Fig. 2.
Regulatory features of 5' and 3' UTRs and their role in environmental responses. (A) UTRs act as hubs for post-transcriptional regulation of mRNA function and thereby ultimately determine the abundance of the encoded protein. Regulatory features of UTRs include binding sites for RBPs, miRNAs, and lncRNAs, uORFs, RNA secondary structures such as hairpins and RNA G-quadruplexes (RG4s), as well as sites for splicing, nucleotide modification, and polyadenylation, the latter determined with the help of far (FUE) and near upstream elements (NUE). (B–I) Examples of UTR-mediated regulatory processes that operate in response to environmental signals. (B) PNT1 recruits the active phyB photoreceptor under red light, inhibiting translation of PORA mRNA and thereby regulating plant greening. (C) PhyB, together with the splicing factors RRC1 and SFPS, triggers intron retention in the PIF3 5' UTR; the retained intron contains a uORF that down-regulates PIF3 translation in the light and thereby promotes seedling de-etiolation. (D) Binding of the lncRNA cis-NATPHO1.2 triggers structural rearrangements in the 5' UTR and coding region of the rice PHO1.2 mRNA under phosphate starvation and thereby increases access of the large ribosomal subunit to the initiation codon. Translation of PHO1.2 increases, and elevated levels of PHO1.2 transporter allow for efficient redistribution of inorganic phosphate (Pi). (E) A thermosensitive hairpin in the PIF7 5' UTR adopts a more relaxed conformation at elevated temperatures, which acts as a translational enhancer. Increased levels of PIF7 subsequently promote temperature-induced hypocotyl elongation. (F) MiR156/157 bind to the 3' UTR of SPL3 and trigger the transcript’s degradation via ARGONAUTE 1 (AGO1). MiR156/157 levels are reduced at elevated temperature, allowing SPL3 protein to accumulate and induce flowering. (G) An m6A modification in the PIF4 3' UTR under red light destabilizes the transcript, thereby promoting photomorphogenesis. (H) Formation of an RG4 in the CORG1 3' UTR at low temperature prevents degradation of the transcript and thereby attenuates growth in the cold. (I) Selection of a distal polyadenylation site in the HKT1 3' UTR enhances translation under salt stress; increased production of the HKT1 transporter subsequently increases export of sodium ions and thereby promotes salt tolerance in Spartina alterniflora. Arrows indicate positive regulation; blunt arrows indicate negative regulation; dotted arrows denote environmental effects. Ribosomes are depicted in bright blue.