Assay for transposase-accessible chromatin with high-throughput sequencing and its application prospect in woody plants

doi:10.12302/j.issn.1000-2006.202205024

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (5): 1-10.doi: 10.12302/j.issn.1000-2006.202205024

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Assay for transposase-accessible chromatin with high-throughput sequencing and its application prospect in woody plants

WANG Ziyue(), ZHEN Yan(), LIU Guangxin, XI Mengli()

Co-Innovation Center for Sustainable Forestry in Southern China,Key Laboratory of Forest Genetics and Biotechnique of Ministry of Education,Nanjing Forestry University,Nanjing 210037,China

Received:2022-05-16 Revised:2022-06-24 Online:2022-09-30 Published:2022-10-19
Contact: XI Mengli E-mail:y20wzy@163.com;zhenyanniso@aliyun.com;ximenglinjfu@126.com

Abstract

Abstract:

Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) is an important technique established in 2013 in human immune cells to study epigenetic regulation. This technique has been used in the identification of genomic regulatory elements, binding sites of transcription factors and analysis of transcriptional regulation mechanism in human and mouse model animals. However, the application of ATAC-seq technique in plants is still in its infancy, and related studies mainly focus on model plants such as Arabidopsis and rice. In this review, we discuss the application of ATAC-seq in plants, including chromatin accessibility sites mapping, stress resistance mechanisms revealing, epigenetic modification and regulatory elements identification. Furthermore, we look at the prospects of applying ATAC-seq in woody plant epigenomics so as to promote its application in woody plant epigenomics research.

Key words: assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq), woody plants, chromatin accessibility, epigenomic

CLC Number:

S722
Q756

WANG Ziyue, ZHEN Yan, LIU Guangxin, XI Mengli. Assay for transposase-accessible chromatin with high-throughput sequencing and its application prospect in woody plants[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2022, 46(5): 1-10.

Figures/Tables 4

Table 1

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Table 2

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方法 method	细胞类型 type of cells	所需细胞数量/万个 number of input cells required	所需时间/d required time	获取原理 principle	特点 specific features
DNase-seq	任何细胞	100~1 000	1~3	使用限制性内切酶(DNase Ⅰ)对样品进行片段化处理,切割不受蛋白保护的染色质区域	1)需要大量细胞作为实验材料 2)可在全基因组范围内检测蛋白质结合位点 3)制备样品过程复杂
FAIRE-seq	任何细胞	100~1 000	2~3	使用超声波打断DNA序列,随后酚-氯仿富集	1)需要大量细胞作为实验材料 2)背景信号高,数据分析困难 3)甲醛交联程度难以确定
ATAC-seq	新鲜分离的细胞或缓慢冷却的冷冻细胞	0.05~5.00	<1	使用Tn5转座酶,完整地获取整个开放染色质区域	1)细胞需求量少 2)操作简便、效率高 3)线粒体和叶绿体对实验结果有影响 4)后续数据分析有局限性
MNase-seq	任何细胞	1~10	2	使用限制性外切酶(微球菌核酸酶),对DNA进行切割,可绘制核小体图谱	1)需要大量细胞作为实验材料 2)可获得单个核小体的DNA 3)酶用量和酶解时间难以确定 4)MNase存在对A/T碱基序列的切割倾向性
NOMe-seq	任何细胞	100	1~2	使用GpC甲基转移酶对DNA进行化学修饰来检测染色质可及性	1)需要大量细胞作为实验材料 2)可同时进行核小体定位和CpG 甲基化分析 3)需要大量的测序读数

方法 method	原理 principle	优点 advantage	植物物种应用 applied species	发表年份 published year
Crude-ATAC-seq	裂解细胞器及蔗糖沉淀获取细胞核	适用于大多数植物, 无须进行转基因操作	拟南芥 (Arabidopsis thaliana)	2017^[23]
INTACT-ATAC-seq	从标记的特定细胞类型中提取细胞核	降低了细胞器 DNA的污染	苜蓿(Medicago sativa)、番茄(Solanun lycopersicum)、水稻(Oryza sativa) 和拟南芥	2017^[23]、2018^[24]
FANS-ATAC-seq	利用流式细胞仪对细胞核进行分选	降低了细胞器 DNA的污染
FANS-ATAC-seq	利用流式细胞仪对细胞核进行分选	拟南芥	2016^[21]

Assay for transposase-accessible chromatin with high-throughput sequencing and its application prospect in woody plants

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[1]	YANG Jiading, LIU Yujie, FENG Jianyuan, ZHANG Yuanlan. Nitrogen resorption machanism during leaf senescence in woody plants [J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2023, 47(5): 1-8.
[2]	HOU Jing, MAO Jinyan, ZHAI Hui, WANG Jie, YIN Tongming. Application of CRISPR/Cas technique in woody plant improvement [J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2021, 45(6): 24-30.
[3]	LI Dong, HUANG Li-li, HAN Su-fen*. 16S rDNA Sequence Analysis of 23 Rhizobium Strains Isolated from Leguminosae Woody Plants [J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2007, 31(06): 117-120.
[4]	PENG Fang-ren1, GUO Hong-yan1, YANG Yu-zhen1,2, GUO Yan-qing1. Progresses of Research on Ammonium Assimilation in Woody Plants [J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2006, 30(06): 117-122.
[5]	GUO Hong-yan, GUO Yan-qing, PENG Fang-ren*. The Research Progresses on the Mechanism of Metabolization of Vegetative Storage Protein in Woody Plants [J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2006, 30(04): 123-128.