Upstream Open Reading Frames and Human Genetic Disease

Abstract

In many eukaryotic messenger ribonucleic acids (mRNAs) one or more short upstream open reading frames (uORFs) precede the initiation codon of the main coding region. For example, in human cells, uORFs are present in about half of the transcripts. Emerging ribosome profiling and peptidomics analyses have recently shown that these uORFs are translated into polypeptides that seem to serve important biological functions. In addition, very interesting examples have shown that these uORFs are cis‐acting RNA elements that can impact gene expression by repressing translation of the downstream main ORF under control conditions and derepressing it under certain pathophysiological stresses. Furthermore, evidence from genetic and bioinformatic studies implicate disturbed uORF‐mediated translational control in the aetiology of human diseases. Identifying more cases and understanding the aberrant mechanisms of uORF‐mediated translational control, as well as discovering the biological function of the uORF‐encoded polypeptides, is fundamental to advance in diagnosis, prognosis and treatment of many human disorders.

Key Concepts:

  • Upstream open reading frames (uORFs) are cis‐acting RNA elements involved in translational regulation, which precede the initiation codon of the main coding region.

  • For a uORF to function as a translational regulatory element, its initiation codon must be recognised, at least at certain times, by the scanning 40S ribosomal subunit and associated translation initiation factors.

  • uORFs can impact gene expression by repressing translation of the downstream main ORF under control conditions, and derepressing it under certain pathophysiological stresses.

  • The impact the uORFs can have on translation depends on variables, such as (1) the distance between the 5′ cap and the uORF, (2) the context in which the uORF AUG (or non‐AUG) is located, (3) the length of the uORF, (4) the sequence and secondary structure of the uORF, (5) the number of uORFs per transcript, (6) the position of the uORF termination codon and (7) the length of the intercistronic sequence(s).

  • uORF‐encoded polypeptides might serve functional roles in cells.

  • Polymorphisms or mutations that introduce/eliminate uORFs or modify the uORF‐encoded peptide can cause human disease.

  • Understanding the mechanisms through which the uORFs regulate gene expression may lead to innovation in diagnosis, prognosis and treatment of many human disorders.

Keywords: upstream open reading frame (uORF); protein synthesis; polypeptide; translational control; gene expression regulation; human genetic disease

Figure 1.

Mechanisms by which uORFs can affect gene expression. (a) The leaky scanning mechanism is dependent on the efficiency of the uAUG (or non‐uAUG) recognition; sometimes the ribosome can translate the uORF, but other timess the scanning machinery bypasses the uAUG, recognising the downstream AUG and translating the main ORF. (b) When a scanning ribosome recognises and translates a functional uORF, there is synthesis of a small peptide; if translation termination of the uORF is efficient, both 60S and 40S ribosomal subunits might dissociate from the transcript and the main ORF is not translated. (c) A uORF can repress translation of the main ORF in a nucleotide or peptide‐dependent manner; in this last case, the uORF‐encoded peptide interacts with the translating machinery and promotes ribosome blockage. Also, the uORF nucleotide sequence can have a role on its translation efficiency, for instance by encoding rare codons that cause the ribosome to stall. (d) After translation termination of the uORF, the 40S ribosomal subunit can remain associated with the transcript, resume scanning and recognise the downstream main AUG – a mechanism designated as translation reinitiation. (e) In response to stress conditions, the presence of one ORF in a transcript can promote an increase of the corresponding protein levels; the higher levels of phosphorylated eIF2α contribute to increase leaky scanning of the uORF and translation of the main ORF is favored. (f) The 5′‐leader sequence containing a uORF, or the uORF, can present a strong secondary structure that impedes the translation of the main ORF by blocking the ribosome. (g) Some uORF‐encoded peptides can affect translation efficiency of the main ORF by trans‐acting in another molecule of transcript. (h) Some uORF‐encoded peptides can play a function in mechanisms other than translational control, for example in DNA repair. (i) The termination codon of a uORF can be recognised as premature and nonsense‐mediated mRNA decay (NMD) is triggered through a mechanism involving the UPF1 protein and ribonucleases. (j) The impact that the uORFs can have on translation depends on (1) distance between the 5′ cap and the uORF (distance to the cap), (2) context in which the uORF AUG (or non‐AUG) is located (AUG context), (3) length of the uORF, (4) number of uORFs per transcript, (5) sequence and secondary structure of the uORF, (6) presence of non‐AUG start codon(s) (7) length of the intercistronic sequence(s) and/or distance between uORFs and (8) position of the uORF termination codon, upstream or downstream of the main initiation codon.

Figure 2.

uORF‐mediated translational deregulation and human disease. Polymorphisms, mutations, alternative processing or other alterations in the transcript that can create, disrupt or modify a uORF (a, b and c, respectively) may affect translational efficiency of the main ORF, as well as the individual phenotype, and culminate in a pathological condition.

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Further Reading

Gebauer F and Hentze MW (2004) Molecular mechanisms of translational control. Nature Review Molecular Cell Biology 5(10): 827–835.

Pestova TV, Lorsch JR and Hellen CUT (2007) The mechanism of translation initiation in eukaryotes. In: Mathews MB, Sonenberg N and Hershey JWB (eds) Translational Control in Biology and Medicine, pp. 87–128. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

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Barbosa, Cristina, Onofre, Cláudia, and Romão, Luísa(Aug 2014) Upstream Open Reading Frames and Human Genetic Disease. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0025714]