The DNA methylome of human peripheral blood mononuclear cells.
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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Public Library of Science (PLoS)
2010
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oai:doaj.org-article:1d216bc828114c5190bf17a5fc9206462021-11-18T05:36:57ZThe DNA methylome of human peripheral blood mononuclear cells.1544-91731545-788510.1371/journal.pbio.1000533https://doaj.org/article/1d216bc828114c5190bf17a5fc9206462010-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21085693/pdf/?tool=EBIhttps://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885DNA 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.Yingrui LiJingde ZhuGeng TianNing LiQibin LiMingzhi YeHancheng ZhengJian YuHonglong WuJihua SunHongyu ZhangQuan ChenRuibang LuoMinfeng ChenYinghua HeXin JinQinghui ZhangChang YuGuangyu ZhouJinfeng SunYebo HuangHuisong ZhengHongzhi CaoXiaoyu ZhouShicheng GuoXueda HuXin LiKarsten KristiansenLars BolundJiujin XuWen WangHuanming YangJian WangRuiqiang LiStephan BeckJun WangXiuqing ZhangPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 8, Iss 11, p e1000533 (2010) |
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DOAJ |
| collection |
DOAJ |
| language |
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| topic |
Biology (General) QH301-705.5 |
| spellingShingle |
Biology (General) QH301-705.5 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 The DNA methylome of human peripheral blood mononuclear cells. |
| 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. |
| format |
article |
| author |
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 |
| author_facet |
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 |
| author_sort |
Yingrui Li |
| title |
The DNA methylome of human peripheral blood mononuclear cells. |
| title_short |
The DNA methylome of human peripheral blood mononuclear cells. |
| title_full |
The DNA methylome of human peripheral blood mononuclear cells. |
| title_fullStr |
The DNA methylome of human peripheral blood mononuclear cells. |
| title_full_unstemmed |
The DNA methylome of human peripheral blood mononuclear cells. |
| title_sort |
dna methylome of human peripheral blood mononuclear cells. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2010 |
| url |
https://doaj.org/article/1d216bc828114c5190bf17a5fc920646 |
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