CIRDES: an efficient genome-wide method for in vivo RNA-RNA interactome analysis.
CIRDES: an efficient genome-wide method for in vivo RNA-RNA interactome analysis.
复制标题
CIRDES：一种有效的全基因组方法，用于体内 RNA-RNA 相互作用组分析。
作者：
Li Yao-Ting;Zhou Nan;Deng Wei-Xi;Zeng Xue-Zhen;Wang Xiao-Juan;Peng Jing-Wen;Yang Bing;Wang Yan-Jie;Liao Jian-You;Yin Dong
复杂的RNA-RNA相互作用是基本生物学过程的基础。然而，大量的RNA-RNA相互作用仍然未知。大多数现有的用于绘制RNA-RNA相互作用的方法都是基于邻近连接，但这些策略也捕获了大量的分子内RNA二级结构，使得几乎不可能检测到大多数RNA-RNA相互作用。为了克服这一限制，我们开发了一种有效的全基因组方法，捕获相互作用RNA和深度测序（CIRDES），用于体内捕获RNA相互作用组。我们设计了多个20-nt的CIRDES探针，平铺感兴趣的整个RNA序列。qRT-PCR结果表明，该策略具有较高的选择性和较低的背景噪声。CIRDES从甲醛交联的细胞中高效富集靶RNA及其相互作用RNA。在杂交和纯化后，基于衔接子连接文库构建，在与3'端红外染料缀合的RNA衔接子高效连接后，将捕获的RNA转化为cDNA文库。使用CIRDES，我们检测到高度丰富的已知相互作用RNA，以及大量的U6 snRNA的新靶点。与U6相互作用的U4 snRNA的富集证实了CIRDES鉴定RNA-RNA相互作用的稳健性。这些结果表明CIRDES是全基因组RNA-RNA相互作用组分析的有效策略。
Complex RNA-RNA interactions underlie fundamental biological processes. However, a large number of RNA-RNA interactions remain unknown. Most existing methods used to map RNA-RNA interactions are based on proximity ligation, but these strategies also capture a huge amount of intramolecular RNA secondary structures, making it almost impossible to detect most RNA-RNA interactions. To overcome this limitation, we developed an efficient, genome-wide method, Capture Interacting RNA and Deep Sequencing (CIRDES) for in vivo capturing of the RNA interactome. We designed multiple 20-nt CIRDES probes tiling the whole RNA sequence of interest. This strategy obtained high selectivity and low background noise proved by qRT-PCR data. CIRDES enriched target RNA and its interacting RNAs from cells crosslinked by formaldehyde in high efficiency. After hybridization and purification, the captured RNAs were converted to the cDNA library after a highly efficient ligation to a 3' end infrared-dye-conjugated RNA adapter based on adapter ligation library construction. Using CIRDES, we detected highly abundant known interacting RNA, as well as a large number of novel targets of U6 snRNA. The enrichment of U4 snRNA, which interacts with U6, confirmed the robustness of the identification of the RNA-RNA interaction by CIRDES. These results suggest that the CIRDES is an efficient strategy for genome-wide RNA-RNA interactome analysis.
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DOI：
10.1016/b978-0-12-809633-8.20106-4
发表时间：
2020-02
期刊：
--
影响因子：
--
作者：
A. Prjibelski;Anton I. Korobeynikov;Alla L. Lapidus
通讯作者：
A. Prjibelski;Anton I. Korobeynikov;Alla L. Lapidus
影响因子：
48
作者：
Van Nostrand EL;Pratt GA;Shishkin AA;Gelboin-Burkhart C;Fang MY;Sundararaman B;Blue SM;Nguyen TB;Surka C;Elkins K;Stanton R;Rigo F;Guttman M;Yeo GW
通讯作者：
Yeo GW
影响因子：
16
作者：
Sharma, Eesha;Sterne-Weiler, Tim;Blencowe, Benjamin J.
通讯作者：
Blencowe, Benjamin J.
DOI：
10.1126/science.1237973
发表时间：
2013-08-16
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Engreitz JM;Pandya-Jones A;McDonel P;Shishkin A;Sirokman K;Surka C;Kadri S;Xing J;Goren A;Lander ES;Plath K;Guttman M
通讯作者：
Guttman M
影响因子：
12.3
作者：
Zhang, Yong;Liu, Tao;Meyer, Clifford A.;Eeckhoute, Jerome;Johnson, David S.;Bernstein, Bradley E.;Nussbaum, Chad;Myers, Richard M.;Brown, Myles;Li, Wei;Liu, X. Shirley
通讯作者：
Liu, X. Shirley