Untranslated regions (UTRs) are sections of the mRNA before the start codon and after the stop codon that are not translated, termed the five prime untranslated region (5 UTR) and three prime untranslated region (3 UTR), respectively. These regions are transcribed with the coding region and thus are exonic as they are present in the mature mRNA. Several roles in gene expression have been attributed to the untranslated regions, including mRNA stability, mRNA localization, and translational efficiency. The ability of a UTR to perform these functions depends on the sequence of the UTR and can differ between mRNAs. Genetic variants in 3' UTR have also been implicated in disease susceptibility because of the change in RNA structure and protein translation.
The stability of mRNAs may be controlled by the 5 UTR and/or 3 UTR due to varying affinity for RNA degrading enzymes called ribonucleases and for ancillary proteins that can promote or inhibit RNA degradation. (See also, C-rich stability element.)
Translational efficiency, including sometimes the complete inhibition of translation, can be controlled by UTRs. Proteins that bind to either the 3 or 5 UTR may affect translation by influencing the ribosomes ability to bind to the mRNA. MicroRNAs bound to the 3 UTR also may affect translational efficiency or mRNA stability.
Cytoplasmic localization of mRNA is thought to be a function of the 3 UTR. Proteins that are needed in a particular region of the cell can also be translated there; in such a case, the 3 UTR may contain sequences that allow the transcript to be localized to this region for translation.
Some of the elements contained in untranslated regions form a characteristic secondary structure when transcribed into RNA. These structural mRNA elements are involved in regulating the mRNA. Some, such as the SECIS element, are targets for proteins to bind. One class of mRNA element, the riboswitches, directly bind small molecules, changing their fold to modify levels of transcription or translation. In these cases, the mRNA regulates itself.