RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats.
RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats.
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DOI：
10.4161/epi.20290
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发表时间：
2012-07
期刊：
影响因子：
3.7
通讯作者：
Meyers BC
中科院分区：
文献类型：
--
作者：
Lee TF;Gurazada SG;Zhai J;Li S;Simon SA;Matzke MA;Chen X;Meyers BC
在植物中，异染色质是由一种基于RNA的小基因沉默机制维持的，这种机制被称为RNA指导的DNA甲基化(RdDM)。RdDM需要两种植物特有的DNA依赖的RNA聚合酶(RNAP IV和RNAP V)的非冗余功能。RNAP IV在siRNA的生物发生中起着重要作用，而RNAP V可能会招募DNA甲基化机制来靶向内源基因座进行沉默。虽然先前已经发现依赖于RNAP IV和RNAP V的小RNA生成区，但RNAP V靶向的siRNA积累和沉默的基因组位点还没有被广泛描述。为了表征拟南芥基因组中依赖RNAP V的异染色质siRNA生成区，我们对野生型和RNAP V缺失突变(Nrpe1)植物的小RNA群体进行了深入测序。我们的结果表明，RNAP V依赖的siRNA生成基因座主要与基因间隔区的短重复序列相关。在包括dms4、drd1、dms3和rdm1在内的RdDM突变体中，对短重复序列产生的小RNA的抑制也很明显，反映了这些RdDM效应器与RNAP V的已知关联。RNAP V靶向的基因组区域很小，估计平均长度为238bp。我们的结果表明，RNAP V影响基因组基因座的siRNA产生，其特征与已知的RNAP IV依赖的基因座不同。RNAP V与RNAP IV和DRM1/2一起，可以靶向并沉默位于分散基因组区域的一组小的基因间转座元件以进行沉默。这些基因座的沉默可能被RdDM积极加强。
In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (RNAP), RNAP IV and RNAP V. RNAP IV plays a major role in siRNA biogenesis, while RNAP V may recruit DNA methylation machinery to target endogenous loci for silencing. Although small RNA-generating regions that are dependent on both RNAP IV and RNAP V have been identified previously, the genomic loci targeted by RNAP V for siRNA accumulation and silencing have not been described extensively. To characterize the RNAP V-dependent, heterochromatic siRNA-generating regions in the Arabidopsis genome, we deeply sequenced the small RNA populations of wild-type and RNAP V null mutant (nrpe1) plants. Our results showed that RNAP V-dependent siRNA-generating loci are associated predominately with short repetitive sequences in intergenic regions. Suppression of small RNA production from short repetitive sequences was also prominent in RdDM mutants including dms4, drd1, dms3 and rdm1, reflecting the known association of these RdDM effectors with RNAP V. The genomic regions targeted by RNAP V were small, with an estimated average length of 238 bp. Our results suggest that RNAP V affects siRNA production from genomic loci with features dissimilar to known RNAP IV-dependent loci. RNAP V, along with RNAP IV and DRM1/2, may target and silence a set of small, intergenic transposable elements located in dispersed genomic regions for silencing. Silencing at these loci may be actively reinforced by RdDM.