Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting
Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting
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DOI：
10.1105/tpc.107.050062
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发表时间：
2007-03-01
期刊：
影响因子：
11.6
通讯作者：
Carrington, James C.
中科院分区：
文献类型：
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作者：
Howell, Miya D.;Fahlgren, Noah;Carrington, James C.
许多内源转录本、病毒和转基因的转录后RNA沉默涉及依赖RNA的RNA聚合酶6/类DICER 4（RDR6/DCL4）的短干扰RNA（siRNA）生物发生途径。拟南芥包含几个反式作用小干扰RNA（tasiRNA）家族，它们通过RDR6/DCL4依赖途径形成21个核苷酸的相位阵列，并对靶转录本进行负调控。利用深度测序技术和计算方法，在野生型植株和沉默缺陷突变体中分析了拟南芥基因组中已知tasiRNA和类tasiRNA位点的相位模式。发现一些基因转录本在被一种或多种微小RNA（miRNA）或tasiRNA初始靶向后，通过RDR6/DCL4依赖途径进行传递，其中最显著的例子是一个不断扩大的编码五肽重复（PPR）蛋白的基因分支。有趣的是，利用毛果杨进行的系统发育分析揭示了在一个类似扩大的PPR基因群内存在小RNA介导的调控机制的证据。我们认为转录后沉默机制在进化尺度上起作用，以缓冲快速扩张的基因家族的影响。
Posttranscriptional RNA silencing of many endogenous transcripts, viruses, and transgenes involves the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 (RDR6/DCL4)-dependent short interfering RNA (siRNA) biogenesis pathway. Arabidopsis thaliana contains several families of trans-acting siRNAs (tasiRNAs) that form in 21-nucleotide phased arrays through the RDR6/DCL4-dependent pathway and that negatively regulate target transcripts. Using deep sequencing technology and computational approaches, the phasing patterns of known tasiRNAs and tasiRNA-like loci from across the Arabidopsis genome were analyzed in wild-type plants and silencing-defective mutants. Several gene transcripts were found to be routed through the RDR6/DCL4-dependent pathway after initial targeting by one or multiple miRNAs or tasiRNAs, the most conspicuous example of which was an expanding clade of genes encoding pentatricopeptide repeat (PPR) proteins. Interestingly, phylogenetic analysis using Populus trichocarpa revealed evidence for small RNA-mediated regulatory mechanisms within a similarly expanded group of PPR genes. We suggest that posttranscriptional silencing mechanisms operate on an evolutionary scale to buffer the effects of rapidly expanding gene families.