The DNA Methylome of Human Peripheral Blood Mononuclear Cells

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	The DNA Methylome of Human Peripheral Blood Mononuclear Cells
	Li YR 1; Zhu JD 2,3; Tian G 1,4,5; Li N 1; Li QB 1; Ye MZ 1; Zheng HC 1; Yu J 2; Wu HL 1; Sun JH 1; Wang W 7; Yang HM 1; Wang J 1; Li RQ 1; Beck S11; Wang J1,8; Zhang XQ*1; s.beck@ucl.ac.uk ; wangj@genomics.org.cn ; zhangxq@genomics.org.cn
	2010
发表期刊	PLOS BIOLOGY
卷号	8 期号:11 页码:e1000533
合作性质	其它
摘要	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.
资助者	This project was supported by the National Natural Science Foundation of China (30725008; 30890032;30811130531), the Chinese 863 program (2006AA02Z177, 2006AA02A301), the Chinese Academy of Science (GJHZ0701-6), the Shenzhen Municipal Government of China (grants JC200903190772A, CXB200903110066A, ZYC200903240077A, ZYC200903240076A and ZYC200903240080A), the Danish Platform for Integrative Biology and the Ole Romer grant from the Danish Natural Science Research Council. This project was also funded by the Yantian District local government of Shenzhen. SB was supported by The Wellcome Trust (grant 084071) and is recipient of a Royal Society Wolfson Research Merit Award. JZ is supported by the funds from National Science Foundation(90919024, and 30921140312), National Research Program for Basic Research(2009CB825606, 2009CB825607 and 2010CB912802), and Shanghai Science Foundation(09JC141300). ; This project was supported by the National Natural Science Foundation of China (30725008; 30890032;30811130531), the Chinese 863 program (2006AA02Z177, 2006AA02A301), the Chinese Academy of Science (GJHZ0701-6), the Shenzhen Municipal Government of China (grants JC200903190772A, CXB200903110066A, ZYC200903240077A, ZYC200903240076A and ZYC200903240080A), the Danish Platform for Integrative Biology and the Ole Romer grant from the Danish Natural Science Research Council. This project was also funded by the Yantian District local government of Shenzhen. SB was supported by The Wellcome Trust (grant 084071) and is recipient of a Royal Society Wolfson Research Merit Award. JZ is supported by the funds from National Science Foundation(90919024, and 30921140312), National Research Program for Basic Research(2009CB825606, 2009CB825607 and 2010CB912802), and Shanghai Science Foundation(09JC141300). ; This project was supported by the National Natural Science Foundation of China (30725008; 30890032;30811130531), the Chinese 863 program (2006AA02Z177, 2006AA02A301), the Chinese Academy of Science (GJHZ0701-6), the Shenzhen Municipal Government of China (grants JC200903190772A, CXB200903110066A, ZYC200903240077A, ZYC200903240076A and ZYC200903240080A), the Danish Platform for Integrative Biology and the Ole Romer grant from the Danish Natural Science Research Council. This project was also funded by the Yantian District local government of Shenzhen. SB was supported by The Wellcome Trust (grant 084071) and is recipient of a Royal Society Wolfson Research Merit Award. JZ is supported by the funds from National Science Foundation(90919024, and 30921140312), National Research Program for Basic Research(2009CB825606, 2009CB825607 and 2010CB912802), and Shanghai Science Foundation(09JC141300). ; This project was supported by the National Natural Science Foundation of China (30725008; 30890032;30811130531), the Chinese 863 program (2006AA02Z177, 2006AA02A301), the Chinese Academy of Science (GJHZ0701-6), the Shenzhen Municipal Government of China (grants JC200903190772A, CXB200903110066A, ZYC200903240077A, ZYC200903240076A and ZYC200903240080A), the Danish Platform for Integrative Biology and the Ole Romer grant from the Danish Natural Science Research Council. This project was also funded by the Yantian District local government of Shenzhen. SB was supported by The Wellcome Trust (grant 084071) and is recipient of a Royal Society Wolfson Research Merit Award. JZ is supported by the funds from National Science Foundation(90919024, and 30921140312), National Research Program for Basic Research(2009CB825606, 2009CB825607 and 2010CB912802), and Shanghai Science Foundation(09JC141300).
收录类别	SCI
语种	英语
资助者	This project was supported by the National Natural Science Foundation of China (30725008; 30890032;30811130531), the Chinese 863 program (2006AA02Z177, 2006AA02A301), the Chinese Academy of Science (GJHZ0701-6), the Shenzhen Municipal Government of China (grants JC200903190772A, CXB200903110066A, ZYC200903240077A, ZYC200903240076A and ZYC200903240080A), the Danish Platform for Integrative Biology and the Ole Romer grant from the Danish Natural Science Research Council. This project was also funded by the Yantian District local government of Shenzhen. SB was supported by The Wellcome Trust (grant 084071) and is recipient of a Royal Society Wolfson Research Merit Award. JZ is supported by the funds from National Science Foundation(90919024, and 30921140312), National Research Program for Basic Research(2009CB825606, 2009CB825607 and 2010CB912802), and Shanghai Science Foundation(09JC141300). ; This project was supported by the National Natural Science Foundation of China (30725008; 30890032;30811130531), the Chinese 863 program (2006AA02Z177, 2006AA02A301), the Chinese Academy of Science (GJHZ0701-6), the Shenzhen Municipal Government of China (grants JC200903190772A, CXB200903110066A, ZYC200903240077A, ZYC200903240076A and ZYC200903240080A), the Danish Platform for Integrative Biology and the Ole Romer grant from the Danish Natural Science Research Council. This project was also funded by the Yantian District local government of Shenzhen. SB was supported by The Wellcome Trust (grant 084071) and is recipient of a Royal Society Wolfson Research Merit Award. JZ is supported by the funds from National Science Foundation(90919024, and 30921140312), National Research Program for Basic Research(2009CB825606, 2009CB825607 and 2010CB912802), and Shanghai Science Foundation(09JC141300). ; This project was supported by the National Natural Science Foundation of China (30725008; 30890032;30811130531), the Chinese 863 program (2006AA02Z177, 2006AA02A301), the Chinese Academy of Science (GJHZ0701-6), the Shenzhen Municipal Government of China (grants JC200903190772A, CXB200903110066A, ZYC200903240077A, ZYC200903240076A and ZYC200903240080A), the Danish Platform for Integrative Biology and the Ole Romer grant from the Danish Natural Science Research Council. This project was also funded by the Yantian District local government of Shenzhen. SB was supported by The Wellcome Trust (grant 084071) and is recipient of a Royal Society Wolfson Research Merit Award. JZ is supported by the funds from National Science Foundation(90919024, and 30921140312), National Research Program for Basic Research(2009CB825606, 2009CB825607 and 2010CB912802), and Shanghai Science Foundation(09JC141300). ; This project was supported by the National Natural Science Foundation of China (30725008; 30890032;30811130531), the Chinese 863 program (2006AA02Z177, 2006AA02A301), the Chinese Academy of Science (GJHZ0701-6), the Shenzhen Municipal Government of China (grants JC200903190772A, CXB200903110066A, ZYC200903240077A, ZYC200903240076A and ZYC200903240080A), the Danish Platform for Integrative Biology and the Ole Romer grant from the Danish Natural Science Research Council. This project was also funded by the Yantian District local government of Shenzhen. SB was supported by The Wellcome Trust (grant 084071) and is recipient of a Royal Society Wolfson Research Merit Award. JZ is supported by the funds from National Science Foundation(90919024, and 30921140312), National Research Program for Basic Research(2009CB825606, 2009CB825607 and 2010CB912802), and Shanghai Science Foundation(09JC141300).
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/353002/6554
专题	基因起源组
通讯作者	s.beck@ucl.ac.uk; wangj@genomics.org.cn; zhangxq@genomics.org.cn
作者单位	1.BGI-Shenzhen, Shenzhen, Guangdong, China 2.Cancer Epigenetics and Gene Therapy Program, Shanghai Cancer Institute, Shanghai Jiaotong University, Shanghai, China 3.Epigentic Laboratory, Bio-X Center, Shanghai JiaoTong University, Shanghai, China 4.Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China, 5.The Graduate University of Chinese Academy of Sciences, Beijing, China 6.School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China 7.Kunming Institute of Zoology, Chinese Academy of Sciences, Yunnan, China 8.Department of Biology, University of Copenhagen, Copenhagen, Denmark, 9.Institute of Human Genetics, University of Aarhus, Aarhus, Denmark 10.Institute of Genetics and Developmental Biology, Chinese Academy of Human Sciences, Beijing, China 11.UCL Cancer Institute, University College London, London, United Kingdom
推荐引用方式 GB/T 7714	Li YR,Zhu JD,Tian G,et al. The DNA Methylome of Human Peripheral Blood Mononuclear Cells[J]. PLOS BIOLOGY,2010,8(11):e1000533.
APA	Li YR.,Zhu JD.,Tian G.,Li N.,Li QB.,...&zhangxq@genomics.org.cn.(2010).The DNA Methylome of Human Peripheral Blood Mononuclear Cells.PLOS BIOLOGY,8(11),e1000533.
MLA	Li YR,et al."The DNA Methylome of Human Peripheral Blood Mononuclear Cells".PLOS BIOLOGY 8.11(2010):e1000533.

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