Impact of the Diversity in the 5′ UTR on Translation Regulation

FIGURE 1. Different types of alternative transcription start site (TSS) selection. (A) Schematic representation of the regulation of alternative first exons and alternative tandem TSSs and their corresponding different 5′ untranslated region (UTR) isoforms. (B) Schematic representation of the impact of alternative first exons including or excluding parts of the coding region, resulting in proteins with different N‐termini. Exons are represented by boxes (open reading frame (ORF)—wide; UTRs—narrow); introns are represented by lines. Constitutive exons are colored in light blue, alternative regions of the 5′ UTR in red and green. The alternative coding region and the corresponding alternative N‐terminus are depicted in gray (B).

FIGURE 2. Different types of alternative splicing events in the 5′ untranslated region (UTR). Schematic representation of the different types of alternative splicing events (cassette exon, mutually exclusive exons, alternative 5′ and 3′ splice sites, and intron retention) and their corresponding 5′ UTR isoforms. Exons are represented by boxes (open reading frame (ORF)—wide; UTRs—narrow); introns are represented by lines. Constitutive exons are colored in light blue, alternative exons in orange and red.

FIGURE 3. Translational inhibition by upstream open reading frames (uORFs). (A) Translation of uORFs overlapping with the main ORF prevents translation of the main ORF, as scanning ribosomes never reach the start codon of the latter. (B) Translation of uORFs residing entirely in the 5′ untranslated region (UTR) inhibits translation of the main ORF by ribosome dissociation or stalling upon translation termination at the uORF stop codon. uORF‐encoded peptides can further induce ribosome stalling at the uORF to inhibit translation of the main ORF. (C) If ribosomes remain associated with the mRNA after uORF termination, they can reinitiate translation at the downstream main ORF, if required initiation factors are recruited in due time.

FIGURE 4. Internal ribosome entry site (IRES)‐dependent translation initiation. (A) IRES‐dependent translation initiation is an alternative mode independent of cap recognition. IRESs are considered to be complex secondary RNA structures within the 5′ UTR, which can directly recruit the ribosomal 40S subunit. Subsequently, the 40S subunit either recruits initiation factors to facilitate scanning for a start codon or, alternatively, the 40S subunit can be directly placed on the start codon. After start codon recognition, the 60S ribosomal subunit is recruited to allow for translation initiation, elongation, and termination. (B) IRES‐mediated translation initiation commonly depends on supporting proteins, the so‐called IRES trans‐acting factors (ITAFs). Binding of ITAFs to the IRES can lead to conformational changes of the mRNA structure, thereby facilitating (or preventing) ribosome recruitment.

FIGURE 5. Impact of alternative splicing or alternative transcription start site (TSS) selection on the presence of translation regulatory elements. (A) Schematic representation of the inclusion and exclusion of an alternative exon containing an upstream open reading frame (uORF). In the depicted example, the inclusion of a uORF results in ribosome stalling and the consequent inhibition of translation, whereas the isoform not including the alternative exon is efficiently translated. (B) Schematic representation of the inclusion or exclusion of an internal ribosome entry site (IRES) element due to the alternative first exon usage mechanism of alternative TSS selection. In the depicted example, under stress conditions, translation is inhibited, whereas the inclusion of the IRES allows for sustained translation. Exons are represented by boxes (open reading frame (ORF)—wide; 5′ untranslated regions (UTR)—narrow); introns are represented by lines. The 5′ m7G cap structure is also depicted. Constitutive exons are colored in light blue, alternative exons in orange (A) and red and green (B).