High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.).
High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.).
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DOI：
10.1371/journal.pone.0027916
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Llave C
中科院分区：
文献类型：
--
作者：
Donaire L;Pedrola L;Rosa Rde L;Llave C
长度为20至25个核苷酸（nt）的小RNA（sRNA）在许多发育和生理过程中维持基因组完整性并控制基因表达。尽管RNA沉默主要是在模式植物中研究的，但高通量测序技术的出现已经使超过40种植物物种的sRNA组分的分析成为可能。在这里，我们使用深度测序和分子方法报告了橄榄（Olea europaea L.）中sRNA的第一个清单。从幼枝和成枝制备的sRNA文库显示，24-nt类在sRNA转录组中占主导地位，并在其他植物物种中积累到从未见过的水平，这表明异染色质沉默在其大基因组的维持和完整性中起着积极的作用。在文库中共鉴定出18个已知的miRNA家族。此外，5个来自潜在发夹样前体的其他sRNA仍然是可信的miRNA候选者。RNA印迹证实了miRNA的表达，并提出了组织和/或发育特异性表达模式。在橄榄cDNA集合中计算预测保守miRNA的靶mRNA，并通过内切核酸裂解测定进行实验验证。最后，我们使用表达数据来揭示miR 156、miR 172和miR 390/TAS 3衍生的反式作用小干扰RNA（tasiRNA）调控节点的遗传组分，这表明这些控制发育转变的交互式网络在橄榄中是完全可操作的。
Small RNAs (sRNAs) of 20 to 25 nucleotides (nt) in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the sRNA component of more than 40 plant species. Here, we used deep sequencing and molecular methods to report the first inventory of sRNAs in olive (Olea europaea L.). sRNA libraries prepared from juvenile and adult shoots revealed that the 24-nt class dominates the sRNA transcriptome and atypically accumulates to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. A total of 18 known miRNA families were identified in the libraries. Also, 5 other sRNAs derived from potential hairpin-like precursors remain as plausible miRNA candidates. RNA blots confirmed miRNA expression and suggested tissue- and/or developmental-specific expression patterns. Target mRNAs of conserved miRNAs were computationally predicted among the olive cDNA collection and experimentally validated through endonucleolytic cleavage assays. Finally, we use expression data to uncover genetic components of the miR156, miR172 and miR390/TAS3-derived trans-acting small interfering RNA (tasiRNA) regulatory nodes, suggesting that these interactive networks controlling developmental transitions are fully operational in olive.
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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：
3.7
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：
3.7
作者：
Donaire, Livia;Wang, Yu;Llave, Cesar
通讯作者：
Llave, Cesar
影响因子：
11.6
作者：
Howell, Miya D.;Fahlgren, Noah;Carrington, James C.
通讯作者：
Carrington, James C.
影响因子：
5.4
作者：
de la Rosa, R;Angiolillo, A;Baldoni, L
通讯作者：
Baldoni, L