The DNA Methylome of Human Peripheral Blood Mononuclear Cells: e1000533
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 s...
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| Veröffentlicht in: | PLoS biology 2010-11, Vol.8 (11) |
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| creator | 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 |
| description | 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. |
| doi_str_mv | 10.1371/journal.pbio.1000533 |
| format | Article |
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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.</description><identifier>ISSN: 1544-9173</identifier><identifier>EISSN: 1545-7885</identifier><identifier>DOI: 10.1371/journal.pbio.1000533</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Blood ; Classification ; Deoxyribonucleic acid ; DNA ; DNA methylation ; Gene expression ; Genetics ; Genomes ; Stem cells</subject><ispartof>PLoS biology, 2010-11, Vol.8 (11)</ispartof><rights>2010 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Li Y, Zhu J, Tian G, Li N, Li Q, et al. (2010) The DNA Methylome of Human Peripheral Blood Mononuclear Cells. PLoS Biol 8(11): e1000533. doi:10.1371/journal.pbio.1000533</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,781,785,865,27929,27930</link.rule.ids></links><search><creatorcontrib>Li, Yingrui</creatorcontrib><creatorcontrib>Zhu, Jingde</creatorcontrib><creatorcontrib>Tian, Geng</creatorcontrib><creatorcontrib>Li, Ning</creatorcontrib><creatorcontrib>Li, Qibin</creatorcontrib><creatorcontrib>Ye, Mingzhi</creatorcontrib><creatorcontrib>Zheng, Hancheng</creatorcontrib><creatorcontrib>Yu, Jian</creatorcontrib><creatorcontrib>Wu, Honglong</creatorcontrib><creatorcontrib>Sun, Jihua</creatorcontrib><creatorcontrib>Zhang, Hongyu</creatorcontrib><creatorcontrib>Chen, Quan</creatorcontrib><creatorcontrib>Luo, Ruibang</creatorcontrib><creatorcontrib>Chen, Minfeng</creatorcontrib><creatorcontrib>He, Yinghua</creatorcontrib><creatorcontrib>Jin, Xin</creatorcontrib><creatorcontrib>Zhang, Qinghui</creatorcontrib><creatorcontrib>Yu, Chang</creatorcontrib><creatorcontrib>Zhou, Guangyu</creatorcontrib><creatorcontrib>Sun, Jinfeng</creatorcontrib><creatorcontrib>Huang, Yebo</creatorcontrib><creatorcontrib>Zheng, Huisong</creatorcontrib><creatorcontrib>Cao, Hongzhi</creatorcontrib><creatorcontrib>Zhou, Xiaoyu</creatorcontrib><creatorcontrib>Guo, Shicheng</creatorcontrib><creatorcontrib>Hu, Xueda</creatorcontrib><creatorcontrib>Li, Xin</creatorcontrib><creatorcontrib>Kristiansen, Karsten</creatorcontrib><creatorcontrib>Bolund, Lars</creatorcontrib><creatorcontrib>Xu, Jiujin</creatorcontrib><creatorcontrib>Wang, Wen</creatorcontrib><creatorcontrib>Yang, Huanming</creatorcontrib><creatorcontrib>Wang, Jian</creatorcontrib><creatorcontrib>Li, Ruiqiang</creatorcontrib><creatorcontrib>Beck, Stephan</creatorcontrib><creatorcontrib>Wang, Jun</creatorcontrib><creatorcontrib>Zhang, Xiuqing</creatorcontrib><title>The DNA Methylome of Human Peripheral Blood Mononuclear Cells: e1000533</title><title>PLoS biology</title><description>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.</description><subject>Blood</subject><subject>Classification</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA methylation</subject><subject>Gene expression</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Stem 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| subjects | Blood Classification Deoxyribonucleic acid DNA DNA methylation Gene expression Genetics Genomes Stem cells |
| title | The DNA Methylome of Human Peripheral Blood Mononuclear Cells: e1000533 |
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