SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data.
SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data.
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DOI：
10.1261/rna.047068.114
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发表时间：
2015-05
期刊：
影响因子：
--
通讯作者：
Vinther J
中科院分区：
文献类型：
--
作者：
Poulsen LD;Kielpinski LJ;Salama SR;Krogh A;Vinther J
引物延伸分析选择性2‘羟基酰化反应(SHAPE)是一种准确探测RNA二级结构的方法。在现有的SHAPE方法中，SHAPE探测信号被归一化为无试剂对照，以校正因逆转录酶过早终止而引起的背景。在这里，我们介绍了一种择形(SHAPE)试剂，N-丙酮异酸酐(NPIA)，它保留了SHAPE试剂准确探测RNA结构的能力，但也允许SHAPE试剂与生物素分子之间的共价偶联。我们证明，在链霉亲和素珠上基于形状选择cDNA-RNA杂交物有效地消除了形状探测数据中存在的绝大多数背景信号，并且基于测序的形状数据包含的RNA结构数据与通过归一化到无试剂对照获得的常规基于测序的形状数据相同。此外，该选择有效地丰富了被探测的RNA，表明形状策略将适用于高背景和低探测信号的应用，如体内RNA结构探测。
Selective 2′ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA–RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing.
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DOI：
10.1007/978-1-61779-292-2_11
发表时间：
2012
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Takahashi, Hazuki;Kato, Sachi;Murata, Mitsuyoshi;Carninci, Piero
通讯作者：
Carninci, Piero
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
DOI：
10.1093/bioinformatics/btp250
发表时间：
2009-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Darty K;Denise A;Ponty Y
通讯作者：
Ponty Y
影响因子：
4.5
作者：
Karabiber, Fethullah;McGinnis, Jennifer L.;Weeks, Kevin M.
通讯作者：
Weeks, Kevin M.
影响因子：
6.8
作者：
Gutell, RR;Lee, JC;Cannone, JJ
通讯作者：
Cannone, JJ