3'UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells.
3'UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells.
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DOI：
10.1371/journal.pgen.1005879
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发表时间：
2016-02
期刊：
影响因子：
4.5
通讯作者：
Pilpel Y
中科院分区：
文献类型：
--
作者：
Hoffman Y;Bublik DR;Ugalde AP;Elkon R;Biniashvili T;Agami R;Oren M;Pilpel Y
大多数哺乳动物基因通常具有可选择的多聚腺苷酸化（阿帕）位点，因此具有不同的3 'UTR长度。据报道，扩增细胞有利于阿帕位点，导致较短的3 'UTR。这种缩短的一个结果是mRNA从其结合位点被消除的微小RNA（miRNA）的靶向中逃逸。这种机制可能会在正常或癌性增殖过程中为增殖相关基因提供表达增益。值得注意的是，与位于更中心的那些相比，位于3 'UTR两端附近的miRNA位点往往更活跃。因此，位于完整3 'UTR中心附近的miRNA位点可能在3' UTR缩短后变得更活跃。为了解决这一猜想，我们进行了3'测序以确定几种细胞系中所有人UTR的3'末端。值得注意的是，我们发现保守的miRNA结合位点优先富集在紧邻阿帕位点的上游，并且这种富集在促分化/抗增殖基因中更为突出。在快速增殖细胞中上调的miR 17 -92簇的结合位点特别富集在阿帕位点的上游，推测在缩短时赋予更强的抑制活性。因此，3 'UTR缩短似乎不仅能够逃避生长促进基因的抑制，而且还增强了抗增殖基因的抑制。microRNA（miRNAs）是基因表达的调节因子。通常，它们识别基因序列中的结合位点并发挥抑制作用。该方案规定了一个调控网络，确定哪个基因由哪个miRNA调控。然而，这是一个静态的基于序列的方案，可能不支持网络布线中的动态变化。基因是否会以一种依赖于细胞生理状态的方式受到或从miRNA的调控中释放出来？在这里，我们描述这样一个动态机制。已经确定，当它们的结合位点位于靶mRNA的末端附近或紧接在编码序列终止密码子之后时，miRNA调控通常更有效。因此，远离mRNA末端的位点可能是潜在的，因为它不能有效地结合其相应的miRNA。然而，在特定的生理状态下，例如癌症或快速增殖的细胞，mRNA末端倾向于变短。到目前为止，有人认为这种缩短可能有助于通过消除mRNA上的结合位点来释放有利于增殖的基因。我们提出了一个镜像，互补的机制，作用于基因，需要在增殖过程中被抑制。具体来说，我们认为mRNA缩短可以通过使mRNA末端靠近它们来动态激活潜在的抑制性miRNA结合位点。我们绘制了增殖细胞中所有mRNA的末端，发现富含癌症的末端明显位于高密度潜在潜在结合位点的下游，这些位点保留在短mRNA中，但现在靠近新末端。这可能使这种潜在的潜在的miRNA位点在增殖时变得动态激活。值得注意的是，这种机制优先靶向促分化和抗增殖基因，这些基因通常在癌症中受到抑制。
Most mammalian genes often feature alternative polyadenylation (APA) sites and hence diverse 3’UTR lengths. Proliferating cells were reported to favor APA sites that result in shorter 3’UTRs. One consequence of such shortening is escape of mRNAs from targeting by microRNAs (miRNAs) whose binding sites are eliminated. Such a mechanism might provide proliferation-related genes with an expression gain during normal or cancerous proliferation. Notably, miRNA sites tend to be more active when located near both ends of the 3’UTR compared to those located more centrally. Accordingly, miRNA sites located near the center of the full 3’UTR might become more active upon 3'UTR shortening. To address this conjecture we performed 3' sequencing to determine the 3' ends of all human UTRs in several cell lines. Remarkably, we found that conserved miRNA binding sites are preferentially enriched immediately upstream to APA sites, and this enrichment is more prominent in pro-differentiation/anti-proliferative genes. Binding sites of the miR17-92 cluster, upregulated in rapidly proliferating cells, are particularly enriched just upstream to APA sites, presumably conferring stronger inhibitory activity upon shortening. Thus 3’UTR shortening appears not only to enable escape from inhibition of growth promoting genes but also to potentiate repression of anti-proliferative genes. MicroRNAs (miRNAs) are regulators of gene expression. Typically they recognize a binding site in genes' sequences and exert a repressive effect. This scheme prescribes a regulatory network that determines which gene is regulated by which miRNA. Yet this is a static sequence-based scheme that might not support dynamic changes in network wiring. Can genes become subject to, or be released, from the regulation of a miRNA in a manner that depends on the physiological state of cells? Here we describe such a dynamic mechanism. It is established that miRNA regulation is often more effective when their binding sites reside near the end of the target mRNA or right after the coding sequence STOP codon. Thus, a site distant from the mRNA’s end might be latent as it will not bind efficiently its corresponding miRNA. Yet, in particular physiological states, e.g. cancer or rapidly proliferating cells, mRNA ends tend to become shortened. So far it was suggested that such shortening may serve to release proliferation-favoring genes from miRNA repression by eliminating their binding sites from the mRNA. We propose a mirror image, complementary mechanism that acts upon genes that need to be repressed during proliferation. Specifically, we propose that mRNA shortening can dynamically activate latent repressive miRNA binding sites by bringing the mRNA end close to them. We mapped the ends of all mRNAs in proliferating cells and found that cancer-enriched ends are strikingly positioned closely downstream to a high density of potentially latent binding sites, which are retained in the short mRNA but are now close to the new ends. This may enable such potentially latent miRNA sites to become dynamically activated upon proliferation. Remarkably, this mechanism targets preferentially pro-differentiation and antiproliferative genes, which are often repressed in cancer.