Identification of novel microRNAs in rice (Oryza sativa) based on the cleavage signals in precursors
Identification of novel microRNAs in rice (Oryza sativa) based on the cleavage signals in precursors
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基于前体裂解信号鉴定水稻 (Oryza sativa) 中的新型 microRNA
DOI：
10.1080/11263504.2018.1524800
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发表时间：
2018-11
期刊：
影响因子：
2
通讯作者：
Shao Chaogang
中科院分区：
文献类型：
--
作者：
Ye Xinghuo;Jiang Yeqin;Yu Lan;Yang Zhihong;Meng Yijun;Shao Chaogang
摘要微RNA（miRNAs）是植物基因表达的重要调控因子，近年来，越来越多的新的miRNA基因在水稻中被克隆。然而，目前还没有证据表明所有的miRNAs都已被发现，尤其是那些常规方法难以发现的低表达miRNAs。利用DCL 1介导的加工miRNA前体的切割信号可以作为发现新miRNA的线索的发现，进行了水稻miRNA候选物的全基因组搜索。结果，发现了51个先前验证的miRNA和24个新的miRNA候选者。经过靶点预测和基于degradome测序数据的验证，结合反向方法复检，进一步确定了10个miRNA候选物-mRNA靶点对，为深入分析这些miRNA候选物的功能提供了基础。此外，本研究中发现的一些异构体更有可能是真实的miRNAs。我们还发现了一个例外的例子，它不遵守22-nt的miRNA有能力从切割的靶点触发分阶段的siRNA产生的规则。
Abstract MicroRNAs (miRNAs) are crucial regulators of gene expression in plants and a growing number of novel miRNA genes have been cloned in rice in recent years. However, there is no evidence that all miRNAs have been discovered, especially for those low expression ones which are difficult to be found by conventional methods. By taking advantage of the finding that DCL1-mediated cleavage signals for the processing of the miRNA precursors could be used as the clues for novel miRNAs’ discovery, a genome-wide search for rice miRNA candidates was carried out. As a result, 51 previously validated miRNAs and 24 novel miRNA candidates were discovered. After target prediction and degradome sequencing data-based validation, coupled with reverse approach retest, 10 miRNA candidate–mRNA target pairs were further identified, providing a basis for in-depth functional analysis of these miRNA candidates. Besides, some isomiRs found in this study showed more likely to be the real miRNAs. We also found an exceptional example which did not obey the rule that 22-nt miRNAs have the ability to trigger the phased siRNAs production from the cleaved targets.
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影响因子：
14.9
作者：
Chen C;Ridzon DA;Broomer AJ;Zhou Z;Lee DH;Nguyen JT;Barbisin M;Xu NL;Mahuvakar VR;Andersen MR;Lao KQ;Livak KJ;Guegler KJ
通讯作者：
Guegler KJ
影响因子：
3.3
作者：
Ziemann M;Bhave M;Zachgo S
通讯作者：
Zachgo S
DOI：
10.1007/s12154-013-0091-8
发表时间：
2013-03
期刊：
Journal of Chemical Biology
影响因子：
--
作者：
Wei Xuan;Evan Murphy;T. Beeckman;D. Audenaert;Ive De Smet
通讯作者：
Wei Xuan;Evan Murphy;T. Beeckman;D. Audenaert;Ive De Smet
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：
27.5
作者：
Zhen Wang;S. Xing;R. Birkenbihl;S. Zachgo
通讯作者：
Zhen Wang;S. Xing;R. Birkenbihl;S. Zachgo