Deep sequencing of microRNAs from hickory reveals an extensive degradation and 3′ end modification
Deep sequencing of microRNAs from hickory reveals an extensive degradation and 3′ end modification
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DOI：
10.1007/s11816-013-0310-3
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发表时间：
2014-03
影响因子：
2.4
通讯作者：
Zhengjia Wang;Jianqin Huang;Youjun Huang;Bingsong Zheng
中科院分区：
文献类型：
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作者：
Zhengjia Wang;Jianqin Huang;Youjun Huang;Bingsong Zheng
植物 microRNA (miRNA) 的降解和 3' 端修饰可能在调节 miRNA 功能和稳定性中发挥至关重要的作用。然而，关于如何进行降解和修饰的机制仍然知之甚少。在这里，我们报告了通过深度测序对两个山核桃花分化阶段的 miRNA 降解和 3' 修饰进行的调查。我们从两个山核桃花分化阶段构建了两个小RNA（sRNA）文库，并获得了大量截短的miRNA和具有3'端修饰的miRNA。如此多的截短 miRNA 的存在表明了一种同时通过两端降解的机制。进一步分析发现，从3'端截断的概率高于从5'端截断的概率。在许多家族中都观察到 3' 端添加了单核苷酸或双核苷酸。我们发现，在 3' 端添加腺嘌呤碱基是最常见的事件，占两个 sRNA 文库中所有 miRNA 3' 端修饰的 50% 以上。尿苷添加是第二种流行的修饰。这些观察结果表明，miRNA 的 3' 末端修饰优先选择山核桃植物中的腺嘌呤和尿苷。此外，我们观察到截短的 miRNA 或 isomiR 的表达与成熟 miRNA 相关。总而言之，我们的研究提供了有关植物中 miRNA 降解和 3' 端修饰的更多信息。
The degradation and 3′ end modification of plant microRNAs (miRNAs) may play crucial roles in regulating miRNA function and stability. However, the mechanism as to how the degradation and the modification are processed are still poorly characterized. Here, we report a survey of miRNA degradation and 3′ modification from two hickory floral differentiation stages through deep sequencing. We constructed two small RNA (sRNA) libraries from two hickory floral differentiation stages and obtained a large number of truncated miRNAs and miRNAs with 3′ end modifications. The presence of so many truncated miRNAs suggests a mechanism degrading through both ends simultaneously. Further analysis reveals that the truncation from the 3′ end has higher probability than from the 5′ end. Single- or double-nucleotide additions to the 3′ end have been observed in many families. We found that the addition of adenine base to the 3′ end is the most common event, accounting for more than 50 % of all miRNA 3′ end modification in the two sRNA libraries. Uridine addition is the second popular modification. These observations suggest that the 3′ end modification of miRNAs preferentially selects adenine and uridine in the hickory plant. Furthermore, we observed that expression of either truncated miRNA or isomiR associates with mature miRNAs. Altogether, our study provides more information regarding the degradation and 3′ end modification of miRNAs in plants.