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.

Disruption ofTWIST1translation by 5′ UTR variants in Saethre-Chotzen syndrome

“…Approximately 50% of mammalian 5′ UTRs contain uORFs that generally act as repressive regulators of gene activity (Calvo et al., ; Johnstone, Bazzini, & Giraldez, ; Ye et al., ), with control of translation mediated through several different mechanisms (Cabrera‐Quio, Herberg, & Pauli, ; Wethmar, ). The number of diseases known to be caused by mutations that introduce or disrupt uORFs is increasing (Barbosa, Onofre, & Romao, ; Calvo et al., ; Chatterjee, Rao, & Pal, ) and, in this work, we show that a uORF‐generating variant (c.‐263C > A) in the 5′ UTR of TWIST1 likely leads to SCS. Although there are >50 different SNVs within the TWIST1 5′ UTR catalogued in the gnomAD database, none creates an uAUG (A), and TWIST1 is unusual in having a relatively long 5′ UTR without an uAUG (B).…”

“…Approximately 50% of mammalian 5 ′ UTRs contain uORFs that generally act as repressive regulators of gene activity (Calvo et al, 2009;Johnstone, Bazzini, & Giraldez, 2016;Ye et al, 2015), with control of translation mediated through several different mechanisms (Cabrera-Quio, Herberg, & Pauli, 2016;Wethmar, 2014). The number of diseases known to be caused by mutations that introduce or disrupt uORFs is increasing (Barbosa, Onofre, & Romao, 2014;Calvo et al, 2009;Chatterjee, Rao, & Pal, 2017) Figure S3A), and TWIST1 is unusual in having a relatively long 5 ′ UTR without an uAUG (Supp. Figure S3B).…”

Upstream ORFs are prevalent translational repressors in vertebrates

“…On the other hand, some uORFs have been shown to function through their encoded peptide sequences (Rahmani et al, 2009;Ebina et al, 2015), and it has not yet been determined whether most uORF-encoded peptides are themselves functional molecules. uORF polymorphism has also been implicated in a variety of human diseases (Calvo et al, 2009;Chatterjee et al, 2010;Barbosa & Gene, 2014), and uORF-containing genes are prominent in key cellular processes and functional classes, such as stress response (Lawless et al, 2009), meiosis (Brar et al, 2012), circadian rhythms (Janich et al, 2015), and tyrosine kinase activity (Wethmar et al, 2015). uORF polymorphism has also been implicated in a variety of human diseases (Calvo et al, 2009;Chatterjee et al, 2010;Barbosa & Gene, 2014), and uORF-containing genes are prominent in key cellular processes and functional classes, such as stress response (Lawless et al, 2009), meiosis (Brar et al, 2012), circadian rhythms (Janich et al, 2015), and tyrosine kinase activity (Wethmar et al, 2015).…”

“…uORFs can control protein isoform selection by influencing alternate AUG usage (Calkhoven et al , ; Kochetov et al , ), engaging nonsense‐mediated decay (NMD) (Mendell et al , ; Hurt et al , ), and modulating internal ribosome entry site (IRES) usage (Fernandez et al , ; Bastide et al , ). uORF polymorphism has also been implicated in a variety of human diseases (Calvo et al , ; Chatterjee et al , ; Barbosa & Gene, ), and uORF‐containing genes are prominent in key cellular processes and functional classes, such as stress response (Lawless et al , ), meiosis (Brar et al , ), circadian rhythms (Janich et al , ), and tyrosine kinase activity (Wethmar et al , ). Finally, proteomic analyses have linked predicted uORFs to lower protein levels (Calvo et al , ; Ye et al , ).…”

Upstream ORFs Prevent MAVS Spontaneous Aggregation and Regulate Innate Immune Homeostasis

“…uORF presence also correlates with lower steady-state RNA levels, as translation of some uORFs causes nonsense-mediated mRNA decay (Matsui et al, 2007;Mendell et al, 2004). In addition, uORF polymorphism has been found to be associated with a variety of human diseases (Barbosa and Gene, 2014;Calvo et al, 2009;Chatterjee et al, 2010). Functional classes of uORF-containing genes are involved in key cellular processes, such as circadian rhythms, meiosis, and stress response (Brar et al, 2012;Janich et al, 2015;Lawless et al, 2009).…”