Gene expression regulation by upstream open reading frames and human disease

Abstract

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.

Figure 1. uORF-mediated translational control can occur through different mechanisms.

(A) The leaky scanning mechanism is dependent on the efficiency of uAUG recognition; sometimes the ribosome can translate the uORF, but other times the scanning machinery bypasses the uAUG, recognizing the downstream AUG and translating the main ORF. (B) When a scanning ribosome recognizes 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 peptide-dependent manner; in this case, the uORF-encoded peptide interacts with the translating machinery and promotes ribosome blockage. (D) The termination codon of a uORF can be recognized as premature and nonsense-mediated mRNA decay (NMD) is triggered through a mechanism involving the UPF1 protein and ribonucleases. (E) After translation termination of the uORF, the 40S ribosomal subunit can remain associated with the transcript, resume scanning, and recognize the downstream main AUG—a mechanism designated as translation reinitiation. (F) The impact that the uORFs can have on translation depends on (i) distance between the 5′ cap (m⁷G) and the uORF (distance to the cap), (ii) context in which the uORF AUG is located (AUG context), (iii) length of the uORF, (iv) number of uORFs per transcript, (v) secondary structure of the uORF, (vi) conservation among species, (vii) length of the intercistronic sequence(s), and (viii) position of the uORF termination codon, upstream or downstream of the main initiation codon (length, number, secondary structure, conservation, position of stop codon). The increase of translational repression exerted by a uORF correlates with increasing distance between the m⁷G and the uORF, increasing length of the uORF and intercistronic sequence, a higher number of uORFs, and a stronger uAUG Kozak context. (G) In response to stress conditions, the presence of more than one uORF in a transcript can promote an increase in translation efficiency of the main ORF; the reinitiation after translation of the uORF1 is less efficient since there is less ternary complex available. Consequently, reinitiation will take more time/distance to occur and the ternary complex will only be available by the time the 40S ribosomal subunit has already bypassed the subsequent uORFs, augmenting the recognition of the main AUG. (H) In response to stress conditions, the presence of one uORF 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.

Figure 2. Examples of human genes encoding mRNAs that, under stress conditions, evade global repression of translation and are upregulated due to the presence of uORFs.

For each mRNA, the schematic representation of the 5′ leader sequence is shown with the length (in nucleotides; nts) indicated below each representation; boxes with numbers represent the uORF(s), where the number indicates the corresponding length in codons.