UTRs

Untranslated regions (UTRs) are portions of mRNA that flank the coding sequence and are not themselves translated into protein. They lie at the 5' and 3' ends of the mature transcript: the 5' UTR is upstream of the start codon, and the 3' UTR lies downstream of the termination codon. Although they do not encode amino acids, UTRs contain sequence motifs and structural elements that regulate gene expression after transcription.

In eukaryotes, the 5' UTR can influence translation initiation. Translation typically begins by ribosome scanning from the 5' cap to the start codon, and features within the 5' UTR, such as the Kozak sequence or upstream open reading frames, can modulate initiation efficiency. The 5' end also interacts with the cap structure to facilitate ribosome recruitment. In prokaryotes, the 5' UTR often contains ribosome binding sites (Shine-Dalgarno sequences) that align the start codon with the ribosome.

The 3' UTR contains signals for mRNA processing and elements that regulate stability, localization, and translation. It often includes binding sites for RNA-binding proteins and microRNAs, which can influence mRNA decay rates and translational efficiency. Elements such as AU-rich motifs may promote degradation, while other motifs can stabilize transcripts or direct cellular localization. The 3' UTR also contributes to the efficiency of polyadenylation and, in some cases, to translational control via cytoplasmic polyadenylation.

UTR length and composition vary by gene and species. Alternative transcription start sites, termination sites, or polyadenylation can produce transcripts with different UTRs, expanding regulatory potential without altering the coding sequence. Mutations or variations in UTRs can affect gene expression and may be associated with disease or phenotypic variation. In research and biotechnology, UTRs are often engineered to tune expression of recombinant transcripts.