Nobuta Kan, Lu Cheng, Shrivastava Roli, Pillay Manoj, De Paoli Emanuele, Accerbi Monica, Arteaga-Vazquez Mario, Sidorenko Lyudmila, Jeong Dong-Hoon, Yen Yang, Green Pamela J, Chandler Vicki L, Meyers Blake C
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.
Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14958-63. doi: 10.1073/pnas.0808066105. Epub 2008 Sep 24.
Small RNAs from plants are known to be highly complex and abundant, with this complexity proportional to genome size. Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of RDR2. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wild-type maize and in the isogenic mop1-1 loss-of-function mutant by using Illumina's sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth. Similar to rdr2 in Arabidopsis, in mop1-1, the 24-nucleotide (nt) endogenous heterochromatic short-interfering siRNAs were dramatically reduced, resulting in an enrichment of miRNAs and transacting siRNAs. In contrast to the Arabidopsis rdr2 mutant, the mop1-1 plants retained a highly abundant heterochromatic approximately 22-nt class of small RNAs, suggesting a second mechanism for heterochromatic siRNA production. The enrichment of miRNAs and loss of 24-nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced.
已知植物中的小RNA高度复杂且数量丰富，这种复杂性与基因组大小成正比。拟南芥中的大多数内源性小干扰RNA（siRNA）的生物合成依赖于RNA依赖性RNA聚合酶2（RDR2）。最近的研究表明，玉米的副突变介导因子1（mop1）基因是RDR2的预测直系同源基因。mop1基因对于副突变的建立以及转座子和转基因转录沉默的维持是必需的，这表明小RNA可能参与其中。我们使用Illumina的合成测序（SBS）技术分析了野生型玉米和同基因mop1-1功能缺失突变体中的小RNA，这使我们能够深入表征玉米小RNA的组成。与拟南芥中的rdr2类似，在mop1-1中，24个核苷酸（nt）的内源性异染色质短干扰siRNA显著减少，导致微小RNA（miRNA）和反式作用siRNA富集。与拟南芥rdr2突变体不同，mop1-1植株保留了高度丰富的约22 nt的异染色质小RNA类别，这表明存在异染色质siRNA产生的第二种机制。随着玉米基因组测序更加全面，mop1-1中miRNA的富集和24 nt异染色质siRNA的缺失对于miRNA的发现应该是有利的。
