Function and Evolution of Upstream ORFs in Eukaryotes

Recent advances in RNA sequencing and ribosome profiling allow the quantitative study of uORFs at the genomic scale. Most uORFs in eukaryotic genomes show evidence of translation, and the translational efficiency of uORFs and their impact on the translation of downstream CDSs are influenced by the sequence context of uORFs. Both positive Darwinian selection and purifying selection have shaped the genome-wide landscapes of uORFs in eukaryotes. uORFs can dynamically modulate the translation of downstream CDSs in various biological contexts. There is growing interest in the role of translational regulation in cellular homeostasis during organismal development. Translation initiation is the rate-limiting step in mRNA translation and is central to translational regulation. Upstream open reading frames (uORFs) are regulatory elements that are prevalent in eukaryotic mRNAs. uORFs modulate the translation initiation rate of downstream coding sequences (CDSs) by sequestering ribosomes. Over the past several years, genome-wide studies have revealed the widespread regulatory functions of uORFs in different species in different biological contexts. Here, we review the current understanding of uORF-mediated translational regulation from the perspective of functional and evolutionary genomics and address remaining gaps that deserve further study. There is growing interest in the role of translational regulation in cellular homeostasis during organismal development. Translation initiation is the rate-limiting step in mRNA translation and is central to translational regulation. Upstream open reading frames (uORFs) are regulatory elements that are prevalent in eukaryotic mRNAs. uORFs modulate the translation initiation rate of downstream coding sequences (CDSs) by sequestering ribosomes. Over the past several years, genome-wide studies have revealed the widespread regulatory functions of uORFs in different species in different biological contexts. Here, we review the current understanding of uORF-mediated translational regulation from the perspective of functional and evolutionary genomics and address remaining gaps that deserve further study. mRNA regions that are upstream of the start codon of the main ORFs. the small subunit of a eukaryotic ribosome. ‘40S’ denotes its sedimentation coefficient during centrifugation in Svedberg units. the large subunit of a eukaryotic ribosome. It has a sedimentation coefficient of 60S. the eukaryotic ribosome, which has a sedimentation coefficient of 80S. a process in which the same nascent RNA molecules are processed into different transcripts. sequence elements that only regulate the same mRNA where they are located. the frequency of an allele reaches 100% in the population. nucleotides flanking the start codon of an ORF (usually from –6 to +4 given that the first nucleotide of ORF start codon is +1). The consensus Kozak sequence of CDSs in vertebrates is GCCRCCAUGG (where R can be A or G). small noncoding RNAs that form a complex with Argonaute proteins and bind to target sites by seed-pairing. miRNAs are usually ~22 nucleotides in length. complex formed by a single ribosome and the associated mRNA fragment. a surveillance pathway that degrades aberrant transcripts with premature stop codons. a sequence of triplets encoding amino acids. An ORF begins with a start codon and is bounded by a stop codon. uORFs that are present in some but not all individuals in the population. a passage in the large ribosomal subunit where the nascent peptide chain exits from the ribosome. a recently developed technique that could separate ribosome-protected RNA fragments for sequencing. It is widely used in studies of mRNA translation. a high-throughput method for determining the sequences of RNA molecules in the transcriptome. the complex formed by eIF2, GTP, and Met-tRNAi. It is required not only for the assembly of the pre-initiation complex, but also for re-initiation. a pattern that repeats every three nucleotides. Here, it refers to the ‘high-low-low’ pattern of RPF 5′ end coverage in a codon. genomic elements that could move into new locations in the genomes.