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Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin
Yang, Xiaofei1; Shao, Xiaojian2; Gao, Lin1; Zhang, Shihua3
2015-08-01
Source PublicationHUMAN MOLECULAR GENETICS
ISSN0964-6906
Volume24Issue:15Pages:4374-4384
AbstractDNA 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.
DOI10.1093/hmg/ddv172
Language英语
Funding ProjectNational 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 Research AreaBiochemistry & Molecular Biology ; Genetics & Heredity
WOS SubjectBiochemistry & Molecular Biology ; Genetics & Heredity
WOS IDWOS:000361314100017
PublisherOXFORD UNIV PRESS
Citation statistics
Cited Times:23[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/20798
Collection应用数学研究所
Affiliation1.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
Recommended Citation
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.
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