BGI researchers sequenced the human methylome at single base-pair resolution

DNA methylation plays an important role in many processes such as animal development, X-chromosome inactivation, and carcinogenesis. Understanding the mechanisms and functions of DNA methylation and how it varies from tissue to tissue and between individuals will have profound implications for human health and disease. A team of Chinese researchers decoded the essentially complete methylome (an inventory of all the bases that are methylated) of the human genome using peripheral blood mononuclear cells (PBMCs). The results will be published in the online, open access journal PLoS Biology next week.

The research is part of YanHuang (YH) Project, which has been launched by BGI (previous known as Beijing Genomics Institute) at Shenzhen, which aims to sequence 100 Chinese individuals in 3 years to accelerate the discovery of disease genes and mutations in an Asian population. The methylome was generated from the same donor whose genome was deciphered in the YH project. The methylome was examined at 20 distinct features including regulatory, protein-coding, non-coding, and repeat sequences. The integration of the data with the previously determined genome sequence of the same Asian individual allowed the identification of allele-specific methylation (ASM) differences between the methylomes of the genomes inherited from either parent. This revealed that ASM was highly correlated with allele-specific gene expression (ASE) which indicated that parental gene imprinting (that is the favored expression of the genes inherited from one parent) may be more common than previously thought.

The research not only provides a comprehensive resource for future epigenomic research but also demonstrates a paradigm for epigenetic studies through new sequencing technology. The PBMC methylome data has been deposited to NCBI . accession number: SRA008544). It is expected to form a lasting resource as part of the International Human Epigenome Project.

Funding: This project was supported by the National Natural Science Foundation of China (30725008; 30890032;30811130531), the Chinese 863 program (2006AA02Z177), 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). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests statement: The authors declare that no competing interests exist.