘宏德,孙啸()   

  1. 东南大学生物科学与医学工程学院生物电子学国家重点实验室,南京 210096
  • 收稿日期:2017-02-27 修回日期:2017-05-08 出版日期:2017-08-20 发布日期:2017-12-25
  • 作者简介:刘亚军,博士,专业方向:生物信息学。E-mail: liuyajun_biology@126.com|张峰,硕士研究生,专业方向:生物信息学。E-mail: zf564js@163.com|孙啸,博士,教授,专业方向:生物信息学。E-mail: xsun@seu.edu.cn
  • 基金资助:
    江苏省重点研发计划项目(BE2016002-3);国家自然科学基金项目(31371339);国家国家重点基础研究发展计划项目(973计划)(2012CB316500)

The application of next-generation sequencing techniques in studying transcriptional regulation in embryonic stem cells

Liu Yajun(),Zhang Feng(),Liu Hongde,Sun Xiao()   

  1. State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
  • Received:2017-02-27 Revised:2017-05-08 Online:2017-08-20 Published:2017-12-25
  • Supported by:
    the Key Research and Development Program of Jiangsu province(BE2016002-3);the National Natural Science Foundation of China(31371339);the National Natural Science Foundation of China (No. 31371339) and the National Basic Research Program of China (973 Program)(2012CB316500)

摘要:

基因转录调控及其机制分析是后基因组时代生物学研究的重点之一。随着高通量测序技术的发展,人们可以从不同层面研究基因的转录调控行为,从转录组、转录因子结合,到染色质局部结构和整体空间构象,可系统分析转录调控的分子机制。干细胞分化过程的转录调控分析对研究再生医学和理解细胞癌变机制等具有重要意义。本文综述了下一代测序技术在干细胞转录调控研究中的应用,包括:(1)基于基因芯片或RNA测序的转录组分析;(2)基于染色体免疫共沉淀(chromatin immunoprecipitation, ChIP)测序的表观基因组和转录因子结合信息的分析;(3)基于DNase 酶切测序(DNase-Seq)的染色质开放性分析;(4)基于高通量染色质构象捕获(high-throughput chromosome conformation capture, Hi-C)技术的染色体远程相互作用分析。从基因表达谱、转录因子结合和基因组三维结构等层面展开介绍,重点关注了一些多能性转录因子(Oct4、Sox2和Nanog等)在维持干细胞干性和分化中的调控作用,以期为干细胞转录调控的研究提供借鉴和参考。

关键词: 胚胎干细胞, 转录组, ChIP, DNase-seq, Hi-C

Abstract:

The mechanism of transcriptional regulation has been the focus of many studies in the post-genomic era. The development of sequencing-based technologies for chromatin profiling enables current researchers to experimentally measure chromatin properties. Moreover, many studies aim at annotating the state of the chromatin into broad categories based on observed chromatin features and/or DNA sequences, then associating the resultant distal regulatory regions with the correct target genes based on DNA sequences, and predicting the dependence of epigenetic features on genetic variation. Stem cell biology has many applications in the area of regenerative medicine and tumorigenesis. In this review, we summarize recent research progresses on the application of next-generation sequencing techniques in studying transcriptional regulation in embryonic stem cells. This review mainly focuses on four areas: (1) microarray or RNA-seq; (2) chromatin immunoprecipitation (ChIP); (3) Dnase I hypersensitive sites (DHSs); (4) high-throughput chromosome conformation capture (Hi-C). These technologies have been utilized in studying chromatin on three levels, i.e., gene expression, transcription factor binding and genome three-dimensional structure. We especially emphasize three master transcription factors of pluripotency: Oct4, Sox2 and Nanog. We aim to track the frontier of stem cell transcriptional regulation research and share important progresses in this field.

Key words: embryonic stem cell, transcriptome, ChIP, DNase-seq, Hi-C