通过 PAR-CLIP 进行 miRNA 靶基因的全基因组鉴定。
Genome-wide identification of miRNA targets by PAR-CLIP.
机构信息
Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
出版信息
Methods. 2012 Oct;58(2):94-105. doi: 10.1016/j.ymeth.2012.08.006. Epub 2012 Aug 19.
Abstract
miRNAs are short (20-23 nt) RNAs that are loaded into proteins of the Argonaute (AGO) family and guide them to partially complementary target sites on mRNAs, resulting in mRNA destabilization and/or translational repression. It is estimated that about 60% of the mammalian genes are potentially regulated by miRNAs, and therefore methods for experimental miRNA target determination have become valuable tools for the characterization of posttranscriptional gene regulation. Here we present a step-by-step protocol and guidelines for the computational analysis for the large-scale identification of miRNA target sites in cultured cells by photoactivatable ribonucleoside enhanced crosslinking and immunoprecipitation (PAR-CLIP) of AGO proteins.
摘要
miRNAs 是短链（20-23 个核苷酸）RNA，可以与 Argonaute（AGO）家族的蛋白质结合，并指导它们与 mRNA 上的部分互补靶位点结合，导致 mRNA 不稳定和/或翻译抑制。据估计，大约 60%的哺乳动物基因可能受到 miRNAs 的调控，因此，实验性 miRNA 靶标确定方法已成为描述转录后基因调控的有价值的工具。这里我们提供了一个分步协议和指南，用于通过 AGO 蛋白的光激活核苷酸增强交联和免疫沉淀（PAR-CLIP）对培养细胞中的 miRNA 靶位点进行大规模鉴定的计算分析。
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Nucleic Acids Res. 2012 Nov 1;40(20):e160. doi: 10.1093/nar/gks697. Epub 2012 Jul 28.
2
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Cell. 2012 Jun 8;149(6):1393-406. doi: 10.1016/j.cell.2012.04.031. Epub 2012 May 31.
3
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