The DNA methylome of human peripheral blood mononuclear cells

Li, Yingrui, Zhu, Jingde, Tian, Geng, Li, Ning, Li, Qibin, Ye, Mingzhi, Zheng, Hancheng, Yu, Jian, Wu, Honglong, Sun, Jihua, Zhang, Hongyu, Chen, Quan, Luo, Ruibang, Chen, Minfeng, He, Yinghua, Jin, Xin, Zhang, Qinghui, Yu, Chang, Zhou, Guangyu, Sun, Jinfeng, Huang, Yebo, Zheng, Huisong, Cao, Hongzhi, Zhou, Xiaoyu, Guo, Shicheng, Hu, Xueda, Li, Xin, Kristiansen, Karsten, Bolund, Lars, Xu, Jiujin, Wang, Wen, Yang, Huanming, Wang, Jian, Li, Ruiqiang, Beck, Stephan, Wang, Jun and Zhang, Xiuqing (2010) The DNA methylome of human peripheral blood mononuclear cells. PLoS Biology, 8 11: . doi:10.1371/journal.pbio.1000533


Author Li, Yingrui
Zhu, Jingde
Tian, Geng
Li, Ning
Li, Qibin
Ye, Mingzhi
Zheng, Hancheng
Yu, Jian
Wu, Honglong
Sun, Jihua
Zhang, Hongyu
Chen, Quan
Luo, Ruibang
Chen, Minfeng
He, Yinghua
Jin, Xin
Zhang, Qinghui
Yu, Chang
Zhou, Guangyu
Sun, Jinfeng
Huang, Yebo
Zheng, Huisong
Cao, Hongzhi
Zhou, Xiaoyu
Guo, Shicheng
Hu, Xueda
Li, Xin
Kristiansen, Karsten
Bolund, Lars
Xu, Jiujin
Wang, Wen
Yang, Huanming
Wang, Jian
Li, Ruiqiang
Beck, Stephan
Wang, Jun
Zhang, Xiuqing
Title The DNA methylome of human peripheral blood mononuclear cells
Journal name PLoS Biology   Check publisher's open access policy
ISSN 1544-9173
1545-7885
Publication date 2010-11-09
Sub-type Article (original research)
DOI 10.1371/journal.pbio.1000533
Open Access Status DOI
Volume 8
Issue 11
Total pages 9
Place of publication San Francisco, CA 94107 United States
Publisher Public Library of Science
Language eng
Abstract DNA methylation plays an important role in biological processes in human health and disease. Recent technological advances allow unbiased whole-genome DNA methylation (methylome) analysis to be carried out on human cells. Using whole-genome bisulfite sequencing at 24.7-fold coverage (12.3-fold per strand), we report a comprehensive (92.62%) methylome and analysis of the unique sequences in human peripheral blood mononuclear cells (PBMC) from the same Asian individual whose genome was deciphered in the YH project. PBMC constitute an important source for clinical blood tests world-wide. We found that 68.4% of CpG sites and < 0.2% of non-CpG sites were methylated, demonstrating that non-CpG cytosine methylation is minor in human PBMC. Analysis of the PBMC methylome revealed a rich epigenomic landscape for 20 distinct genomic features, including regulatory, protein-coding, non-coding, RNA-coding, and repeat sequences. Integration of our methylome data with the YH genome sequence enabled a first comprehensive assessment of allele-specific methylation (ASM) between the two haploid methylomes of any individual and allowed the identification of 599 haploid differentially methylated regions (hDMRs) covering 287 genes. Of these, 76 genes had hDMRs within 2 kb of their transcriptional start sites of which > 80% displayed allele-specific expression (ASE). These data demonstrate that ASM is a recurrent phenomenon and is highly correlated with ASE in human PBMCs. Together with recently reported similar studies, our study provides a comprehensive resource for future epigenomic research and confirms new sequencing technology as a paradigm for large-scale epigenomics studies.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 152 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 185 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Tue, 01 Sep 2015, 12:33:10 EST by System User on behalf of Learning and Research Services (UQ Library)