Mechanisms of miRNA-Mediated Gene Regulation from Common Downregulation to mRNA-Specific Upregulation

Abstract

Discovered in 1993, micoRNAs (miRNAs) are now recognized as one of the major regulatory gene families in eukaryotes. To date, 24521 microRNAs have been discovered and there are certainly more to come. It was primarily acknowledged that miRNAs result in gene expression repression at both the level of mRNA stability by conducting mRNA degradation and the level of translation (at initiation and after initiation) by inhibiting protein translation or degrading the polypeptides through binding complementarily to 3'UTR of the target mRNAs. Nevertheless, some studies revealed that miRNAs have the capability of activating gene expression directly or indirectly in respond to different cell types and conditions and in the presence of distinct cofactors. This reversibility in their posttranslational gene regulatory natures enables the bearing cells to rapidly response to different cell conditions and consequently block unnecessary energy wastage or maintain the cell state. This paper provides an overview of the current understandings of the miRNA characteristics including their genes and biogenesis, as well as their mediated downregulation. We also review up-to-date knowledge of miRNA-mediated gene upregulation through highlighting some notable examples and discuss the emerging concepts of their associations with other posttranscriptional gene regulation processes.

Figure 1

Potential mechanisms of miRNA-mediated downregulation. Ribonucleoproteins (miRNPs) target mRNAs through sequence complementation. The association between miRNPs and mRNAs can have one or several consequences. miRNP-mediated downregulation may have direct and indirect mechanisms and occur before translation is triggered or after translation initiation. (a–c) Translation initiation mechanisms. miRNP interferes with early steps of translation before elongation. (a) miRNPs recruit several factors and enzymes for mRNA cleavage and degradation including decapping enzymes, deadenylase, 3′ and 5′ exonucleases, and endonucleases. (b, c) Argonaute protein competes with cap binding proteins (CBPs) and elf4E for binding to cap structure and inhibits translation initiation by interfering with mRNA circularization and formation of closed-loop achieved through cap structure interaction with CBPs and elf4E/G required for translation initiation. (d–h) Postinitiation mechanisms. miRNPs repress translation elongation and termination or involve in protein degradation and sequestration. (d, e) miRNP interferes with ribosome subunit by inhibiting its joining or promoting its dissociation. (f, g) miRNP obstructs translation elongation by competing with elongation factors or cotranslationally recruiting protein decay factors such as exosomes. (h) Target mRNA is sequestered from translation machinery and stored or sometimes is degraded by enzymes. However, alternatively, translationally inhibited mRNA along with associated proteins could be sequestered at the same bodies. For explanations in support of illustrations, refer to the main text.

Figure 2

miRNA-mediated upregulation according to cell cycle phase. miR-334 and miR-27a bind to the 3′UTR of KLF4 and Myt1 mRNA in proliferating and cancerous cells and subsequently downregulate mRNA expression by both translational inhibition and mRNA degradation. miRNP-mediated repression requires factors including AGO, GW182, deadenylases, and nucleases. However, in G0 cells and immature oocytes, GW182 is downregulated and FXR1 is associated with AGO2 bearing miRNP and leads to gene expression upregulation. miR-206 is associated with KLF4 mRNA in G0 cells and xmiR-16 is associated with Myt1 mRNA in immature Xenopus oocyte. miR-206 and xmiR-16 activate KLF4 and Myt1 expression, respectively, by binding to their 3′UTRs and recruiting special factors such as FXR1, since AGO2 is associated with gene expression activation in these cells and lacks slicer activity.

Figure 3

Activation of hepatitis C virus (HCV) expression by miR-122, a liver-specific microRNA. The mature single-stranded miR-122 is processed from its double- stranded precursor and incorporated into functional miRNP, bearing AGO2. miRNPs target one or two tandem binding sites in the 5′ noncoding region (5′NCR) of HCV RNA. HCV appears to usurp the miRNP to increase its RNA accumulation by a number of mechanisms. (a) First, miR-122 complexes provide a scaffold for the binding of essential factors such polymerase for RNA replication. (b) In addition, miRNP complexes increase the association of 40s ribosome subunit, and thus, result in increased translation and protein yield. (c) They also form an unusual oligomeric complex in 5′ end of HCV RNA and result in HCV RNA stability enhancement by masking its single-stranded 5′end through hiding 5′NCR from 5′ cytoplasmic exonucleases and immune sensors. (d) Also, miR-122 binding was reported to lead to increased propagation and life cycle of virus by some ill-defined mechanisms.

Figure 4

Relief of miRNA-mediated CAT-1 repression according to cell response to radiation. High AMP/ADP in cell is accompanied by the cell exposure to radiation. Consequently, AMP-kinase activity is enhanced, which then leads to HuR (an RNA binding protein that interacts with ARE in 3′UTR of the mRNA) dephosphorylation, releasing from nucleus to cytoplasm and entering to processing bodies (PBs). In P bodies, HuR dissociates miRNP from CAT-1 mRNA and mobilizes it to stress granules (SGs). Within SGs, CAT-1 expression is elevated via recruiting polysomes and relieved from miR-122-mediated downregulation by HuR replacement of miRNP in PBs. Moreover, HuR binds to ARE sites of mRNAs in nucleus and chaperones them to the cytoplasm which then are relocalized in polysomes and contributes in delays onset of RNA decay by competing with AMD effectors.