PDF(Pubmed)
Abstract：
RNA-directed DNA methylation (RdDM) is driven by small RNAs (sRNAs) complementary to the nascent transcript of RNA polymerase V (Pol V). sRNAs associated with ARGONAUTE (AGO) proteins are tethered to Pol V mainly by the AGO-hook domain of its subunit NRPE1. We found, by in silico analyses, that Pol V strongly colocalizes on chromatin with another AGO-hook protein, SPT6-like (SPT6L), which is a known essential transcription elongation factor of Pol II. Our phylogenetic analysis revealed that SPT6L acquired its AGO-binding capacity already in the most basal streptophyte algae, even before the emergence of Pol V, suggesting that SPT6L might be a driving force behind the RdDM evolution. Since its emergence, SPT6L with the AGO-hook represents the only conserved SPT6 homolog in Viridiplantae, implying that the same protein is involved in both Pol II and Pol V complexes. To better understand the role of SPT6L in the Pol V complex, we characterized genomic loci where these two colocalize and uncovered that DNA methylation there is more dynamic, driven by higher levels of sRNAs often from non-canonical RdDM pathways and more dependent on chromatin modifying and remodeling proteins like MORC. Pol V loci with SPT6L are highly depleted in helitrons but enriched in gene promoters for which locally and temporally precise methylation is necessary. In view of these results, we discuss potential roles of multiple AGO-hook domains present in the Pol V complex and speculate that SPT6L mediates de novo methylation of naïve loci by interconnecting Pol II and Pol V activities.
摘要：
RNA指导的DNA甲基化（RdDM）由与RNA聚合酶V（PolV）的新生转录物互补的小RNA（sRNA）驱动。与ARGONAUTE（AGO）蛋白相关的sRNA主要通过其亚基NRPE1的AGO-hook结构域连接到PolV。我们发现,通过计算机模拟分析，PolV与另一种AGO-hook蛋白强烈共定位在染色质上，类似SPT6（SPT6L），它是PolII的已知必需转录延伸因子。我们的系统发育分析显示，SPT6L已经在最基础的链球菌藻类中获得了AGO结合能力，甚至在PolV出现之前，这表明SPT6L可能是RdDM进化背后的驱动力。自从它出现以来,带有AGO钩的SPT6L代表了Viridiplantae中唯一保守的SPT6同源物，暗示相同的蛋白质参与PolII和PolV复合物。为了更好地理解SPT6L在PolV复合物中的作用，我们对这两个共定位的基因组基因座进行了表征，并发现DNA甲基化更具动态性，由高水平的sRNA驱动，通常来自非规范的RdDM途径，并且更依赖于染色质修饰和重塑蛋白，如MORC。具有SPT6L的PolV基因座在Helitron中高度耗尽，但在基因启动子中富集，因此需要局部和时间上精确的甲基化。鉴于这些结果,我们讨论了PolV复合物中存在的多个AGO-hook结构域的潜在作用，并推测SPT6L通过互连PolII和PolV活性来介导初始基因座的从头甲基化。
