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Review
. 2018 Mar;23(3):248-259.
doi: 10.1016/j.tplants.2017.11.003. Epub 2017 Dec 6.

UTR-Dependent Control of Gene Expression in Plants

Ashish Kumar Srivastava  1 , Yuming Lu  2 , Gaurav Zinta  2 , Zhaobo Lang  2 , Jian-Kang Zhu  3
Affiliations
Review

UTR-Dependent Control of Gene Expression in Plants

Ashish Kumar Srivastava et al. Trends Plant Sci. 2018 Mar.

Abstract

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.

Keywords: adenosine methylation; alternative splicing; epigenetics; nonsense-mediated decay; polyadenylation; riboswitch.

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Figures

Figure I
Figure I. Functional enrichment analysis of UTR-containing genes in Arabidopsis and rice
UTR-containing genes of Arabidopsis and rice genomes were sorted according to their 3′ and 5′UTR length before functional enrichment analysis was independently performed for genes with short (1–500 bp), medium (501–1000 and 1001–2000 bp), and long (> 2000 bp) UTRs using Bioconductor package topGO in R software (version 3.1.1). On the basis of p value, top five GO terms related to biological process are represented, independently for 3′ and 5′UTRs. The colour of bars such as blue (1–500 bp), black (501–1,000 bp), green (1,001–2,000 bp) and red (>2,000 bp) signifies variable UTR length. In rice, relatively fewer GO terms were enriched, especially in medium (1,001–2,000 bp) and long (>2,000 bp) UTR categories.
Figure 1
Figure 1. Percentages of CDS and UTR elements in arabidopsis and rice and their lengths
(A) Genome-scale survey showing the percentage of transcript bases involved in protein-coding (CDS; coding sequence) and in gene regulation (UTR; untranslated region) in Arabidopsis thaliana and Oryza sativa.(B) Percentage of 5′and 3′ UTRs in different length categories along with average UTR length (bp) at whole genome level and in orthologs.
Figure 2
Figure 2. Various modes of UTR-dependent regulation of genes
(A) Alternative polyadenylation: either more than one polyA site is utilized to produce mRNA variants that differ in 3′UTR length or, if the polyA is located upstream of the stop codon, truncated transcripts are produced. (B) Riboswitching: 3′ or 5′UTRs form folding structures that sense a particular metabolite and modulate transcript stability. (C) Adenosine methylation (m6A): The presence of m6A in 5′UTR promotes CAP-independent translation. (D) Short-peptide translation: A short open reading frame in 5′UTR (uORF) can either repress the translation of the main ORF or induce mRNA decay via the NMD pathway. (E) Nonsense-mediated decay (NMD): A pre-mature termination codon (PTC) upstream of the regular termination codon (TC) recruits NMD factors that mediate mRNA decay. (F) Alternative splicing: Retention of intronic elements in 5′UTR can either promote or repress translation, while retention of intronic elements in 3′UTR can modulate miRNA-mediated cleavage.
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