染色质转座酶可及性测序研究进展

doi:10.16288/j.yczz.19-279

遗传 ›› 2020, Vol. 42 ›› Issue (4): 333-346.doi: 10.16288/j.yczz.19-279

• 综述 • 下一篇

染色质转座酶可及性测序研究进展

吴杰¹, 全建平¹, 叶勇¹, 吴珍芳¹, 杨杰¹, 杨明²(), 郑恩琴¹()

^1. 华南农业大学动物科学学院,国家生猪种业工程技术研究中心,广州 510642
^2. 仲恺农业工程学院,动物科技学院,广州 510225

收稿日期:2019-11-14 修回日期:2020-01-29 出版日期:2020-04-20 发布日期:2020-02-26
通讯作者: 杨明,郑恩琴 E-mail:yangming@zhku.edu.cn;eqzheng@scau.edu.cn
作者简介:吴杰,硕士研究生,专业方向：分子遗传与动物育种。E-mail: wujiezi163@163.com
基金资助:
广东省“扬帆计划”引进创新创业团队项目编号(2016YT03H062);广东省现代农业产业技术体系生猪创新团队项目编号(2019KJ126);广东省自然科学基金项目资助编号(2017A030313213)

Advances in assay for transposase-accessible chromatin with high-throughput sequencing

Jie Wu¹, Jianping Quan¹, Yong Ye¹, ZhenFang Wu¹, Jie Yang¹, Ming Yang²(), Enqin Zheng¹()

^1. National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
^2. College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China

Received:2019-11-14 Revised:2020-01-29 Online:2020-04-20 Published:2020-02-26
Contact: Yang Ming,Zheng Enqin E-mail:yangming@zhku.edu.cn;eqzheng@scau.edu.cn
Supported by:
Supported by Guangdong YangFan Innovative and Entrepreneurial Research Team Program No(2016YT03H062);Guangdong Modern Agricultural Industry Technology System Pig Innovation Team Project No(2019KJ126);Guangdong Natural Science Foundation(2017A030313213)

摘要/Abstract

摘要：

染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing, ATAC-seq)诞生于2013年,具有比脱氧核糖核酸酶I超敏感位点测序(deoxyribonuclease I hypersensitive site sequencing, DNase-seq)和微球菌核酸酶敏感位点测序(micrococcal nuclease sequencing, MNase-seq)更快速、灵敏、简便的优点,是目前分析全基因组范围染色质开放区域的热点技术。通过该技术能获得染色质开放区域的相关信息,从而映射出转录因子等调控蛋白的结合区域和核小体定位等信息,对于研究表观遗传分子机制具有重要意义。本文比较了5种获取染色质开放区域技术的优缺点,重点介绍了ATAC-seq的原理和主要流程,描述了利用ATAC-seq技术研究染色质开放区域的发展概况以及ATAC-seq的相关应用,期望对真核生物全基因组水平的染色质开放区域研究、顺式调控元件鉴定以及遗传调控网络的解析等提供借鉴。

关键词: 染色质转座酶可及性测序, 染色质开放区域, Tn5转座酶, 表观遗传修饰, 转录因子

Abstract:

Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) was developed in 2013. It has the advantages of more convenient operation and higher efficiency for DNA recovery than DNase I hypersensitive site sequencing (DNase-seq) and micrococcal nuclease sequencing (MNase-seq). ATAC-seq currently is the most popular technique of genome-wide mapping for chromatin accessibility. It provides information on binding regions of transcription factors and nucleosome localization on the chromatin. Thus, ATAC-seq is of great significance for studying the epigenetics and molecular mechanisms in chromatin structure. In this review, we compare the advantages and disadvantages of multiple techniques for profiling chromatin accessibility, and summarize the principles, main process, development and applications of ATAC-seq. We hope this review will provide a reference for study of genome-wide mapping for chromatin accessibility, identification of cis-regulatory elements, and dissection of the epigenetic and genetic regulatory networks using the ATAC-seq technology in eukaryotes.

Key words: assay for transposase-accessible chromatin with high-throughput sequencing, open chromatin regions, Tn5 transposase, epigenetic modification, transcription factor

吴杰, 全建平, 叶勇, 吴珍芳, 杨杰, 杨明, 郑恩琴. 染色质转座酶可及性测序研究进展[J]. 遗传, 2020, 42(4): 333-346.

Jie Wu, Jianping Quan, Yong Ye, ZhenFang Wu, Jie Yang, Ming Yang, Enqin Zheng. Advances in assay for transposase-accessible chromatin with high-throughput sequencing[J]. Hereditas(Beijing), 2020, 42(4): 333-346.

图/表 2

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技术	细胞类型及数量	获取方式	目的	特点	参考文献
DNase-seq	需要1,000,000~ 10,000,000的任何细胞类型	DNase I 酶切	获取染色质开放信息	(1)比传统方法操作更简便; (2)细胞需要量大; (3)酶最优酶切浓度确定过程繁琐; (4)样品制备过程复杂且耗时	[20,24]
MNase-seq	需要1,000,000~ 10,000,000的任何细胞类型	微球菌核酸酶酶切	绘制核小体图谱以间接探测染色质可及性	(1)操作简单,后期数据处理方便; (2)细胞样本需要量大; (3)酶浓度和切割温度难以确定	[26,27]
FAIRE-seq	需要100,000~ 10,000,000的任何细胞类型	超声波物理断裂	获取染色质开放信息	(1)不用酶切、不需要分离出细胞核; (2)没有序列切割特异性; (3)细胞需要量大; (4)甲醛最佳交联程度难以确定	[21,24,31]
NOMe-seq	至少1,000,000 的任何细胞类型	甲基化修饰	获得内源DNA甲基化的信息并定位核小体	(1)不需要使DNA断裂,不会产生富集偏差; (2)同时获得含GpC和CpG二核苷酸的信息; (3)细胞需要量大	[22,34]
ATAC-seq	500~50,000个新鲜分离的细胞	Tn5转座酶酶切	获取染色质可及性、转录因子结合以及核小体定位信息	(1)过程简便、效率高; (2)数据分析工具不够成熟; (3)线粒体、叶绿体中的DNA污染; (4)冷冻组织细胞DNA提取效率低; (5) DNA片段损失过多	[36~38]

染色质转座酶可及性测序研究进展

Advances in assay for transposase-accessible chromatin with high-throughput sequencing

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