UTR-Dependent Control of Gene Expression in Plants

Plant mRNAs contain untranslated regions (UTRs) that significantly enhance the coding capacity of the genome by producing multiple mRNA variants from the same gene. Approximately 18–19% of transcribed sequences in Arabidopsis thaliana and Oryza sativa genomes are UTRs. The length-wise distribution of UTRs indicates greater complexity in rice than in A. thaliana. In general, UTRs are longer in rice than in Arabidopsis. At the whole-genome level, UTRs provide functional specificity to genes in a length-dependent manner. Despite the conserved nature of many UTR-associated cis-regulatory elements across plant families, the existence of plant-specific mechanisms is expected. Multiple ways exist by which UTR elements can exert control over gene expression and the functioning of translated proteins. Throughout their lives, plants sense many developmental and environmental stimuli, and activation of optimal responses against these stimuli requires extensive transcriptional reprogramming. To facilitate this activation, plant mRNA contains untranslated regions (UTRs) that significantly increase the coding capacity of the genome by producing multiple mRNA variants from the same gene. In this review we compare UTRs of arabidopsis (Arabidopsis thaliana) and rice (Oryza sativum) at the genome scale to highlight their complexity in crop plants. We discuss different modes of UTR-based regulation with emphasis on genes that regulate multiple plant processes, including flowering, stress responses, and nutrient homeostasis. We demonstrate functional specificity in genes with variable UTR length and propose future research directions. Throughout their lives, plants sense many developmental and environmental stimuli, and activation of optimal responses against these stimuli requires extensive transcriptional reprogramming. To facilitate this activation, plant mRNA contains untranslated regions (UTRs) that significantly increase the coding capacity of the genome by producing multiple mRNA variants from the same gene. In this review we compare UTRs of arabidopsis (Arabidopsis thaliana) and rice (Oryza sativum) at the genome scale to highlight their complexity in crop plants. We discuss different modes of UTR-based regulation with emphasis on genes that regulate multiple plant processes, including flowering, stress responses, and nutrient homeostasis. We demonstrate functional specificity in genes with variable UTR length and propose future research directions. methylation of guanosine in the 5′ terminus of mRNAs. a conserved epitranscriptomic modification of mRNA that is directed by a methyltransferase complex containing METTL3 as the SAM-binding subunit. a process in which one pre-mRNA transcript is processed to produce multiple mRNAs that generally differ in their 3′-UTR length. a process by which pre-mRNAs are processed differentially to generate multiple isoforms that differ in biological activity. the sequence of a transcript that is translated into protein. A CDS starts with a start codon (AUG) and stops at one of the three stop codons (UAA, UGA, or UAG). the collective term for a group of antisense long noncoding transcripts that undergo APA to repress the expression of the flowering time regulator FLC. a protein complex formed at the junction of two exons on a pre-mRNA strand joined together during RNA splicing. the ability of an intron sequence to enhance the expression of a gene containing that intron. a translation-coupled mechanism that eliminates mRNAs containing PTCs. Its main function is to reduce errors in gene expression. a part of the reading frame that has potential to be translated; usually contains start (AUG) and stop (UAA, UAG, or UGA) codons. a stop codon (UAA, UAG, or UGA) is a nucleotide triplet within mRNA that signals the termination of translation into proteins. refers to the two sections on each side of a CDS on an mRNA strand. an ORF within the 5′ UTR of an mRNA.