MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps
文献类型：期刊论文
| 作者 | Ye, Yusen3; Gao, Lin3; Zhang, Shihua1,2,4
|
| 刊名 | NUCLEIC ACIDS RESEARCH
 |
| 出版日期 | 2019-06-20 |
| 卷号 | 47期号:11页码:11 |
| ISSN号 | 0305-1048 |
| DOI | 10.1093/nar/gkz201 |
| 英文摘要 | The chromosome conformation capture (3C) technique and its variants have been employed to reveal the existence of a hierarchy of structures in three-dimensional (3D) chromosomal architecture, including compartments, topologically associating domains (TADs), sub-TADs and chromatin loops. However, existing methods for domain detection were only designed based on symmetric Hi-C maps, ignoring long-range interaction structures between domains. To this end, we proposed a generic and efficient method to identify multi-scale topological domains (MSTD), including cis-and trans-interacting regions, from a variety of 3D genomic datasets. We first applied MSTD to detect promoter-anchored interaction domains (PADs) from promoter capture Hi-C datasets across 17 primary blood cell types. The boundaries of PADs are significantly enriched with one or the combination of multiple epigenetic factors. Moreover, PADs between functionally similar cell types are significantly conserved in terms of domain regions and expression states. Cell type-specific PADs involve in distinct cell type-specific activities and regulatory events by dynamic interactions within them. We also employed MSTD to define multi-scale domains from typical symmetric Hi-C datasets and illustrated its distinct superiority to the-state-of-art methods in terms of accuracy, flexibility and efficiency. |
| 资助项目 | National Natural Science Foundation of China[61873198] ; National Natural Science Foundation of China[61532014] ; National Natural Science Foundation of China[61432010] ; National Natural Science Foundation of China[61672407] ; National Natural Science Foundation of China[11661141019] ; National Natural Science Foundation of China[61621003] ; National Natural Science Foundation of China[61422309] ; National Natural Science Foundation of China[61379092] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040600] ; Key Research Program of the Chinese Academy of Sciences[KFZD-SW-219] ; National Key Research and Development Program of China[2017YFC0908405] ; CAS Frontier Science Research Key Project for Top Young Scientist[QYZDB-SSW-SYS008] |
| WOS研究方向 | Biochemistry & Molecular Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:000475702000005 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/35298]  |
| 专题 | 应用数学研究所 |
| 通讯作者 | Gao, Lin; Zhang, Shihua |
| 作者单位 | 1.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China 2.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China 3.Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Shaanxi, Peoples R China 4.Chinese Acad Sci, Acad Math & Syst Sci, NCMIS, CEMS,RCSDS, Beijing 100190, Peoples R China |
| 推荐引用方式 GB/T 7714 | Ye, Yusen,Gao, Lin,Zhang, Shihua. MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps[J]. NUCLEIC ACIDS RESEARCH,2019,47(11):11. |
| APA | Ye, Yusen,Gao, Lin,&Zhang, Shihua.(2019).MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps.NUCLEIC ACIDS RESEARCH,47(11),11. |
| MLA | Ye, Yusen,et al."MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps".NUCLEIC ACIDS RESEARCH 47.11(2019):11. |
入库方式： OAI收割
来源：数学与系统科学研究院
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。