Wu Jiejun, Wang Shu-Huei, Potter Dustin, Liu Joseph C, Smith Laura T, Wu Yue-Zhong, Huang Tim H-M, Plass Christoph
Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA.
BMC Genomics. 2007 May 24;8:131. doi: 10.1186/1471-2164-8-131.
Previous studies of individual genes have shown that in a self-enforcing way, dimethylation at histone 3 lysine 9 (dimethyl-H3K9) and DNA methylation cooperate to maintain a repressive mode of inactive genes. Less clear is whether this cooperation is generalized in mammalian genomes, such as mouse genome. Here we use epigenomic tools to simultaneously interrogate chromatin modifications and DNA methylation in a mouse leukemia cell line, L1210.
Histone modifications on H3K9 and DNA methylation in L1210 were profiled by both global CpG island array and custom mouse promoter array analysis. We used chromatin immunoprecipitation microarray (ChIP-chip) to examine acetyl-H3K9 and dimethyl-H3K9. We found that the relative level of acetyl-H3K9 at different chromatin positions has a wider range of distribution than that of dimethyl-H3K9. We then used differential methylation hybridization (DMH) and the restriction landmark genome scanning (RLGS) to analyze the DNA methylation status of the same targets investigated by ChIP-chip. The results of epigenomic profiling, which have been independently confirmed for individual loci, show an inverse relationship between DNA methylation and histone acetylation in regulating gene silencing. In contrast to the previous notion, dimethyl-H3K9 seems to be less distinct in specifying silencing for the genes tested.
This study demonstrates in L1210 leukemia cells a diverse relationship between histone modifications and DNA methylation in the maintenance of gene silencing. Acetyl-H3K9 shows an inverse relationship between DNA methylation and histone acetylation in regulating gene silencing as expected. However, dimethyl-H3K9 seems to be less distinct in relation to promoter methylation. Meanwhile, a combination of epigenomic tools is of help in understanding the heterogeneity of epigenetic regulation, which may further our vision accumulated from single-gene studies.
先前对单个基因的研究表明，组蛋白3赖氨酸9位点的二甲基化（二甲基 - H3K9）与DNA甲基化以一种自我强化的方式协同作用，维持非活性基因的抑制模式。这种协同作用在哺乳动物基因组（如小鼠基因组）中是否普遍存在尚不清楚。在此，我们使用表观基因组学工具同时研究小鼠白血病细胞系L1210中的染色质修饰和DNA甲基化。
通过全基因组CpG岛阵列和定制小鼠启动子阵列分析对L1210细胞中的H3K9组蛋白修饰和DNA甲基化进行了分析。我们使用染色质免疫沉淀微阵列（ChIP - chip）检测乙酰化 - H3K9和二甲基化 - H3K9。我们发现，不同染色质位置的乙酰化 - H3K9相对水平的分布范围比二甲基化 - H3K9的分布范围更广。然后，我们使用差异甲基化杂交（DMH）和限制性地标基因组扫描（RLGS）分析ChIP - chip所研究的相同靶点的DNA甲基化状态。表观基因组分析结果已在个别位点得到独立验证，结果显示在调节基因沉默方面，DNA甲基化与组蛋白乙酰化之间存在负相关关系。与先前的观点相反，对于所测试的基因，二甲基化 - H3K9在指定沉默方面似乎不那么明显。
本研究表明，在L1210白血病细胞中，组蛋白修饰与DNA甲基化在维持基因沉默方面存在多种关系。正如预期的那样，乙酰化 - H3K9在调节基因沉默时，DNA甲基化与组蛋白乙酰化之间呈现负相关关系。然而，二甲基化 - H3K9与启动子甲基化的关系似乎不那么明显。同时，表观基因组学工具的组合有助于理解表观遗传调控的异质性，这可能拓展我们从单基因研究中积累的认知。
