The Bioinformatics Centre, Department of Biology, and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen 2200, Denmark.
Genome Res. 2010 Aug;20(8):1010-9. doi: 10.1101/gr.103259.109. Epub 2010 May 27.
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs), bound to Argonaute proteins (RISC), destabilize mRNAs through base-pairing with the mRNA. However, the gene expression changes after perturbations of these small RNAs are only partially explained by predicted miRNA/siRNA targeting. Targeting may be modulated by other mRNA sequence elements such as binding sites for the hundreds of RNA binding proteins (RNA-BPs) expressed in any cell, and this aspect has not been systematically explored. Across a panel of published experiments, we systematically investigated to what extent sequence motifs in 3' untranslated regions (UTRs) correlate with expression changes following transfection of small RNAs. The most significantly overrepresented motifs in down-regulated mRNAs are two novel U-rich motifs (URMs), UUUUAAA and UUUGUUU, recently discovered as binding sites for the ELAVL4 (also known as HuD) RNA-BP. Surprisingly, the most significantly overrepresented motif in up-regulated mRNAs is the heptanucleotide AU-rich element (ARE), UAUUUAU, which is known to affect mRNA stability via at least 20 different RNA-BPs. We show that destabilization mediated by the transfected miRNA is generally attenuated by ARE motifs and augmented by URM motifs. These ARE and URM signatures were confirmed in different types of published experiments covering eight different cell lines. Finally, we show that both ARE and URM motifs couple to presumed endogenous miRNA binding sites in mRNAs bound by Argonaute proteins. This is the first systematic investigation of 3' UTR motifs that globally couple to regulation by miRNAs and may potentially antagonize or cooperate with miRNA/siRNA regulation. Our results suggest that binding sites of miRNAs and RNA-BPs should be considered in combination when interpreting and predicting miRNA regulation in vivo.
微小 RNA（miRNA）和小干扰 RNA（siRNA）与 Argonaute 蛋白（RISC）结合，通过与 mRNA 碱基配对使 mRNA 不稳定。然而，这些小 RNA 干扰后基因表达的变化仅部分可以通过预测的 miRNA/siRNA 靶向来解释。靶向可能受到其他 mRNA 序列元件的调节，例如结合数百种在任何细胞中表达的 RNA 结合蛋白（RNA-BP）的结合位点，而这一方面尚未得到系统的探索。在一组已发表的实验中，我们系统地研究了 3'非翻译区（UTR）中的序列基序在小 RNA 转染后与表达变化相关的程度。下调 mRNA 中最显著过表达的基序是两个新的 U 丰富基序（URM），UUUUAAA 和 UUUGUUU，最近被发现是 ELAVL4（也称为 HuD）RNA-BP 的结合位点。令人惊讶的是，上调 mRNA 中最显著过表达的基序是七核苷酸 AU 丰富元件（ARE），UUUUAU，该基序通过至少 20 种不同的 RNA-BP 影响 mRNA 稳定性。我们表明，转染 miRNA 介导的失稳通常被 ARE 基序减弱，而被 URM 基序增强。这些 ARE 和 URM 特征在涵盖八种不同细胞系的八种不同类型的已发表实验中得到了证实。最后，我们表明，ARE 和 URM 基序都与 Argonaute 蛋白结合的 mRNAs 中的假定内源性 miRNA 结合位点相关联。这是首次对与 miRNA 调节全局相关的 3'UTR 基序进行的系统研究，这些基序可能与 miRNA/siRNA 调节拮抗或合作。我们的结果表明，在体内解释和预测 miRNA 调节时，应考虑 miRNA 和 RNA-BP 的结合位点。
