染色质转座酶可及性测序及其在木本植物中的应用前景

doi:10.12302/j.issn.1000-2006.202205024

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南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (5): 1-10.doi: 10.12302/j.issn.1000-2006.202205024

染色质转座酶可及性测序及其在木本植物中的应用前景

王子玥(), 甄艳(), 刘光欣, 席梦利()

南京林业大学,南方现代林业协同创新中心,林木遗传与生物技术省部共建教育部重点实验室,江苏南京 210037

收稿日期:2022-05-16 修回日期:2022-06-24 出版日期:2022-09-30 发布日期:2022-10-19
通讯作者: 席梦利
基金资助:
国家自然科学基金项目(31670603)

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

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)是2013年在人类免疫细胞中建立的用于研究表观遗传调控的重要技术。该技术已在人类及小鼠等模式动物的基因组调控元件鉴定、转录因子结合位点识别及转录调控机制的解析等研究领域发挥了重要作用。然而,ATAC-seq技术在植物领域中的研究应用还处于起步阶段,相关研究主要集中在拟南芥和水稻等模式植物中。笔者主要概述了ATAC-seq技术在植物中的应用,包括染色质可及性图谱绘制、抗逆机制解析、表观修饰鉴定及调控元件识别等领域的研究进展,并进一步阐述了ATAC-seq在木本植物中的应用潜力,以推动ATAC-seq技术在木本植物表观基因组学研究中的应用。

关键词: 染色质转座酶可及性测序, 木本植物, 染色质可及性, 表观基因组学

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

中图分类号:

S722
Q756

王子玥,甄艳,刘光欣,等. 染色质转座酶可及性测序及其在木本植物中的应用前景[J]. 南京林业大学学报（自然科学版）, 2022, 46(5): 1-10.

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 (Natural Science Edition), 2022, 46(5): 1-10.DOI: 10.12302/j.issn.1000-2006.202205024.

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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]

染色质转座酶可及性测序及其在木本植物中的应用前景

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

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