RNA structure probing reveals the structural basis of Dicer binding and cleavage.
RNA structure probing reveals the structural basis of Dicer binding and cleavage.
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RNA 结构探测揭示了 Dicer 结合和切割的结构基础
DOI：
10.1038/s41467-021-23607-w
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发表时间：
2021-06-07
影响因子：
16.6
通讯作者：
Zhang QC
中科院分区：
文献类型：
--
作者：
Luo QJ;Zhang J;Li P;Wang Q;Zhang Y;Roy-Chaudhuri B;Xu J;Kay MA;Zhang QC
众所周知，RNA的结构决定其生物学功能，然而目前的RNA结构探测方法仅捕获部分结构信息。测量完整性的能力（即，全长）RNA结构将有助于研究小RNA的功能和调节机制，并鉴定功能位点的短片段。在这里，我们提出了icSHAPE-MaP，一种结合体内选择性2′-羟基酰化和突变分析来探测完整RNA结构的方法。我们进一步展示了基于RNA免疫沉淀下拉和icSHAPE-MaP小RNA结构分析相结合的人Dicer结合底物的RNA结构景观。我们发现不同的结构类别的切丁酶底物的结合亲和力和切割效率。通过对icSHAPE-MaP RNA结构数据约束的三级结构建模，我们发现空间距离度量是影响Dicer切割位点选择的重要参数。开发了诸如icSHAPE的测序方法以探测细胞中转录组范围的RNA结构。为了探测完整的RNA结构，作者开发了icSHAPE-MaP并应用于Dicer结合的底物，表明距离测量对于pre-miRNA的Dicer切割是重要的。
It is known that an RNA’s structure determines its biological function, yet current RNA structure probing methods only capture partial structure information. The ability to measure intact (i.e., full length) RNA structures will facilitate investigations of the functions and regulation mechanisms of small RNAs and identify short fragments of functional sites. Here, we present icSHAPE-MaP, an approach combining in vivo selective 2′-hydroxyl acylation and mutational profiling to probe intact RNA structures. We further showcase the RNA structural landscape of substrates bound by human Dicer based on the combination of RNA immunoprecipitation pull-down and icSHAPE-MaP small RNA structural profiling. We discover distinct structural categories of Dicer substrates in correlation to both their binding affinity and cleavage efficiency. And by tertiary structural modeling constrained by icSHAPE-MaP RNA structural data, we find the spatial distance measuring as an influential parameter for Dicer cleavage-site selection. Sequencing methods such as icSHAPE were developed to probe RNA structures transcriptome-wide in cells. To probe intact RNA structures, the authors develop icSHAPE-MaP and apply to Dicer-bound substrates showing that distance measuring is important for Dicer cleavage of pre-miRNAs.
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影响因子：
14.9
作者：
Chan PP;Lowe TM
通讯作者：
Lowe TM
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：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
影响因子：
10.5
作者：
Babiarz, Joshua E.;Ruby, J. Graham;Blelloch, Robert
通讯作者：
Blelloch, Robert
影响因子：
16
作者：
Krol, Jacelk;Fiszer, Agnieszka;Krzyzosiak, Wlodzimierz J.
通讯作者：
Krzyzosiak, Wlodzimierz J.