SNF2 chromatin remodeler-family proteins FRG1 and-2 are required for RNA-directed DNA methylation
SNF2 chromatin remodeler-family proteins FRG1 and-2 are required for RNA-directed DNA methylation
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DOI：
10.1073/pnas.1420515111
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发表时间：
2014-12-09
影响因子：
11.1
通讯作者：
Ausin, Israel
中科院分区：
文献类型：
--
作者：
Groth, Martin;Stroud, Hume;Ausin, Israel
拟南芥中的DNA甲基化由至少四种不同的酶维持：DNA甲基转移酶1（MET 1）、染色体甲基化酶3（CMT 3）、结构域重排甲基转移酶2（DRM 2）和染色体甲基化酶2（CMT 2）。然而，DNA甲基化仅由酶DRM 2建立，其在RNA指导的DNA甲基化（RdDM）途径中起作用。一些RdDM成分属于基因家族，具有部分冗余功能，例如内切核糖核酸酶DICER-LIKE 2、3和4，并参与DE NOVO 2（IDN 2）相互作用物IDN 2-LIKE 1和2。传统的诱变筛选通常无法检测到多余的基因，因为一个基因的丢失可以通过相关基因来补偿。为了避免这个问题，我们使用共表达数据来鉴定与RdDM途径中的基因共调控的密切相关的基因。在这里，我们报告了两个冗余的蛋白质，SNF 2-RING-HELICASE-LIKE 1和-2（FRG 1和-2）的发现，它们是属于SNF 2家族的解旋酶样蛋白质的假定染色质修饰剂。全基因组亚硫酸氢盐测序分析表明，FRG 1和-2的同时突变导致特定RdDM靶向位点的甲基化缺陷。我们还表明，FRG 1物理协会与苏（var）3-9相关的SUVR 2，一个已知的RdDM组件，在体内。结合起来，我们的研究结果确定FRG 1和FRG 2作为以前未识别的RdDM机器的组成部分。
DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: DNA METHYLTRANSFERASE1 (MET1), CHROMOMETHYLASE3 (CMT3), DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2), and CHROMOMETHYLASE2 (CMT2). However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families and have partially redundant functions, such as the endoribonucleases DICER-LIKE 2, 3, and 4, and INVOLVED IN DE NOVO2 (IDN2) interactors IDN2-LIKE 1 and 2. Traditional mutagenesis screens usually fail to detect genes if they are redundant, as the loss of one gene can be compensated by a related gene. In an effort to circumvent this issue, we used coexpression data to identify closely related genes that are coregulated with genes in the RdDM pathway. Here we report the discovery of two redundant proteins, SNF2-RING-HELICASE-LIKE1 and -2 (FRG1 and -2) that are putative chromatin modifiers belonging to the SNF2 family of helicase-like proteins. Analysis of genome-wide bisulfite sequencing shows that simultaneous mutations of FRG1 and -2 cause defects in methylation at specific RdDM targeted loci. We also show that FRG1 physically associates with Su(var)3-9-related SUVR2, a known RdDM component, in vivo. Combined, our results identify FRG1 and FRG2 as previously unidentified components of the RdDM machinery.