遗传 ›› 2019, Vol. 41 ›› Issue (3): 254-261.doi: 10.16288/j.yczz.18-296

• 研究报告 • 上一篇    下一篇

Alu元件在染色质三维结构层次上的生物信息学分析

何超1,2,沈文龙2,李平2,张彦2,曾晶1,殷作明1(),赵志虎2()   

  1. 1. 西藏军区总医院,拉萨 850000
    2.军事科学院军事医学研究院生物工程研究所,北京 100071
  • 收稿日期:2018-10-30 修回日期:2019-01-01 出版日期:2019-01-14 发布日期:2019-01-14
  • 通讯作者: 殷作明,赵志虎 E-mail:yinzuoming@163.com;zhaozh@bmi.ac.cn
  • 作者简介:何超,硕士,工程师,研究方向：生物信息学。E-mail: hechao2010@tsinghua.org.cn
  • 基金资助:
    国家自然科学基金项目资助(31370762);国家自然科学基金项目资助(31030026);国家自然科学基金项目资助(31272416);国家自然科学基金项目资助(81372218)

Bioinformatics analysis of Alu components at the level of genome 3D structure

Chao He1,2,Wenlong Shen2,Ping Li2,Yan Zhang2,Jing Zeng1,Zuoming Yin1(),Zhihu Zhao2()   

  1. 1.General Hospital of Tibet Military Region, Lhasa 850000, China
    2.Beijing Institute of Biotechnology, Beijing 100071, China
  • Received:2018-10-30 Revised:2019-01-01 Online:2019-01-14 Published:2019-01-14
  • Contact: Yin Zuoming,Zhao Zhihu E-mail:yinzuoming@163.com;zhaozh@bmi.ac.cn
  • Supported by:
    Supported by the National Natural Science Foundation of China(31370762);Supported by the National Natural Science Foundation of China(31030026);Supported by the National Natural Science Foundation of China(31272416);Supported by the National Natural Science Foundation of China(81372218)

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摘要：

染色质在细胞核内三维高级结构包括最底层的核小体、核小体组成的“串珠”结构、螺线管纤维结构、染色质/DNA环结构(chromatin/DNA loop)、拓扑结构域(topologically associated domain, TAD)等多层次结构。其中,TAD因在不同的细胞类型中相对稳定且保守,被认为是染色质三维结构的基本单元。Alu元件是一种哺乳动物基因组中占据了较大比例的短散在重复元件,其广泛存在且种类繁多,目前关于Alu元件功能上的研究尚不透彻。本研究对Alu元件与染色质三维结构的关系进行研究,分析了Alu元件在染色质三维结构形成中的作用,并通过染色质三维结构上的距离关系对Alu元件子族的演化流程进行了探索。结果发现,Alu元件参与的染色质间相互作用在高强度的染色质相互作用中的比例随着强度增加而逐渐增高,表明Alu在染色质三维结构构建的过程中发挥了重要的作用。同时,研究还发现Alu元件在染色质上相互作用的强度与进化上的关系存在着一定的正相关性,表现在一维序列进化距离上比较接近的Alu元件在染色质的三维结构上也会彼此相互靠近。

关键词: 染色质三维结构, Alu元件, 生物信息, 进化树

Abstract:

The interphase chromatin is folded in the nucleus in a hierarchical manner, including the nucleosome, the "beads on a string" structure composed of nucleosomes, the solenoid fiber structure, the chromatin/DNA loop structure (chromatin/DNA loop), and the topologically associated domain (TAD). Among them, TAD is considered to be the basic unit of the 3D structure of chromatin because it is relatively stable and conserved in different cell types. Alu elements occupy a large proportion in the mammalian genomes. There are a wide variety of Alu elements, but their functional characterizations are limited to date. This study investigates the role of Alu elements in the assembly of 3D chromatin conformation. The evolutionary process of the Alu subfamily was explored by the distance relationship of the 3D structure of chromatin. We found that the proportion of Alu elements in high-density chromatin interaction increased with higher similarity, indicating that Alu plays an important role in the construction of chromatin 3D structure. There is a certain positive correlation between the strength of the upper interaction and the evolutionary relationship. In sum, the Alu elements with relatively close distances in the 1D sequence will also be close to each other in the 3D structure of chromatin.

Key words: genome 3D structure, Alu component, bioinformatics, evolutionary tree