Research Progress in Chromatin Immunoprecipitation Followed by Sequencing

doi:10.13560/j.cnki.biotech.bull.1985.2021-0807

Abstract

Abstract:

Chromatin immunoprecipitation followed by sequencing（ChIP-seq）is an important method to study the interaction between DNA and target proteins,it has been widely used to study transcription factor and the functions and distributions of post-translation histone modification. In recent years,researchers have been optimizing the key steps of this method,including cell separation,chromatin fragmentation,immunoprecipitation and sequencing library construction,allowing the ChIP-seq suitable for the analysis of small amount of cells. In cleavage under targets and release using nucleus（CUT&RUN）and cleavage under targets and tagmentation（CUT&Tag）,the enzyme is “targeted” to the target protein through specific antibodies,and the chromatin near the target protein is digested by MNase or Tn5 transposase,which simplifies the operation process. The paper provided an overview of the principle behind ChIP-seq and its data analysis methods,compared the ChIP-based optimization methods and derived methods,and summarized the studies of transcription factors and histone modification in the regulation of biological clock,hormone signal transduction,signal transduction pathway and stress response in the process of plant growth and development,as well as the application of ChIP-seq technique.

Key words: chromatin immunoprecipitation, transcription factors, histone modification, data analysis

CHEN Gui-fang, YANG Jia-yi, GAO Yun-hua, REN Ge. Research Progress in Chromatin Immunoprecipitation Followed by Sequencing[J]. Biotechnology Bulletin, 2022, 38(7): 40-50.

Figures/Tables 5

References 76

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	ULI-NChIP-seq	scChIP-seq	ChIP-exo	MOW ChIP-seq	ChIP-nexus	Nano-ChIP-seq
细胞分离/ 单细胞捕获	流式细胞分选	液滴微流控芯片	-	微流控芯片	-	-
染色质制备	MNase酶切	MNase酶切	甲醛交联超声断裂 lambda核酸外切酶 RecJ_f 核酸外切酶	甲醛交联超声断裂	甲醛交联超声断裂	甲醛交联超声断裂
文库制备	-	-	-	-	使用含有BamH I酶切位点的测序接头,环化连接酶使DNA成环,酶切后进一步建库	使用发夹结构引物; BciV I酶切DNA,使含有突出末端便于连接测序接头
细胞数	10³-10^5[39]	单细胞建库^[42]	10^6[43-44]	10²-10^4[45]	10^6[47]	10^4[49]

	ULI-NChIP-seq	scChIP-seq	ChIP-exo	MOW ChIP-seq	ChIP-nexus	Nano-ChIP-seq
细胞分离/ 单细胞捕获	流式细胞分选	液滴微流控芯片	-	微流控芯片	-	-
染色质制备	MNase酶切	MNase酶切	甲醛交联超声断裂 lambda核酸外切酶 RecJ_f 核酸外切酶	甲醛交联超声断裂	甲醛交联超声断裂	甲醛交联超声断裂
文库制备	-	-	-	-	使用含有BamH I酶切位点的测序接头,环化连接酶使DNA成环,酶切后进一步建库	使用发夹结构引物; BciV I酶切DNA,使含有突出末端便于连接测序接头
细胞数	10³-10^5[39]	单细胞建库^[42]	10^6[43-44]	10²-10^4[45]	10^6[47]	10^4[49]

	ChIP-seq	CUT&RUN	CUT&Tag
细胞处理	甲醛交联/裂解细胞	改变细胞膜通透性	改变细胞膜通透性
染色质制备	超声断裂/MNase酶切	染色质与特异性抗体、pA-MN反应;Ca²⁺激活MNase酶切处理染色质	染色质与特异性抗体、pA-Tn5反应;Mg²⁺激活Tn5,进行切割与接头连接
细胞数	10⁶-10⁷	10²-10^3[54] 可实现单细胞建库^[55]	10²-10³ 可实现单细胞建库^[59]

	ChIP-seq	CUT&RUN	CUT&Tag
细胞处理	甲醛交联/裂解细胞	改变细胞膜通透性	改变细胞膜通透性
染色质制备	超声断裂/MNase酶切	染色质与特异性抗体、pA-MN反应;Ca²⁺激活MNase酶切处理染色质	染色质与特异性抗体、pA-Tn5反应;Mg²⁺激活Tn5,进行切割与接头连接
细胞数	10⁶-10⁷	10²-10^3[54] 可实现单细胞建库^[55]	10²-10³ 可实现单细胞建库^[59]