Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin

doi:10.1093/hmg/ddv172

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	Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin
	Yang, Xiaofei 1; Shao, Xiaojian 2; Gao, Lin 1; Zhang, Shihua3
	2015-08-01
发表期刊	HUMAN MOLECULAR GENETICS
ISSN	0964-6906
卷号	24 期号:15 页码:4374-4384
摘要	DNA methylation is a key functional regulatory mechanism in human genome, which plays critical roles in development, differentiation and many diseases. With rapid progress of large-scale projects (e.g. ENCODE), many DNA methylation data across diverse cell lines have been produced. However, common methylation patterns, cell lineage-and cell line-specific DNA methylation patterns across multiple cell lines have not yet been explored completely. Using the DNA methylation data across 54 human cell lines, we identified 35 276 local DNA methylation regions called local clusters of CpG sites (LCCSs). We constructed an LCCS co-methylation network and investigated the common DNA methylation patterns across all cell lines, which reveal two distinct groups in terms of their methylation level and genomic characteristics. We further detected diverse sets of cell lineage-specific high-and low-methylation patterns, which were depleted in promoter, CpG island (CGI) and repeat regions but enriched in gene body and non-CGI regions, especially the CGI shore regions. We discovered that the cell lineage-specific low-methylated LCCSs were enriched with functional transcriptional factor binding motif regions. Moreover, the detected cell line-specific high-and low-methylated patterns show distinct enrichments in cell line-specific chromatin states and functional relevance with the corresponding cell lines.
DOI	10.1093/hmg/ddv172
语种	英语
资助项目	National Natural Science Foundation of China[61379092] ; National Natural Science Foundation of China[61422309] ; National Natural Science Foundation of China[61432010] ; National Natural Science Foundation of China[61303118] ; National Natural Science Foundation of China[31201002] ; Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040600] ; Outstanding Young Scientist Program of CAS ; Key Laboratory of Random Complex Structures and Data Science at CAS ; Fundamental Research Funds for the Central Universities[BDZ021404]
WOS研究方向	Biochemistry & Molecular Biology ; Genetics & Heredity
WOS类目	Biochemistry & Molecular Biology ; Genetics & Heredity
WOS记录号	WOS:000361314100017
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/20798
专题	应用数学研究所
通讯作者	Gao, Lin
作者单位	1.Xidian Univ, Sch Comp Sci & Technol, Xian 710071, Shaanxi, Peoples R China 2.Binzhou Univ, Dept Math, Binzhou 256603, Shandong, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Yang, Xiaofei,Shao, Xiaojian,Gao, Lin,et al. Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin[J]. HUMAN MOLECULAR GENETICS,2015,24(15):4374-4384.
APA	Yang, Xiaofei,Shao, Xiaojian,Gao, Lin,&Zhang, Shihua.(2015).Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin.HUMAN MOLECULAR GENETICS,24(15),4374-4384.
MLA	Yang, Xiaofei,et al."Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin".HUMAN MOLECULAR GENETICS 24.15(2015):4374-4384.