Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.
mRNA surveillance pathways selectively clear defective mRNAs from the cell. As such, these pathways serve as important modifiers of genetic disorders. Nonsense-mediated decay (NMD), the most intensively studied surveillance pathway, recognizes mRNAs with premature termination codons (PTCs). In mammalian systems the location of a PTC more than 50 nucleotides 59 to the terminal exon-exon junction is a critical determinant of NMD. However, mRNAs with nonsense codons that fulfill this requirement but are located very early in the open reading frame can effectively evade NMD. The unexpected resistance of such mRNAs with AUG-proximal PTCs to accelerated decay suggests that important determinants of NMD remain to be identified. Here, we report that an NMD-sensitive mRNA can be stabilized by artificially tethering the cytoplasmic poly(A) binding protein 1, PABPC1, at a PTC-proximal position. Remarkably, the data further suggest that NMD of an mRNA with an AUG-proximal PTC can also be repressed by PABPC1, which might be brought into proximity with the PTC during cap-dependent translation and 43S scanning. These results reveal a novel parameter of NMD in mammalian cells that can account for the stability of mRNAs with AUG-proximal PTCs. These findings serve to expand current mechanistic models of NMD and mRNA translation.
Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that degrades mRNAs containing premature translation termination codons. In mammalian cells, a termination codon is ordinarily recognized as "premature" if it is located greater than 50 -54 nucleotides 5 to the final exon-exon junction. We have described a set of naturally occurring human -globin gene mutations that apparently contradict this rule. The corresponding -thalassemia genes contain nonsense mutations within exon 1, and yet their encoded mRNAs accumulate to levels approaching wild-type -globin ( WT ) mRNA. In the present report we demonstrate that the stabilities of these mRNAs with nonsense mutations in exon 1 are intermediate between WT mRNA and -globin mRNA carrying a prototype NMD-sensitive mutation in exon 2 (codon 39 nonsense; 39). Functional analyses of these mRNAs with 5-proximal nonsense mutations demonstrate that their relative resistance to NMD does not reflect abnormal RNA splicing or translation re-initiation and is independent of promoter identity and erythroid specificity. Instead, the proximity of the nonsense codon to the translation initiation AUG constitutes a major determinant of NMD. Positioning a termination mutation at the 5 terminus of the coding region blunts mRNA destabilization, and this effect is dominant to the "50 -54 nt boundary rule." These observations impact on current models of NMD.Nonsense-mediated mRNA decay (NMD) 1 is an mRNA surveillance mechanism that rapidly degrades mRNAs carrying premature translation termination codons (1). Nonsense-containing mRNAs targeted by NMD can be generated by naturally occurring frameshift and nonsense mutations, splicing errors, leaky 40 S scanning, and utilization of minor AUG initiation sites (2, 3). A major function of the NMD pathway is to block the synthesis of truncated proteins that could have dominant negative effects on cell function (2, 4).Recent studies have shown that the NMD pathway in mammalian cells is linked to splicing-dependent deposition of a protein complex 20 -24 nucleotides (nt) 5Ј of each exon-exon junction (exon-junction complex; EJC). The EJC contains the general splicing activator RNPS1, the RNA export factor Aly/ REF, the shuttling protein Y14, the nuclear matrix-localized serine-arginine-containing protein SRm160, the oncoprotein DEK, and the Y14 binding protein magoh. The interaction of magoh with Y14 may have a role in cytoplasmic localization of mRNAs and in anchoring the NMD-specific factors Upf3 and Upf2 to the mRNA (5-18). Previous published data have shown that Upf3 and Upf2 join the EJC in different subcellular compartments: Upf3 (Upf3a and Upf3b) is loaded onto mRNAs in the nucleus during splicing via interactions with components of the EJC. In contrast, Upf2 joins the complex soon after cytoplasmic export is initiated (14,19,20). According to the present models, translating ribosomes displace EJCs from the open reading frame (ORF) during the "pioneer" round of cytoplasmic translation (21). If, however, the mRNA contains a pr...
The scanning model for eukaryotic mRNA translation initiation states that the small ribosomal subunit, along with initiation factors, binds at the cap structure at the 5' end of the mRNA and scans the 5' untranslated region (5'UTR) until an initiation codon is found. However, under conditions that impair canonical cap-dependent translation, the synthesis of some proteins is kept by alternative mechanisms that are required for cell survival and stress recovery. Alternative modes of translation initiation include cap- and/or scanning-independent mechanisms of ribosomal recruitment. In most cap-independent translation initiation events there is a direct recruitment of the 40S ribosome into a position upstream, or directly at, the initiation codon via a specific internal ribosome entry site (IRES) element in the 5'UTR. Yet, in some cellular mRNAs, a different translation initiation mechanism that is neither cap- nor IRES-dependent seems to occur through a special RNA structure called cap-independent translational enhancer (CITE). Recent evidence uncovered a distinct mechanism through which mRNAs containing N -methyladenosine (mA) residues in their 5'UTR directly bind eukaryotic initiation factor 3 (eIF3) and the 40S ribosomal subunit in order to initiate translation in the absence of the cap-binding proteins. This review focuses on the important role of cap-independent translation mechanisms in human cells and how these alternative mechanisms can either act individually or cooperate with other cis-acting RNA regulons to orchestrate specific translational responses triggered upon several cellular stress states, and diseases such as cancer. Elucidation of these non-canonical mechanisms reveals the complexity of translational control and points out their potential as prospective novel therapeutic targets.
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