Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding.
Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding.
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DOI：
10.1016/j.cell.2013.03.043
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发表时间：
2013-04-25
期刊：
影响因子：
64.5
通讯作者：
Tollervey D
中科院分区：
文献类型：
--
作者：
Helwak A;Kudla G;Dudnakova T;Tollervey D
微小RNA（miRNAs）在基因调控中起着关键作用，但对其靶标的可靠的生物信息学或实验鉴定仍然很困难。为了提供对人类miRNA靶点的公正看法，我们开发了一种用于连接和测序与人类AGO 1相关的miRNA-靶RNA双链体的技术。在这里，我们报告了超过18，000个高置信度miRNA-mRNA相互作用的数据集。大多数miRNAs的结合包括5′种子区域，但大约60%的种子相互作用是非典型的，包含凸起或错配的核苷酸。此外，种子相互作用通常伴随着特定的非种子碱基配对。18%的miRNA-mRNA相互作用涉及miRNA 3′端，几乎没有证据表明5′端接触，其中一些在功能上得到了验证。对miRNA：mRNA碱基配对的分析表明，miRNA物种在其靶RNA相互作用方面存在系统性差异，并且在几种miRNA的相互作用位点中发现了强烈过度表达的基序。我们推测这些影响RISC对miRNA靶结合的反应。一种实验方法鉴定了miRNA的体内靶点miRNA显示出频繁的mRNA非经典靶向非种子相互作用是常见的，功能性miRNA碱基配对显示出不同的模式和过度表达的基序CLASH方法鉴定了人类细胞中miRNA和mRNA分子之间的18，000多种相互作用，揭示了许多涉及凸出或错配核苷酸的非经典相互作用，以及miRNAs 5′“种子”区域外的相互作用。
MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5′ seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3′ end, with little evidence for 5′ contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding. A experimental approach identifies in vivo targets for miRNAs miRNAs show frequent noncanonical targeting of mRNAs Nonseed interactions are common and functional miRNA base pairing shows distinct patterns and overrepresented motifs The CLASH approach identifies more than 18,000 interactions between miRNA and mRNA molecules in human cells, revealing many noncanonical interactions involving bulged or mismatched nucleotides, as well as interactions outside the proposed 5′ “seed” region of miRNAs.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
DOI：
10.3791/2034
发表时间：
2010-07-02
期刊：
Journal of visualized experiments : JoVE
影响因子：
--
作者：
Hafner, Markus;Landthaler, Markus;Tuschl, Thomas
通讯作者：
Tuschl, Thomas
影响因子：
16
作者：
Lal A;Navarro F;Maher CA;Maliszewski LE;Yan N;O'Day E;Chowdhury D;Dykxhoorn DM;Tsai P;Hofmann O;Becker KG;Gorospe M;Hide W;Lieberman J
通讯作者：
Lieberman J
影响因子：
64.5
作者：
Elkayam E;Kuhn CD;Tocilj A;Haase AD;Greene EM;Hannon GJ;Joshua-Tor L
通讯作者：
Joshua-Tor L