Advances in Chromatin Immunoprecipitation Sequencing and Its Application in Horticultural Plants

doi:10.16420/j.issn.0513-353x.2023-0125

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (1): 39-52.doi: 10.16420/j.issn.0513-353x.2023-0125

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Advances in Chromatin Immunoprecipitation Sequencing and Its Application in Horticultural Plants

ZHAI Tingkai, MA Xiangwei, CHEN Yan, ZHANG Xueying, LI Zhuoyun, XÜ Luzhen, FU Zhuoran, LAI Zhongxiong, LIN Yuling^*()

Institute of Horticultural Biotechnology，Fujian Agriculture and Forestry University，Fuzhou 350002，China

Received:2023-03-01 Revised:2023-07-24 Online:2024-01-25 Published:2024-01-16
Contact: *（E-mail：buliang84@163.com）

Abstract

Abstract:

In recent years，chromatin immunoprecipitation sequencing technology (ChIP-seq) based on the combination of chromatin immunoprecipitation technology (ChIP) and second-generation sequencing technology has been widely used to study the interaction between DNA and proteins. It has great advantages in analyzing the expression and regulation of horticultural plant genes，screening and mapping of target genes，construction of regulatory networks，and confirmation of chromatin openness. This paper reviews the development history of ChIP-seq technology and its progress in the modification of transcription factors and histones in horticultural plants，with the aim of providing theoretical reference for the study of DNA-protein interactions in horticultural plants.

Key words: DNA and protein interaction, chromatin immunoprecipitation sequencing, transcription factor, histone modification

ZHAI Tingkai, MA Xiangwei, CHEN Yan, ZHANG Xueying, LI Zhuoyun, XÜ Luzhen, FU Zhuoran, LAI Zhongxiong, LIN Yuling. Advances in Chromatin Immunoprecipitation Sequencing and Its Application in Horticultural Plants[J]. Acta Horticulturae Sinica, 2024, 51(1): 39-52.

Figures/Tables 3

References 72

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发展阶段 Stage	技术名称 Technical name	细胞数 Number of cell	新/优化技术 New/optimization technology	优点 Advantage	缺点 Disadvantage	细胞/组织水平Cell/ tissue level	参考文献 Reference
初期 Initial （1984— 2010）	ChIP	10⁷	新技术 New technology	有利于富集与蛋白相结合的DNA片段It’s good for enriching DNA fragments that bind to proteins	交联效果差；样本需求量大Formaldehyde crosslinking effect is poor；High demand for samples	组织 Tissue	Gilmour & Lis,1984
	ChIP-chip	10⁷	新技术 New technology	基因组微阵列技术对DNA定位Genomic microarray technique for DNA localization	试验重复性低 Low test repeatability	组织 Tissue	Bernstein et al.,2002
	ChIP-seq	10⁷	新技术 New technology	转录因子结合位点与组蛋白修饰区域定位Localization of transcription factor binding sites and histone modification regions	样本需求量大；试验重复性低；易出现假阳性 Large sample demand; Low test repeatability; Prone to false positives	组织 Tissue	Johnson et al.,2007
探索发展 Explorative （2011— 2018）	ChIP-exo	10⁶	优化：酶切 Optimization：MNase cutting	降低测序假阳性；提高单bp准确性Reduce false positive sequencing results; Improve the accuracy of single bp	样本需求量大；对技术要求高Large sample demand; High technical requirements	组织 Tissue	Rhee & Pugh,2011
	Nano- ChIP-seq	10⁴	优化：文库构建 Optimization：library construction	抑制DNA中GC含量；降低样本需求量Inhibition of GC content in DNA; Lower the quantity of samples	易出现假阳性 Prone to false positives	组织 Tissue	Adli & Bernstein,2011
	scChIP-seq	单细胞 Single cell	新技术 New technology	高度集成化；实现单细胞测序Highly integrated; Single cell sequencing was realized	成本昂贵；对技术要求高Expensive; High technical requirements	单细胞 Single cell	Rotem et al.,2015
	ChIP-nexus	10⁶	优化：文库构建 Optimization： library construction	降低文库构建的DNA需求量Reduce the DNA requirement for library construction	样本需求量大 Large sample demand	组织 Tissue	He et al.,2015
	ULI- NChIP	10³	优化：细胞分离 Optimization：cell separation	降低样本需求量；无需甲醛交联Lower the quantity of samples；No formaldehyde crosslinking required	ChIP时损失DNA影响测序准确性DNA loss during ChIP affects the accuracy of subsequent sequencing results	组织 Tissue	Brind’ Amour et al.,2015
	CUT&RUN	10² ~ 10³	新技术 New technology	富集和染色质片段化同时进行；省去ChIP；降低背景噪音Enrichment occurs simultaneously with chromatin fragmentation; Omit ChIP; Reduce background noise	易发生DNA损失 Prone to DNA loss	组织 Tissue	Skene & Henikoff,2017
快速发展 Rapid （2019—）	ULI-CUT& RUN	10 ~ 10²	优化： CUT&RUN Optimization：CUT&RUN	采用流式细胞分选实现极少数细胞测序Very few cells were sequenced by flow cytometry	易发生DNA损失 Prone to DNA loss	组织 Tissue	Hainer et al.,2019
	CUT&Tag	10²~ 10³	新技术 New technology	靶向切割产物可以直接进行文库扩增 Targeted cleavage products can be directly amplified into the library	易出现假阳性 Prone to false positives	组织 Tissue	Kaya-Okur et al.,2019
	TAF-ChIP	10²	优化：细胞分离 Optimization：cell separation	无需DNA纯化与文库构建；降低对样本需求量No DNA purification and library construction；Lower the quantity of samples	易出现假阳性 Prone to false positives	组织 Tissue	Akhtar et al.,2019
	MOW ChIP-seq	10² ~ 10⁴	优化：免疫共沉Optimization：ChIP	降低对试剂消耗；便于自动化 Reduce the consumption of reagents; Facilitate automation	对技术要求高High technical requirements	组织 Tissue	Zhu et al.,2019
快速发展 Rapid （2019—）	CoBATCH	10⁴	新技术 New technology	实现不同样本高通量单细胞测序Achieve high throughput single cell sequencing of different samples	无法直接在单细胞水平进行分析Samples cannot be analyzed directly at the single-cell level	组织 Tissue	Wang et al.,2019
	scCUT&Tag	单细胞 Single cell	优化：CUT&Tag Optimization： CUT&Tag	单细胞水平测序；高信噪比 Single-cell level sequencing; High signal-to-noise ratio	成本昂贵；对技术要求高Expensive; High technical requirements	单细胞 Single cell	Bartosovic et al.,2021
	Greenscreen	10⁷	新技术 New technology	提高样本间可重复性；消除假阳性Improve repeatability between samples; Eliminate false positives	对数据处理技术要求高 High requirements on data processing technology	组织 Tissue	Klasfeld et al.,2022

发展阶段 Stage	技术名称 Technical name	细胞数 Number of cell	新/优化技术 New/optimization technology	优点 Advantage	缺点 Disadvantage	细胞/组织水平Cell/ tissue level	参考文献 Reference
初期 Initial （1984— 2010）	ChIP	10⁷	新技术 New technology	有利于富集与蛋白相结合的DNA片段It’s good for enriching DNA fragments that bind to proteins	交联效果差；样本需求量大Formaldehyde crosslinking effect is poor；High demand for samples	组织 Tissue	Gilmour & Lis,1984
	ChIP-chip	10⁷	新技术 New technology	基因组微阵列技术对DNA定位Genomic microarray technique for DNA localization	试验重复性低 Low test repeatability	组织 Tissue	Bernstein et al.,2002
	ChIP-seq	10⁷	新技术 New technology	转录因子结合位点与组蛋白修饰区域定位Localization of transcription factor binding sites and histone modification regions	样本需求量大；试验重复性低；易出现假阳性 Large sample demand; Low test repeatability; Prone to false positives	组织 Tissue	Johnson et al.,2007
探索发展 Explorative （2011— 2018）	ChIP-exo	10⁶	优化：酶切 Optimization：MNase cutting	降低测序假阳性；提高单bp准确性Reduce false positive sequencing results; Improve the accuracy of single bp	样本需求量大；对技术要求高Large sample demand; High technical requirements	组织 Tissue	Rhee & Pugh,2011
	Nano- ChIP-seq	10⁴	优化：文库构建 Optimization：library construction	抑制DNA中GC含量；降低样本需求量Inhibition of GC content in DNA; Lower the quantity of samples	易出现假阳性 Prone to false positives	组织 Tissue	Adli & Bernstein,2011
	scChIP-seq	单细胞 Single cell	新技术 New technology	高度集成化；实现单细胞测序Highly integrated; Single cell sequencing was realized	成本昂贵；对技术要求高Expensive; High technical requirements	单细胞 Single cell	Rotem et al.,2015
	ChIP-nexus	10⁶	优化：文库构建 Optimization： library construction	降低文库构建的DNA需求量Reduce the DNA requirement for library construction	样本需求量大 Large sample demand	组织 Tissue	He et al.,2015
	ULI- NChIP	10³	优化：细胞分离 Optimization：cell separation	降低样本需求量；无需甲醛交联Lower the quantity of samples；No formaldehyde crosslinking required	ChIP时损失DNA影响测序准确性DNA loss during ChIP affects the accuracy of subsequent sequencing results	组织 Tissue	Brind’ Amour et al.,2015
	CUT&RUN	10² ~ 10³	新技术 New technology	富集和染色质片段化同时进行；省去ChIP；降低背景噪音Enrichment occurs simultaneously with chromatin fragmentation; Omit ChIP; Reduce background noise	易发生DNA损失 Prone to DNA loss	组织 Tissue	Skene & Henikoff,2017
快速发展 Rapid （2019—）	ULI-CUT& RUN	10 ~ 10²	优化： CUT&RUN Optimization：CUT&RUN	采用流式细胞分选实现极少数细胞测序Very few cells were sequenced by flow cytometry	易发生DNA损失 Prone to DNA loss	组织 Tissue	Hainer et al.,2019
	CUT&Tag	10²~ 10³	新技术 New technology	靶向切割产物可以直接进行文库扩增 Targeted cleavage products can be directly amplified into the library	易出现假阳性 Prone to false positives	组织 Tissue	Kaya-Okur et al.,2019
	TAF-ChIP	10²	优化：细胞分离 Optimization：cell separation	无需DNA纯化与文库构建；降低对样本需求量No DNA purification and library construction；Lower the quantity of samples	易出现假阳性 Prone to false positives	组织 Tissue	Akhtar et al.,2019
	MOW ChIP-seq	10² ~ 10⁴	优化：免疫共沉Optimization：ChIP	降低对试剂消耗；便于自动化 Reduce the consumption of reagents; Facilitate automation	对技术要求高High technical requirements	组织 Tissue	Zhu et al.,2019
快速发展 Rapid （2019—）	CoBATCH	10⁴	新技术 New technology	实现不同样本高通量单细胞测序Achieve high throughput single cell sequencing of different samples	无法直接在单细胞水平进行分析Samples cannot be analyzed directly at the single-cell level	组织 Tissue	Wang et al.,2019
	scCUT&Tag	单细胞 Single cell	优化：CUT&Tag Optimization： CUT&Tag	单细胞水平测序；高信噪比 Single-cell level sequencing; High signal-to-noise ratio	成本昂贵；对技术要求高Expensive; High technical requirements	单细胞 Single cell	Bartosovic et al.,2021
	Greenscreen	10⁷	新技术 New technology	提高样本间可重复性；消除假阳性Improve repeatability between samples; Eliminate false positives	对数据处理技术要求高 High requirements on data processing technology	组织 Tissue	Klasfeld et al.,2022

物种 Species	样品 Sample	方法 Method	应用方向 Application direction	定位基因/定位组蛋白 Localization gene/ histone	参考文献 Reference
龙眼 Dimocarpus longan	胚性愈伤组织 Embryonic callus	X-ChIP	组蛋白修饰 Histone modification	H3K4me1	Ma et al.,2022；Chen et al.,2023
葡萄Vitis vinifera L.	叶片Leaf	X-ChIP	转录因子Transcription factor	VlbZIP30	涂明星,2021
	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K4me1、H3K4me3、 H3K27ac	Schwope et al.,2021
	叶片Leaf	X-ChIP	转录因子Transcription factor	VaMYB4a	俞沁含,2022；俞沁含等,2023
柑橘Citrus reticulata	叶片Leaf	X-ChIP	转录因子Transcription factor	CsbZIP40	窦万福,2020
	叶片Leaf	X-ChIP	转录因子Transcription factor	CsLOB1	Zou et al.,2021
苹果Malus × domestica	叶片Leaf	X-ChIP	转录因子Transcription factor	MdMYB88、MdMYB124	Xie et al.,2018
	根系Root	X-ChIP	转录因子Transcription factor	MdMYB88、MdMYB124	Geng et al.,2018
	叶片Leaf	X-ChIP	转录因子Transcription factor	MdDof54	Chen et al.,2020
	叶片Leaf	X-ChIP	转录因子Transcription factor	B-BOX 7/CONSTANS-LIKE 9 (MdBBX7/MdCOL9)	Chen et al.,2022
	果实Fruit	X-ChIP	转录因子Transcription factor	MdERF4	Hu et al.,2022；Zhang et al.,2022
桃Amygdalus persica	花蕾Flower bud	X-ChIP	组蛋白修饰Histone modification	H3K4me3、H3K27me3	Canton et al.,2022
杏Prunus	花蕾Flower bud	X-ChIP	转录因子Transcription factor	PmTCP4	Iqbal et al.,2020
猕猴桃Actinidia	叶片Leaf	X-ChIP	转录因子Transcription factor	SHORT VEGETATIVE PHASE (SVP2)	Wu et al.,2018
香蕉Musa nana	果实Fruit	X-ChIP	转录因子Transcription factor	Dehydration-responsive element binding (MaDREB)	Kuang et al.,2017
梨Pyrus communis	愈伤组织Callus	X-ChIP	转录因子Transcription factor	PpDAM2、PpDAM3、 PpDAM4	杨锋,2021
沙棘 Hippophae rhamnoides	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K9ac	高国日等,2018
草莓Fragaria ananassa	果实Fruit	N-ChIP	组蛋白修饰Histone modification	H3K27me3	黄晓荣,2019
	果实Fruit	N-ChIP	组蛋白修饰Histone modification	H3K9me2、H3K27me3	林莹,2020
黄瓜Cucumis sativus	卷须Tendril	X-ChIP	转录因子Transcription factor	TCP（TEN）	许梦楠,2015
	果实Fruit	X-ChIP	组蛋白修饰Histone modification	HDAC（SF2）	张震,2019
油菜Brassica napus	种子Seed	X-ChIP	转录因子Transcription factor	SHORT HYPOCOTYL UNDER BLUE1 (SHB1)	Zhang et al.,2017
	叶、根、花芽、角果 Leaf，root，flower bud，horn fruit	X-ChIP	组蛋白修饰 Histone modification	H3K4me1、H3K27me3	Zhang et al.,2021
	叶片Leaf	eChIP	组蛋白修饰Histone modification	H3K4me1、H3K27me3	章清,2021
番茄	叶片Leaf	X-ChIP	转录因子Transcription factor	SlMYC2	Du et al.,2017
Solanum lycopersicum	果实Fruit	X-ChIP	转录因子Transcription factor	Constans-like4 (SlCOL4)	吴琼,2019
	果实Fruit	X-ChIP	转录因子Transcription factor	SNAC4-9	冯炎春,2019
	果实Fruit	X-ChIP	转录因子Transcription factor	BEL1-LIKE HOMEODOMAIN4（SlBL4）	Yan et al.,2020
	果实Fruit	X-ChIP	转录因子Transcription factor	SlGRAS4	Liu et al.,2020
	果皮Pericarp	X-ChIP	组蛋白修饰Histone modification	H3K27me3	Li et al.,2020
	花序原基 Inflorescence primordium	X-ChIP	转录因子 Transcription factor	SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)、 SISTER OF TM3 (STM3)	王晓甜,2021
	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K4me3	Liu et al.,2022
	果皮Pericarp	X-ChIP	组蛋白修饰Histone modification	H3K4me3	Ding et al.,2022
莲藕Nelumbo nucifera	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	NnCenH3	朱之轩,2015
莴苣 Lactuca sativa var. ramosa	叶片Leaf	X-ChIP	转录因子Transcription factor	LsSAW1	安光辉,2022
茄子Solanum melongena	根系Root	X-ChIP	转录因子Transcription factor	SmTCP7a	Xiao et al.,2022
甜菜Beta vulgaris	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	H3K9me2	Kowar et al.,2016
白菜Brassica rapa var. glabra	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	H3K27me3	Poza-Viejo et al.,2022
桂花Osmanthus fragrans	花瓣Petal	X-ChIP	转录因子Transcription factor	COfCCD1、OfCCD4	Han et al.,2022
矮牵牛Pharbitis nil	花冠Corolla	X-ChIP	转录因子Transcription factor	ODORANT 1 (ODO1)	Boersma et al.,2022

物种 Species	样品 Sample	方法 Method	应用方向 Application direction	定位基因/定位组蛋白 Localization gene/ histone	参考文献 Reference
龙眼 Dimocarpus longan	胚性愈伤组织 Embryonic callus	X-ChIP	组蛋白修饰 Histone modification	H3K4me1	Ma et al.,2022；Chen et al.,2023
葡萄Vitis vinifera L.	叶片Leaf	X-ChIP	转录因子Transcription factor	VlbZIP30	涂明星,2021
	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K4me1、H3K4me3、 H3K27ac	Schwope et al.,2021
	叶片Leaf	X-ChIP	转录因子Transcription factor	VaMYB4a	俞沁含,2022；俞沁含等,2023
柑橘Citrus reticulata	叶片Leaf	X-ChIP	转录因子Transcription factor	CsbZIP40	窦万福,2020
	叶片Leaf	X-ChIP	转录因子Transcription factor	CsLOB1	Zou et al.,2021
苹果Malus × domestica	叶片Leaf	X-ChIP	转录因子Transcription factor	MdMYB88、MdMYB124	Xie et al.,2018
	根系Root	X-ChIP	转录因子Transcription factor	MdMYB88、MdMYB124	Geng et al.,2018
	叶片Leaf	X-ChIP	转录因子Transcription factor	MdDof54	Chen et al.,2020
	叶片Leaf	X-ChIP	转录因子Transcription factor	B-BOX 7/CONSTANS-LIKE 9 (MdBBX7/MdCOL9)	Chen et al.,2022
	果实Fruit	X-ChIP	转录因子Transcription factor	MdERF4	Hu et al.,2022；Zhang et al.,2022
桃Amygdalus persica	花蕾Flower bud	X-ChIP	组蛋白修饰Histone modification	H3K4me3、H3K27me3	Canton et al.,2022
杏Prunus	花蕾Flower bud	X-ChIP	转录因子Transcription factor	PmTCP4	Iqbal et al.,2020
猕猴桃Actinidia	叶片Leaf	X-ChIP	转录因子Transcription factor	SHORT VEGETATIVE PHASE (SVP2)	Wu et al.,2018
香蕉Musa nana	果实Fruit	X-ChIP	转录因子Transcription factor	Dehydration-responsive element binding (MaDREB)	Kuang et al.,2017
梨Pyrus communis	愈伤组织Callus	X-ChIP	转录因子Transcription factor	PpDAM2、PpDAM3、 PpDAM4	杨锋,2021
沙棘 Hippophae rhamnoides	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K9ac	高国日等,2018
草莓Fragaria ananassa	果实Fruit	N-ChIP	组蛋白修饰Histone modification	H3K27me3	黄晓荣,2019
	果实Fruit	N-ChIP	组蛋白修饰Histone modification	H3K9me2、H3K27me3	林莹,2020
黄瓜Cucumis sativus	卷须Tendril	X-ChIP	转录因子Transcription factor	TCP（TEN）	许梦楠,2015
	果实Fruit	X-ChIP	组蛋白修饰Histone modification	HDAC（SF2）	张震,2019
油菜Brassica napus	种子Seed	X-ChIP	转录因子Transcription factor	SHORT HYPOCOTYL UNDER BLUE1 (SHB1)	Zhang et al.,2017
	叶、根、花芽、角果 Leaf，root，flower bud，horn fruit	X-ChIP	组蛋白修饰 Histone modification	H3K4me1、H3K27me3	Zhang et al.,2021
	叶片Leaf	eChIP	组蛋白修饰Histone modification	H3K4me1、H3K27me3	章清,2021
番茄	叶片Leaf	X-ChIP	转录因子Transcription factor	SlMYC2	Du et al.,2017
Solanum lycopersicum	果实Fruit	X-ChIP	转录因子Transcription factor	Constans-like4 (SlCOL4)	吴琼,2019
	果实Fruit	X-ChIP	转录因子Transcription factor	SNAC4-9	冯炎春,2019
	果实Fruit	X-ChIP	转录因子Transcription factor	BEL1-LIKE HOMEODOMAIN4（SlBL4）	Yan et al.,2020
	果实Fruit	X-ChIP	转录因子Transcription factor	SlGRAS4	Liu et al.,2020
	果皮Pericarp	X-ChIP	组蛋白修饰Histone modification	H3K27me3	Li et al.,2020
	花序原基 Inflorescence primordium	X-ChIP	转录因子 Transcription factor	SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)、 SISTER OF TM3 (STM3)	王晓甜,2021
	叶片Leaf	X-ChIP	组蛋白修饰Histone modification	H3K4me3	Liu et al.,2022
	果皮Pericarp	X-ChIP	组蛋白修饰Histone modification	H3K4me3	Ding et al.,2022
莲藕Nelumbo nucifera	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	NnCenH3	朱之轩,2015
莴苣 Lactuca sativa var. ramosa	叶片Leaf	X-ChIP	转录因子Transcription factor	LsSAW1	安光辉,2022
茄子Solanum melongena	根系Root	X-ChIP	转录因子Transcription factor	SmTCP7a	Xiao et al.,2022
甜菜Beta vulgaris	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	H3K9me2	Kowar et al.,2016
白菜Brassica rapa var. glabra	叶片Leaf	N-ChIP	组蛋白修饰Histone modification	H3K27me3	Poza-Viejo et al.,2022
桂花Osmanthus fragrans	花瓣Petal	X-ChIP	转录因子Transcription factor	COfCCD1、OfCCD4	Han et al.,2022
矮牵牛Pharbitis nil	花冠Corolla	X-ChIP	转录因子Transcription factor	ODORANT 1 (ODO1)	Boersma et al.,2022

Advances in Chromatin Immunoprecipitation Sequencing and Its Application in Horticultural Plants

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