Isolation and initial structure-functional characterization of endogenous tRNA-derived stress-induced RNAs
Isolation and initial structure-functional characterization of endogenous tRNA-derived stress-induced RNAs
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DOI：
10.1080/15476286.2020.1732702
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发表时间：
2020-03-02
期刊：
影响因子：
4.1
通讯作者：
Ivanov, Pavel
中科院分区：
文献类型：
--
作者：
Akiyama, Yasutoshi;Kharel, Prakash;Ivanov, Pavel
最近的转录组研究已经确定了不同的转移RNA(TRNA)来源的RNA或tRNA来源的片段(TRF)。这些RNA中的一些已经被证明具有功能，并参与了从基因表达调控到跨代表观遗传等多种生物学过程。TRNAs的转录后成熟包括各种加工事件，包括各种RNA修饰的广泛修饰，这是正确的tRNA折叠和稳定性所必需的。此外，tRNA修饰决定了tRNA切割的模式和特异性。许多在TRFs领域的研究的主要缺点是大多数使用的是合成的RNAs，这些RNAs在序列上与内源性TRFs非常相似，但缺乏体内发现的RNA修饰。在这里，我们开发了一种简单的方法来分离tRNA衍生的应力诱导RNAs(TiRNAs)，这是TRFs的一个特定子集。我们的方法是可扩展的，具有成本效益，并且依赖于基于使用DNA探针的序列特异性RNA/DNA分离技术的单个tiRNAs的纯化。我们的方法通过研究tRNA片段中的生理性RNA修饰如何影响其生物活性，从而促进了tiRNAs的功能研究。在这里，我们报告了一些内源性tiRNA的初步功能研究，即tiRNA(Ala)和tiRNA(Gly)。我们发现，天然的5修饰字母Prime-tiRNA(Ala)分子组装成G-四链结构，内源性的5修饰字母Prime-tiRNA(Gly)具有翻译抑制活性。
Recent transcriptome-wide studies have identified a diverse pool of transfer RNA (tRNA)-derived RNAs or tRNA-derived fragments (tRFs). Some of these RNAs have been demonstrated to be functional and involved in multiple biological processes ranging from the regulation of gene expression to transgenerational epigenetic inheritance. Post-transcriptional maturation of tRNAs includes various processing events including extensive decoration by various RNA modifications, which are required for correct tRNA folding and stability. Moreover, tRNA modifications determine the pattern and specificity of tRNA cleavage. The major drawbacks of many studies in the field of tRFs are that most of them used synthetic RNAs that closely mimic endogenous tRFs in their sequence, yet lack RNA modification that is found in vivo. Here, we developed a simple method to isolate tRNA-derived stress-induced RNAs (tiRNAs), a specific subset of tRFs. Our approach is scalable, cost-effective and relies on the purification of individual tiRNAs based on a sequence-specific RNA/DNA isolation technique using DNA probes. Our method facilitates functional studies of tiRNAs by addressing how physiological RNA modifications within tRNA fragments affect their biological activities. Here, we report pilot functional studies on selected endogenous tiRNAs, namely tiRNA(Ala) and tiRNA(Gly). We show that natural 5MODIFIER LETTER PRIME-tiRNA(Ala) molecules assemble into G-quadruplex structures, and endogenous 5MODIFIER LETTER PRIME-tiRNA(Gly) possesses translation inhibition activity.