MNase-seq与核小体定占位研究

doi:10.16288/j.yczz.20-178

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Hereditas(Beijing) ›› 2020, Vol. 42 ›› Issue (12): 1143-1155.doi: 10.16288/j.yczz.20-178

• Review • Previous Articles Next Articles

Resolving nucleosomal positioning and occupancy with MNase-seq

Weihang Deng, Xinhui Li()

Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China

Received:2020-09-04 Revised:2020-10-18 Online:2020-12-17 Published:2020-11-03
Contact: Li Xinhui E-mail:xhli@sjtu.edu.cn
Supported by:
Supported by the National Natural Science Foundation of China No(81972909)

Abstract

Abstract:

Nucleosomes are the basic unit of the three-dimensional structure of chromatin. It is now widely accepted that the positioning and occupancy of nucleosomes play important roles in fundamental genomic processes such as DNA transcription, replication and repair. Among the methods used to provide genome-wide nucleosomal positions and occupancy levels, MNase-seq has proven to be highly effective. Indeed, with this method, the nucleosomal landscapes of a variety of organisms have now been investigated, revealing both commonalities and differences. In this review, we first introduce the technical principles underlying MNase-seq, focusing on details essential to precisely resolve nucleosome positioning and occupancy. We then describe recent advances with this method, as well as future perspectives of its role in chromatin biology, with a particular focus of uncovering mechanistic insights of many disease process.

Key words: nucleosome, chromatin structure, chromatin remodeling, next-generation sequencing (NGS), micrococcal nuclease

Weihang Deng, Xinhui Li. Resolving nucleosomal positioning and occupancy with MNase-seq[J]. Hereditas(Beijing), 2020, 42(12): 1143-1155.

Figures/Tables 3

Fig. 1

Table 1

Fig. 2

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技术名称	测序类型	实验流程	优势	缺陷	参考文献
MNase-seq	双端或单端测序	1. 对染色质进行MNase酶切 2. 文库构建 3. 凝胶电泳筛选单核小体长度片段	1. 可以对全基因组范围内核小体进行测量 2. 技术难度较小 3. 酶切特性使其具有较高分辨率	1. 传统方法需要大量细胞 2. 无法分辨核小体与其他DNA-蛋白质复合物 3. 容易造成技术误差	[7,22~25]
ChIP-seq	双端或单端测序	1. 甲醛交联 2. 超声将染色质片段化 3. 利用特异性抗体沉淀特定蛋白质	1. 方法较成熟,适用范围广泛 2. 技术难度较低 3. 针对特定的蛋白靶点, 特异性较高	1. 分辨率较低 2. 数据质量依赖抗体质量,筛选抗体费时费力 3. 成本较高	[11,26,27]
ATAC-seq	双端测序	1. 利用Tn5转座酶将开放染色质区域的DNA片段化并加上接头 2. 文库构建并上机测序	1. 灵敏性高,低细胞起始量 2. 方法简单,耗时短 3. 分辨率较高 4. 重复性较好	1. Tn5酶价格昂贵 2. 常规数据分析方法不可用或存在限制	[28~30]
DNase-seq	双端或单端测序	1. 利用DNaseⅠ切割开放染色质区域 2. 连接接头、片段筛选	1. 分辨率较高 2. 实验方法较简单	1. 样品准备复杂,实验流程耗时 2. 需要大量细胞 3. 需精确控制酶量	[31,32]
NoMe-seq	双端测序	1. 利用GpC甲基转移酶处理固定的染色质 2. DNA片段的重亚硫酸盐转化 3. 文库构建并上机测序	可对同一样品同时进行核小体定位及DNA甲基化程度的分析	1. 需要大量细胞 2. 数据分析存在挑战	[33,34]

Resolving nucleosomal positioning and occupancy with MNase-seq

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