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 <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.
authors.affiliation: BGI-Shenzhen, Shenzhen, Guangdong, China.
authors.forename: Yingrui
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authors.lastname: Li
authors.forename: Jingde
authors.initials: J
authors.lastname: Zhu
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authors.lastname: Tian
authors.forename: Ning
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authors.forename: Qibin
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authors.forename: Mingzhi
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authors.forename: Honglong
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authors.forename: Hongyu
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authors.lastname: Zhang
authors.forename: Quan
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authors.lastname: Luo
authors.forename: Minfeng
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authors.lastname: Chen
authors.forename: Yinghua
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authors.lastname: He
authors.forename: Xin
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authors.forename: Chang
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authors.forename: Guangyu
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authors.lastname: Zhou
authors.forename: Jinfeng
authors.initials: J
authors.lastname: Sun
authors.forename: Yebo
authors.initials: Y
authors.lastname: Huang
authors.forename: Huisong
authors.initials: H
authors.lastname: Zheng
authors.forename: Hongzhi
authors.initials: H
authors.lastname: Cao
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhou
authors.forename: Shicheng
authors.initials: S
authors.lastname: Guo
authors.forename: Xueda
authors.initials: X
authors.lastname: Hu
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.forename: Karsten
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authors.lastname: Kristiansen
authors.forename: Lars
authors.initials: L
authors.lastname: Bolund
authors.forename: Jiujin
authors.initials: J
authors.lastname: Xu
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Stephan
authors.initials: S
authors.lastname: Beck
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
mesh_terms: D000483:Alleles; D018899:CpG Islands; D019175:DNA Methylation; D006238:Haploidy; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000378:metabolism*; D022661:RNA, Untranslated / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D022661:RNA, Untranslated