Lee Inhan, Ajay Subramanian S, Yook Jong In, Kim Hyun Sil, Hong Su Hyung, Kim Nam Hee, Dhanasekaran Saravana M, Chinnaiyan Arul M, Athey Brian D
Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48109, USA.
Genome Res. 2009 Jul;19(7):1175-83. doi: 10.1101/gr.089367.108. Epub 2009 Mar 31.
MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant interaction sites in the human-enriched, less conserved 5'-UTR miRNA motifs, while human-specific miRNAs have significant interaction sites only in the conserved 5'-UTR motifs, implying both miRNA and 5'-UTR are actively evolving in response to each other. Additionally, many miRNAs with their 3'-end interaction sites in the 5'-UTRs turn out to simultaneously contain 5'-end interaction sites in the 3'-UTRs. Based on these findings we demonstrate combinatory interactions between a single miRNA and both end regions of an mRNA using model systems. We further show that genes exhibiting large-scale protein changes due to miRNA overexpression or deletion contain both UTR interaction sites predicted. We provide the predicted targets of this new miRNA target class, miBridge, as an efficient way to screen potential targets, especially for nonconserved miRNAs, since the target search space is reduced by an order of magnitude compared with the 3'-UTR alone. Efficacy is confirmed by showing SEC24D regulation with hsa-miR-605, a miRNA identified only in primate, opening the door to the study of nonconserved miRNAs. Finally, miRNAs (and associated proteins) involved in this new targeting class may prevent 40S ribosome scanning through the 5'-UTR and keep it from reaching the start-codon, preventing 60S association.
已知微小RNA（miRNA）通过3'-非翻译区（3'-UTR）在转录后调控靶mRNA，在动物中，3'-UTR主要与miRNA的5'-端相互作用。在此，我们在人类5'-UTR中鉴定出许多特定于miRNA 3'-端的内源性基序。尤其是保守miRNA的3'-端在人类富集的、保守性较低的5'-UTR miRNA基序中有显著的相互作用位点，而人类特异性miRNA仅在保守的5'-UTR基序中有显著的相互作用位点，这意味着miRNA和5'-UTR都在相互响应中积极进化。此外，许多在5'-UTR中有3'-端相互作用位点的miRNA在3'-UTR中同时也含有5'-端相互作用位点。基于这些发现，我们使用模型系统证明了单个miRNA与mRNA两端区域之间的组合相互作用。我们进一步表明，由于miRNA过表达或缺失而表现出大规模蛋白质变化的基因含有预测的两个UTR相互作用位点。我们提供了这种新的miRNA靶标类别miBridge的预测靶标，作为筛选潜在靶标的有效方法，特别是对于非保守miRNA，因为与仅3'-UTR相比，靶标搜索空间减少了一个数量级。通过用hsa-miR-605（一种仅在灵长类动物中鉴定出的miRNA）调控SEC24D证实了其有效性，这为非保守miRNA的研究打开了大门。最后，参与这种新靶向类别的miRNA（及相关蛋白）可能会阻止40S核糖体扫描5'-UTR并使其无法到达起始密码子，从而阻止60S的结合。
