植物三维染色质构型研究进展

doi:10.16288/j.yczz.19-326

遗传 ›› 2020, Vol. 42 ›› Issue (1): 73-86.doi: 10.16288/j.yczz.19-326

植物三维染色质构型研究进展

董芊里, 王金宾, 李晓宠, 宫磊()

东北师范大学生命科学学院,分子表观遗传学教育部重点实验室,长春 130024

收稿日期:2019-10-29 修回日期:2019-12-19 出版日期:2020-01-20 发布日期:2019-12-27
通讯作者: 宫磊 E-mail:gongl100@nenu.edu.cn
作者简介:董芊里,博士研究生,专业方向：遗传学。E-mail: dongql043@nenu.edu.cn|王金宾,博士研究生,专业方向：遗传学。E-mail: wangjb702@nenu.edu.cn|李晓宠,博士研究生,专业方向：遗传学。E-mail:lixc800@nenu.edu.cn; 董芊里、王金宾和李晓宠并列第一作者
基金资助:
国家重点研发计划项目编号(2016YFD0101004);国家自然科学基金项目编号(31670220);2015“长白山学者计划”特聘教授专项资助

Progresses in the plant 3D chromatin architecture

Qianli Dong, Jinbin Wang, Xiaochong Li, Lei Gong()

Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China

Received:2019-10-29 Revised:2019-12-19 Online:2020-01-20 Published:2019-12-27
Contact: Gong Lei E-mail:gongl100@nenu.edu.cn
Supported by:
Supported by the National Key Research and Development Program of China No(2016YFD0101004);the National Natural Science Foundation of China No(31670220);the Program of Changbai Mountain Scholar

摘要/Abstract

摘要：

染色质在细胞核内的缠绕、折叠及其在细胞核内的空间排布是真核生物染色质构型的主要特征。在经典DNA探针荧光原位杂交显微观察的基础上,基于新一代测序技术的Hi-C及ChIA-PET染色质构型捕获技术已经被广泛应用于动物及植物细胞核染色质构型的研究中,并以新的角度定义了包括：染色体(质)域(chromosome territory)、A/B染色质区室(compartment A/B)、拓扑偶联结构域(topological associated domains, TADs)、染色质环(chromatin loops)等在内的多个更为精细的染色质构型。利用以上两种主流技术,越来越多的植物物种染色质构型特征被鉴定、分析和比较。本文系统分析和总结了近年来以植物细胞为模型的细胞核染色构型领域取得的重要成果,包括各级染色质构型特征的组成、建立机制和主要影响因素等。在此基础上,分析了目前研究植物染色质构型技术的瓶颈和突破性的技术进展,并对后续研究主要关注的问题和研究内容进行了展望,以期为相关领域的研究提供更多的理论参考和依据。

关键词: 染色质构型, 高通量染色质构象捕获测序, 末端配对标签测序, 染色质区室, 拓扑偶联结构域

Abstract:

Chromatin architecture involves the patterns of chromatin coiling and packing as well as the mutual relative allocations of different chromatins. Besides the canonical microscopic observations, the chromatin architectural capture techniques, including the Hi-C and ChIA-PET, have been widely applied in characterization of chromatin architecture in various plant and animal model species, in which chromatin architectural features, such as the chromosome territory, compartment A/B, topological associated domains (TADs) and chromatin loops, were defined. As for the studies in plant species, replying on the two techniques above (with differences in experimental techniques and data structures), scientists have compared the variation of specific chromatin architecture features across species and/or in different cell types of the same plant species, besides detailed analyses in each individual model. Here, we mainly review the recent progresses in studies of plant chromatin architectures, in which their composition, establishing mechanism and effective factors were described and discussed. We also propose the main technical bottlenecks, describe the breaking-through progresses, and anticipate future research directions, which may offer more theoretical references for related researches in the field.

Key words: chromatin architecture, high-throughput chromosome conformation capture (Hi-C), chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), compartment A/B, topological associated domains (TAD)

董芊里, 王金宾, 李晓宠, 宫磊. 植物三维染色质构型研究进展[J]. 遗传, 2020, 42(1): 73-86.

Qianli Dong, Jinbin Wang, Xiaochong Li, Lei Gong. Progresses in the plant 3D chromatin architecture[J]. Hereditas(Beijing), 2020, 42(1): 73-86.

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技术	互作方式	覆盖范围	检测方法	技术优势	技术局限	研究应用
Hi-C	全部互作 (all vs. all)	全基因组范围	新一代测序技术	可以获得较高分辨率的互作矩阵	需大量细胞进行建库,以产出较高分辨率Hi-C矩阵。基于由此得到的高分辨率Hi-C矩阵,所反映的染色体(质)特征为大量组织样本中大量细胞的平均值;使用限制性内切酶对染色体进行剪切时,可能会由于酶的剪切偏好性,对互作结果产生一定程度的影响	可产出较高分辨率互作矩阵,用以分析目前已知的各级染色体(质)构型(compartment、TAD、chromatin loop等);Hi-C技术亦可用于辅助基因组拼接
scHi-C	全部互作 (all vs. all)			可以获得单个细胞的互作热图,观察单个细胞内的染色体(质)特征	单个细胞中DNA含量较少,无法绘制较高分辨率的Hi-C热图,所以无法分析需要较高分辨率下可以分析的TAD结构或chromatin loop结构;使用限制性内切酶对染色体进行剪切时,可能会由于酶的剪切偏好性,对互作结果产生一定程度的影响。	可研究单个细胞内的染色体(质)构型,可以更精准的阐述染色体(质)构型特征
ChIA-PET	特定蛋白介导的全部互作(many vs. all)			可以构建已知转录因子介导的染色体(质)互作网络;由于使用超声的方法进行机械破碎,不会由于限制性内切酶的剪切偏好性对互作结果产生影响;具有更高的分辨率(100 bp水平)^[15]	由于ChIA-PET实验优先使用特异性的蛋白抗体,其选择性捕获与目标蛋白交联在一起的DNA片段,可能会忽略其他的互作	主要包含靶蛋白结合位点和由靶蛋白介导的结合位点之间的染色质相互作用信息

物种	技术	染色体 (质)域	A/B染色质区室	拓扑偶联结构域	染色质环	IHIs/KEEs	参考文献
深山南芥 (Arabidopsis lyrata)	Hi-C					√	[17]
拟南芥 (Arabidopsis thaliana)	Hi-C	√	√			√	[18]
	Hi-C	√	√			√	[19]
	Hi-C	√	√	√	√		[20]
四倍体拟南芥 (Arabidopsis thaliana (4×Columbia))	Hi-C	√	√			√	[21]
甘蓝 (Brassica oleracea)	Hi-C	√	√	√		√	[22]
芜菁 (Brassica rapa)	Hi-C	√	√	√		√	[22]
树棉 (Gossypium arboreum)	Hi-C	√	√	√			[23]
海岛棉 (Gossypium barbadense)	Hi-C	√	√	√			[23]
陆地棉 (Gossypium hirsutum)	Hi-C			√			[24]
雷蒙德氏棉 (Gossypium raimondii)	Hi-C	√	√	√			[23]
大麦 (Hordeum vulgare)	Hi-C		√				[25]
水稻明恢63 (Oryza Sativa L. spp. indica (Minghui63))	Hi-C		√	√	√		[26]
水稻日本晴 (Oryza sativa L. spp. Japonica)	Hi-C	√	√	√	√	√	[27]
	Hi-C	√	√	√	√		[28]
	scHi-C	√	√				[29]
	ChIA-PET	√	√		√		[15]
粟 (Setaria italic)	Hi-C	√	√	√	√		[28]
番茄 (Solanum lycopersicum)	Hi-C	√	√	√	√		[28]
高粱 (Sorghum bicolor)	Hi-C	√	√	√	√		[28]
玉米 (Zea mays)	Hi-C	√	√	√	√		[28]
玉米 (Zea mays)	ChIA-PET				√		[30]

植物三维染色质构型研究进展

Progresses in the plant 3D chromatin architecture

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