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
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:
WANG Ziyue(), ZHEN Yan(), LIU Guangxin, XI Mengli()
Received:
2022-05-16
Revised:
2022-06-24
Online:
2022-09-30
Published:
2022-10-19
Contact:
XI Mengli
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。
中图分类号:
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.
表1
5种研究染色质可及性方法的比较"
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 |
表2
3种纯化细胞核方法的比较"
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[ |
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[ |
FANS-ATAC-seq | 利用流式细胞仪对 细胞核进行分选 | |||
拟南芥 | 2016[ |
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