Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice.
Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice.
复制标题
DOI：
10.1007/s10142-013-0313-8
复制
发表时间：
2013-06
影响因子：
2.9
通讯作者：
Rock, Christopher D.
中科院分区：
文献类型：
--
作者：
Ou-Yang, Fangqian;Luo, Qing-Jun;Zhang, Yue;Richardson, Casey R.;Jiang, Yingwen;Rock, Christopher D.
microRNA（miRNAs）是一类长度约为21个核苷酸（nt）的小RNA（sRNA），由DICER-LIKE 1（DCL 1）或DCL 4从折返发夹加工而成。它们通过RNA诱导沉默复合物（RISC）通过碱基配对调节靶mRNA的表达。在RISC中，ARGONAUTE 1（AGO 1）是在miRNA：靶标双链体的第10位切割miRNA靶标的关键蛋白。许多注释的水稻miRNA发夹的真实性正在争论中，因为它们与重复序列的同源性。其中一些，如miR 1884 b，已根据不完整的信息从当前版本的miRBase中删除。在这项研究中，我们使用公开的深度测序数据集研究了转座因子（TE）衍生的miRNA与典型miRNA通路（DCL 1/4依赖性和AGO 1依赖性）的关联。AGO 1免疫沉淀样品中特异性富集了7种具有13种独特sRNA的miRNA发夹，而在DCL 1/4敲除基因型中相对减少。有趣的是，这些种类的长度为~21-nt，而不是miRBase和文献中注释的24-nt。它们的表达谱符合当前miRNA功能注释的标准。此外，在预测的靶mRNA的degradome数据集中发现了诊断性切割标签。这些miRNA发夹大多数与水稻中大量存在的一种DNA转座子--微型反向重复转座元件（MITEs）具有显著的同源性。最后，通过针对新EST的RNA印迹证实了24 nt miRNA样sRNA的根特异性产生，所述新EST定位于与miR 1884 b发夹具有广泛序列同源性的候选假基因的3 '-UTR。我们的数据是一致的假设，即TE可以作为一个驱动力的一些MIRNAs的进化，其中选择的DICER-LIKE 1/4加工和整合到AGO 1可以exapt转录TE相关的发夹到典型的miRNA途径。
microRNAs (miRNAs) are a class of small RNAs (sRNAs) of ~21 nucleotides (nt) in length processed from foldback hairpins by DICER-LIKE1 (DCL1) or DCL4. They regulate the expression of target mRNAs by base pairing through RNA-Induced Silencing Complex (RISC). In the RISC, ARGONAUTE1 (AGO1) is the key protein that cleaves miRNA targets at position ten of a miRNA:target duplex. The authenticity of many annotated rice miRNA hairpins is under debate because of their homology to repeat sequences. Some of them, like miR1884b, have been removed from the current release of miRBase based on incomplete information. In this study, we investigated the association of transposable element (TE)-derived miRNAs with typical miRNA pathways (DCL1/4- and AGO1-dependent) using publicly available deep sequencing datasets. Seven miRNA hairpins with 13 unique sRNAs were specifically enriched in AGO1 immunoprecipitation samples and relatively reduced in DCL1/4 knockdown genotypes. Interestingly, these species are ~21-nt long, instead of 24-nt as annotated in miRBase and the literature. Their expression profiles meet current criteria for functional annotation of miRNAs. In addition, diagnostic cleavage tags were found in degradome datasets for predicted target mRNAs. Most of these miRNA hairpins share significant homology with miniature inverted-repeat transposable elements (MITEs), one type of abundant DNA transposons in rice. Finally, the root-specific production of a 24 nt miRNA-like sRNA was confirmed by RNA blot for a novel EST that maps to the 3'-UTR of a candidate pseudogene showing extensive sequence homology to miR1884b hairpin. Our data are consistent with the hypothesis that TEs can serve as a driving force for the evolution of some MIRNAs, where co-opting of DICER-LIKE1/4 processing and integration into AGO1 could exapt transcribed TE-associated hairpins into typical miRNA pathways.
登录
查看更多内容
影响因子：
14.9
作者：
Dai X;Zhao PX
通讯作者：
Zhao PX
影响因子：
3.7
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
影响因子：
11.6
作者：
Lanet, Elodie;Delannoy, Etienne;Robaglia, Christophe
通讯作者：
Robaglia, Christophe
影响因子：
9.2
作者：
Addo-Quaye, Charles;Eshoo, Tifani W.;Axtell, Michael J.
通讯作者：
Axtell, Michael J.
影响因子：
3.7
作者：
Li Y;Li C;Xia J;Jin Y
通讯作者：
Jin Y