fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
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DOI：
10.1016/j.xpro.2021.100762
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发表时间：
2021-09-17
期刊：
影响因子：
--
通讯作者：
Yeo GW
中科院分区：
文献类型：
--
作者：
Corley M;Flynn RA;Blue SM;Yee BA;Chang HY;Yeo GW
引物延伸（SHAPE）结构探针技术分析了RNA分子的选择性2′-羟基酰化反应，从而表征了RNA分子的二级结构，而二级结构影响RNA分子的功能和相互作用。SHAPE的一种变体，足迹法SHAPE（fSHAPE），在蛋白质存在和不存在的情况下探测RNA，以鉴定与蛋白质氢键结合的RNA碱基。SHAPE或fSHAPE与增强的交联和免疫沉淀（SHAPE-eCLIP或fSHAPE-eCLIP）偶联，拉下与任何感兴趣的蛋白质结合的RNA，并分别返回它们的结构或蛋白质相互作用信息。在这里，我们描述了SHAPE-eCLIP和fSHAPE-eCLIP的详细协议以及fSHAPE的分析协议。有关这些方案的使用和执行的完整详细信息，请参阅。蛋白质-RNA氢键（fSHAPE）和RNA结构（SHAPE）探测方案fSHAPE-eCLIP和SHAPE-eCLIP探针与免疫沉淀蛋白结合的RNA区域在不同条件下平行探测的样品是每个方案的基础探针区域在核苷酸分辨率下产生fSHAPE或SHAPE反应性通过引物延伸（SHAPE）分析选择性2′-羟基酰化结构探测技术表征RNA分子的二级结构，其影响RNA分子的功能和相互作用。SHAPE的一种变体，足迹SHAPE（fSHAPE），在蛋白质存在和不存在的情况下探测RNA以鉴定与蛋白质氢键结合的RNA碱基。SHAPE或fSHAPE与增强的交联和免疫沉淀（SHAPE-eCLIP或fSHAPE-eCLIP）偶联，拉下与任何感兴趣的蛋白质结合的RNA，并分别返回它们的结构或蛋白质相互作用信息。在这里，我们描述了SHAPE-eCLIP和fSHAPE-eCLIP的详细协议以及fSHAPE的分析协议。
Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein to identify RNA bases that hydrogen-bond with protein. SHAPE or fSHAPE coupled with enhanced crosslinking and immunoprecipitation (SHAPE-eCLIP or fSHAPE-eCLIP) pulls down RNAs bound by any protein of interest and returns their structure or protein interaction information, respectively. Here, we describe detailed protocols for SHAPE-eCLIP and fSHAPE-eCLIP and an analysis protocol for fSHAPE. For complete details on the use and execution of these protocols, please refer to. Protocols for probing protein-RNA hydrogen bonds (fSHAPE) and RNA structure (SHAPE) fSHAPE-eCLIP and SHAPE-eCLIP probe RNA regions bound by immunoprecipitated protein Samples probed in parallel under different conditions is the basis of each protocol Probed regions yield fSHAPE or SHAPE reactivities at nucleotide resolution Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein to identify RNA bases that hydrogen-bond with protein. SHAPE or fSHAPE coupled with enhanced crosslinking and immunoprecipitation (SHAPE-eCLIP or fSHAPE-eCLIP) pulls down RNAs bound by any protein of interest and returns their structure or protein interaction information, respectively. Here, we describe detailed protocols for SHAPE-eCLIP and fSHAPE-eCLIP and an analysis protocol for fSHAPE.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
5.8
作者：
Barnett, Derek W.;Garrison, Erik K.;Marth, Gabor T.
通讯作者：
Marth, Gabor T.
DOI：
10.1007/978-1-4939-6433-8_4
发表时间：
2016-01-01
期刊：
RNA STRUCTURE DETERMINATION
影响因子：
--
作者：
DiChiacchio, Laura;Mathews, David H.
通讯作者：
Mathews, David H.
DOI：
10.1186/1748-7188-6-26
发表时间：
2011-11-24
期刊：
Algorithms for molecular biology : AMB
影响因子：
--
作者：
Lorenz R;Bernhart SH;Höner Zu Siederdissen C;Tafer H;Flamm C;Stadler PF;Hofacker IL
通讯作者：
Hofacker IL
影响因子：
14.8
作者：
Flynn RA;Zhang QC;Spitale RC;Lee B;Mumbach MR;Chang HY
通讯作者：
Chang HY