美国科学家14日公布首张人类表观基因组图谱。这一成果将对人类表观遗传学研究作出贡献。表观遗传学被称为基因、疾病和环境之间“迷失的桥梁”。
美国萨克研究所（Salk）的研究人员利用功能强大的计算机和新技术绘制了两种人类细胞的表观基因组图谱，它们分别为胚胎干细胞和肺部纤维原细胞。
索尔克生物研究所研究员约瑟夫·埃克说：“以往，我们仅局限于表观基因组片段图。能够研究表观基因组的全部图谱将方便我们更好地体会基因组究竟如何影响健康和疾病，也可以使我们明白饮食和环境如何作用于基因表达。”
表观遗传学是与遗传学相对应的概念。遗传学是指基于基因序列改变所致基因表达水平变化；而在不改变脱氧核糖核酸（DNA）序列的情况下，激活和关闭基因行为或使之低调发挥的机制，称作“表观遗传”。
每个生物体都有一个基本的表观基因组，相当于控制基因功能的“使用手册”。生物体通过与环境互动编辑“使用手册”，不断添加或删除“使用说明”。换句话说，我们日常所吃的食物或接触的毒素都可对激活或关闭基因行为产生遗传性改变。
这份研究报告刊登于英国《自然》杂志网络版上。（生物谷Bioon.com）
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Nature advance online publication 14 October 2009 | doi:10.1038/nature08514
Human DNA methylomes at base resolution show widespread epigenomic differences
Ryan Lister1,9, Mattia Pelizzola1,9, Robert H. Dowen1, R. David Hawkins2, Gary Hon2, Julian Tonti-Filippini4, Joseph R. Nery1, Leonard Lee2, Zhen Ye2, Que-Minh Ngo2, Lee Edsall2, Jessica Antosiewicz-Bourget5,6, Ron Stewart5,6, Victor Ruotti5,6, A. Harvey Millar4, James A. Thomson5,6,7,8, Bing Ren2,3 & Joseph R. Ecker1
1 Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
2 Ludwig Institute for Cancer Research,
3 Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California 92093, USA
4 ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia
5 Morgridge Institute for Research, Madison, Wisconsin 53707, USA
6 Genome Center of Wisconsin, Madison, Wisconsin 53706, USA
7 Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
8 Department of Anatomy, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
9 These authors contributed equally to this work.
10 Correspondence to: Joseph R. Ecker1 Correspondence and requests for materials should be addressed to J.R.E.
DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA–protein interaction for several key regulatory factors. Widespread differences were identified in the composition and patterning of cytosine methylation between the two genomes. Nearly one-quarter of all methylation identified in embryonic stem cells was in a non-CG context, suggesting that embryonic stem cells may use different methylation mechanisms to affect gene regulation. Methylation in non--CG contexts showed enrichment in gene bodies and depletion in protein binding sites and enhancers. Non--CG methylation disappeared upon induced differentiation of the embryonic stem cells, and was restored in induced pluripotent stem cells. We identified hundreds of differentially methylated regions proximal to genes involved in pluripotency and differentiation, and widespread reduced methylation levels in fibroblasts associated with lower transcriptional activity. These reference epigenomes provide a foundation for future studies exploring this key epigenetic modification in human disease and development.
