Ramani Vijay, Qiu Ruolan, Shendure Jay
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
Nat Biotechnol. 2015 Sep;33(9):980-4. doi: 10.1038/nbt.3289. Epub 2015 Aug 3.
We present an unbiased method to globally resolve RNA structures through pairwise contact measurements between interacting regions. RNA proximity ligation (RPL) uses proximity ligation of native RNA followed by deep sequencing to yield chimeric reads with ligation junctions in the vicinity of structurally proximate bases. We apply RPL in both baker's yeast (Saccharomyces cerevisiae) and human cells and generate contact probability maps for ribosomal and other abundant RNAs, including yeast snoRNAs, the RNA subunit of the signal recognition particle and the yeast U2 spliceosomal RNA homolog. RPL measurements correlate with established secondary structures for these RNA molecules, including stem-loop structures and long-range pseudoknots. We anticipate that RPL will complement the current repertoire of computational and experimental approaches in enabling the high-throughput determination of secondary and tertiary RNA structures.
我们提出了一种通过相互作用区域之间的成对接触测量来全局解析RNA结构的无偏方法。RNA邻近连接（RPL）利用天然RNA的邻近连接，然后进行深度测序，以产生在结构上邻近碱基附近具有连接接头的嵌合读数。我们在面包酵母（酿酒酵母）和人类细胞中应用RPL，并生成核糖体RNA和其他丰富RNA的接触概率图，包括酵母snoRNA、信号识别颗粒的RNA亚基和酵母U2剪接体RNA同源物。RPL测量结果与这些RNA分子已建立的二级结构相关，包括茎环结构和长程假结。我们预计RPL将补充当前的计算和实验方法，以实现高通量确定RNA的二级和三级结构。
