Function and Evolution of Upstream ORFs in Eukaryotes

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. 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.