专题：Nature系列
尽管RNA结构对其调控和功能很重要，但在实验中已经了解的RNA结构相对很少，而且也没有对RNA结构进行高通过量测量的实验方法。相反，计算方法是全基因组应用的标准方法。不过，新技术已使人们能够在更大规模上对RNA结构进行计算。
Kertesz等人利用一种深度测序方法来确定酿酒酵母整个转录组的结构。他们获得的结果为二级结构在翻译中的作用提供了有趣的提示，并且为研究这类结构何以能根据环境条件而改变搭建了舞台。
生物谷推荐英文摘要：
Nature doi:10.1038/nature09322
Genome-wide measurement of RNA secondary structure in yeast
Michael Kertesz,Yue Wan,Elad Mazor,John L. Rinn,Robert C. Nutter,Howard Y. Chang Eran segal
The structures of RNA molecules are often important for their function and regulation1, 2, 3, 4, 5, 6, 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 messenger RNAs (mRNAs) of the budding yeast Saccharomyces cerevisiae and obtain structural profiles for over 3,000 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 with untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions and an anti-correlation between the efficiency with which an mRNA is translated and the 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.
