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MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps
Ye, Yusen1; Gao, Lin1; Zhang, Shihua2,3,4
2019-06-20
Source PublicationNUCLEIC ACIDS RESEARCH
ISSN0305-1048
Volume47Issue:11Pages:11
AbstractThe 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.
DOI10.1093/nar/gkz201
Language英语
Funding ProjectNational 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 Research AreaBiochemistry & Molecular Biology
WOS SubjectBiochemistry & Molecular Biology
WOS IDWOS:000475702000005
PublisherOXFORD UNIV PRESS
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Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/35299
Collection应用数学研究所
Corresponding AuthorGao, Lin; Zhang, Shihua
Affiliation1.Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Shaanxi, Peoples R China
2.Chinese Acad Sci, Acad Math & Syst Sci, NCMIS, CEMS,RCSDS, Beijing 100190, Peoples R China
3.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
4.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
Recommended Citation
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.
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