Genome-wide measurement of RNA secondary structure in yeast.
Genome-wide measurement of RNA secondary structure in yeast.
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RNA分子的结构对于它们的功能和调节通常是重要的，但是没有用于RNA结构的基因组规模测量的实验技术。在这里，我们描述了一种称为RNA结构平行分析（PARS）的新策略，该策略基于用结构特异性酶处理的RNA的深度测序片段，从而以单核苷酸分辨率提供数千种RNA种类的二级结构的同时体外分析。我们应用PARS分析了芽殖酵母S.酿酒酵母和获得超过3000个不同的转录本的结构概况。对这些图谱的分析揭示了酵母转录物的几种RNA结构特性，包括与非翻译区相比，编码区存在更多的二级结构，编码区二级结构的三核苷酸周期性，以及mRNA翻译效率与其翻译起始位点缺乏结构之间的关系。PARS很容易适用于其他生物体，并在不同条件下分析RNA结构，从而能够在基因组尺度上研究二级结构的动态。
The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.
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遗传密码产生的mRNA二级结构的周期性模式。
影响因子：
14.9
作者：
Shabalina, Svetlana A.;Ogurtsov, Aleksey Y.;Spiridonov, Nikolay A.
通讯作者：
Spiridonov, Nikolay A.
影响因子：
9.8
作者：
Palazzo AF;Springer M;Shibata Y;Lee CS;Dias AP;Rapoport TA
通讯作者：
Rapoport TA
DOI：
10.1073/pnas.2033246100
发表时间：
2003-09-30
影响因子：
11.1
作者：
Shepard, KA;Gerber, AP;Vale, RD
通讯作者：
Vale, RD
影响因子：
64.5
作者：
Rinn, John L.;Kertesz, Michael;Chang, Howard Y.
通讯作者：
Chang, Howard Y.
DOI：
10.1073/pnas.092538799
发表时间：
2002-04-30
影响因子：
11.1
作者：
Wang, YL;Liu, CL;Brown, PO
通讯作者：
Brown, PO