Bernatavichute Yana V, Zhang Xiaoyu, Cokus Shawn, Pellegrini Matteo, Jacobsen Steven E
Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America.
PLoS One. 2008 Sep 8;3(9):e3156. doi: 10.1371/journal.pone.0003156.
Methylation of histone H3 lysine 9 (H3K9) is a hallmark of transcriptional silencing in many organisms. In Arabidopsis thaliana, dimethylation of H3K9 (H3K9m2) is important in the silencing of transposons and in the control of DNA methylation. We constructed a high-resolution genome-wide map of H3K9m2 methylation by using chromatin immunoprecipitation coupled with whole genome Roche Nimblegen microarrays (ChIP-chip). We observed a very high coincidence between H3K9m2 and CHG methylation (where H is either A,T or C) throughout the genome. The coding regions of genes that are associated exclusively with methylation in a CG context did not contain H3K9m2. In addition, we observed two distinct patterns of H3K9m2. Transposons and other repeat elements present in the euchromatic arms contained small islands of H3K9m2 present at relatively low levels. In contrast, pericentromeric/centromeric regions of Arabidopsis chromosomes contained long, rarely interrupted blocks of H3K9m2 present at much higher average levels than seen in the chromosome arms. These results suggest a complex interplay between H3K9m2 and different types of DNA methylation and suggest that distinct mechanisms control H3K9m2 in different compartments of the genome.
组蛋白H3赖氨酸9（H3K9）的甲基化是许多生物体转录沉默的一个标志。在拟南芥中，H3K9的二甲基化（H3K9m2）在转座子沉默和DNA甲基化控制中起重要作用。我们通过使用染色质免疫沉淀结合全基因组罗氏Nimblegen微阵列（ChIP-chip）构建了H3K9m2甲基化的高分辨率全基因组图谱。我们观察到在整个基因组中H3K9m2与CHG甲基化（其中H为A、T或C）之间有非常高的一致性。仅与CG背景下甲基化相关的基因编码区不包含H3K9m2。此外，我们观察到H3K9m2的两种不同模式。常染色质臂中的转座子和其他重复元件含有少量水平相对较低的H3K9m2小岛。相比之下，拟南芥染色体的着丝粒周围/着丝粒区域含有长的、很少中断的H3K9m2片段，其平均水平比染色体臂中观察到的要高得多。这些结果表明H3K9m2与不同类型的DNA甲基化之间存在复杂的相互作用，并表明不同的机制在基因组的不同区域控制H3K9m2。
