染色质转座酶可及性测序研究进展

doi:10.16288/j.yczz.19-279

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

• Review • Next Articles

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)

Abstract

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

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.

Figures/Tables 2

Table 1

Fig. 1

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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]

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

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