The DNA methylome of human peripheral blood mononuclear cells

Yingrui Li; Jingde Zhu; Geng Tian; Ning Li; Qibin Li; Mingzhi Ye; Hancheng Zheng; Jian Yu; Honglong Wu; Jihua Sun; Hongyu Zhang; Quan Chen; Ruibang Luo; Minfeng Chen; Yinghua He; Xin Jin; Qinghui Zhang; Chang Yu; Guangyu Zhou; Jinfeng Sun; Yebo Huang; Huisong Zheng; Hongzhi Cao; Xiaoyu Zhou; Shicheng Guo; Xueda Hu; Xin Li; Karsten Kristiansen; Lars Bolund; Jiujin Xu; Wen Wang; Huanming Yang; Jian Wang; Ruiqiang Li; Stephan Beck; Jun Wang; Xiuqing Zhang

doi:10.1371/journal.pbio.1000533

The DNA methylome of human peripheral blood mononuclear cells

Yingrui Li, Jingde Zhu, Geng Tian, Ning Li, Qibin Li, Mingzhi Ye, Hancheng Zheng, Jian Yu, Honglong Wu, Jihua Sun, Hongyu Zhang, Quan Chen, Ruibang Luo, Minfeng Chen, Yinghua He, Xin Jin, Qinghui Zhang, Chang Yu, Guangyu Zhou, Jinfeng SunYebo Huang, Huisong Zheng, Hongzhi Cao, Xiaoyu Zhou, Shicheng Guo, Xueda Hu, Xin Li, Karsten Kristiansen, Lars Bolund, Jiujin Xu, Wen Wang, Huanming Yang, Jian Wang, Ruiqiang Li, Stephan Beck, Jun Wang, Xiuqing Zhang

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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 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.

Originalsprog	Engelsk
Tidsskrift	PLoS - Biology
Vol/bind	8
Udgave nummer	11
Sider (fra-til)	e1000533-e1000533
ISSN	1544-9173
DOI	https://doi.org/10.1371/journal.pbio.1000533
Status	Udgivet - nov. 2010

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Li, Y, Zhu, J, Tian, G, Li, N, Li, Q, Ye, M, Zheng, H, Yu, J, Wu, H, Sun, J, Zhang, H, Chen, Q, Luo, R, Chen, M, He, Y, Jin, X, Zhang, Q, Yu, C, Zhou, G, Sun, J, Huang, Y, Zheng, H, Cao, H, Zhou, X, Guo, S, Hu, X, Li, X, Kristiansen, K, Bolund, L, Xu, J, Wang, W, Yang, H, Wang, J, Li, R, Beck, S, Wang, J & Zhang, X 2010, 'The DNA methylome of human peripheral blood mononuclear cells', PLoS - Biology, bind 8, nr. 11, s. e1000533-e1000533. https://doi.org/10.1371/journal.pbio.1000533

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title = "The DNA methylome of human peripheral blood mononuclear cells",

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 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.",

keywords = "Alleles, CpG Islands, DNA Methylation, Haploidy, Humans, Leukocytes, Mononuclear, RNA, Untranslated, Sequence Alignment",

author = "Yingrui Li and Jingde Zhu and Geng Tian and Ning Li and Qibin Li and Mingzhi Ye and Hancheng Zheng and Jian Yu and Honglong Wu and Jihua Sun and Hongyu Zhang and Quan Chen and Ruibang Luo and Minfeng Chen and Yinghua He and Xin Jin and Qinghui Zhang and Chang Yu and Guangyu Zhou and Jinfeng Sun and Yebo Huang and Huisong Zheng and Hongzhi Cao and Xiaoyu Zhou and Shicheng Guo and Xueda Hu and Xin Li and Karsten Kristiansen and Lars Bolund and Jiujin Xu and Wen Wang and Huanming Yang and Jian Wang and Ruiqiang Li and Stephan Beck and Jun Wang and Xiuqing Zhang",

year = "2010",

month = nov,

doi = "10.1371/journal.pbio.1000533",

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T1 - The DNA methylome of human peripheral blood mononuclear cells

AU - Li, Yingrui

AU - Zhu, Jingde

AU - Tian, Geng

AU - Li, Ning

AU - Li, Qibin

AU - Ye, Mingzhi

AU - Zheng, Hancheng

AU - Yu, Jian

AU - Wu, Honglong

AU - Sun, Jihua

AU - Zhang, Hongyu

AU - Chen, Quan

AU - Luo, Ruibang

AU - Chen, Minfeng

AU - He, Yinghua

AU - Jin, Xin

AU - Zhang, Qinghui

AU - Yu, Chang

AU - Zhou, Guangyu

AU - Sun, Jinfeng

AU - Huang, Yebo

AU - Zheng, Huisong

AU - Cao, Hongzhi

AU - Zhou, Xiaoyu

AU - Guo, Shicheng

AU - Hu, Xueda

AU - Li, Xin

AU - Kristiansen, Karsten

AU - Bolund, Lars

AU - Xu, Jiujin

AU - Wang, Wen

AU - Yang, Huanming

AU - Wang, Jian

AU - Li, Ruiqiang

AU - Beck, Stephan

AU - Wang, Jun

AU - Zhang, Xiuqing

PY - 2010/11

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N2 - 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 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.

AB - 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 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.

KW - Alleles

KW - CpG Islands

KW - DNA Methylation

KW - Haploidy

KW - Humans

KW - Leukocytes, Mononuclear

KW - RNA, Untranslated

KW - Sequence Alignment

U2 - 10.1371/journal.pbio.1000533

DO - 10.1371/journal.pbio.1000533

M3 - Journal article

C2 - 21085693

SN - 1544-9173

VL - 8

SP - e1000533-e1000533

JO - PLoS Biology

JF - PLoS Biology

IS - 11

ER -

The DNA methylome of human peripheral blood mononuclear cells

Abstract

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