Local and global crosstalk among heterochromatin marks drives epigenome patterning in Arabidopsis

Transposable elements (TEs) are robustly silenced by multiple epigenetic marks, but dynamics of crosstalk among these marks remains enigmatic. In Arabidopsis, TEs are silenced by cytosine methylation in both CpG and non-CpG contexts (mCG and mCH) and histone H3 lysine 9 methylation (H3K9me). While mCH and H3K9me are mutually dependent for their maintenance, mCG and mCH/H3K9me are independently maintained. Here we show that establishment, rather than maintenance, of mCH depends on mCG, accounting for the synergistic colocalization of these silent marks in TEs. When mCG is lost, establishment of mCH is abolished in TEs. mCG also guides mCH in active genes, although the resulting mCH/H3K9me is removed thereafter. Unexpectedly, targeting efficiency of mCH depends on relative, rather than absolute, levels of mCG within the genome, suggesting underlying global negative controls. We propose that local positive feedback in heterochromatin dynamics, together with global negative feedback, drive robust and balanced DNA methylome patterning. Overall design: Examination of DNA methylation (WGBS) and transcription (RNA-seq) in Arabidopsis WT, several DNA methylase and histone modification mutants, and their genetic hybrids.

转座因子（Transposable Elements, TEs）可被多种表观遗传标记稳健沉默，但这些标记间的串扰动态仍不甚明晰。在拟南芥中，TEs的沉默依赖于CpG与非CpG序列环境中的胞嘧啶甲基化（mCG和mCH）以及组蛋白H3赖氨酸9甲基化（H3K9me）。其中mCH与H3K9me的维持过程相互依赖，而mCG与mCH/H3K9me的维持则彼此独立。本研究发现，mCH的建立而非维持依赖于mCG，这解释了上述沉默标记在TEs中的协同共定位现象。当mCG缺失时，TEs中mCH的建立过程会被完全阻断。mCG还可在活跃基因中引导mCH的沉积，但由此产生的mCH/H3K9me随后会被清除。出乎意料的是，mCH的靶向效率取决于基因组内mCG的相对水平而非绝对水平，这提示存在潜在的全局负调控机制。我们提出，异染色质动态中的局部正反馈与全局负反馈共同作用，可驱动形成稳定且均衡的DNA甲基化组模式。
实验整体设计：对拟南芥野生型（Wild Type, WT）、多种DNA甲基转移酶及组蛋白修饰突变体及其遗传杂交系，开展DNA甲基化（全基因组亚硫酸氢盐测序，Whole Genome Bisulfite Sequencing, WGBS）与转录组（RNA测序，RNA Sequencing, RNA-seq）分析。