Non-coding RNAs and Their Roles in Stress Response in Plants

Abstract

Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance.

Keywords: RNA-directed DNA methylation; Small RNA; Stress response; lncRNA; miRNA.

Figure 1

miRNAs with altered expression during nutrient deficiency Altered expression of miRNAs leads to a decrease (red blunt arrow) or increase (green arrow) in the expression of their target genes and corresponding proteins. ARF, auxin response factor; SPL, sporocyteless; SCL, scarecrow-like 3; NHD, Na⁺/H antiporter; AOP2, alkenyl hydroxalkyl producing 2; HAP2, heme activator protein 2; AP2, apetala 2; APS, ATP sulfurylase; SULTR, sulfate transporter; CSD, copper/zinc superoxide dismutase; cox5b-1, cytochrome C oxidase subunit 5b-1; CCS1, cytochrome C biogenesis protein; UBC24/PHO2, ubiquitin-conjugating Enzyme E2/phosphate 2; NLA, nitrogen limitation adaptation; ARPN, plantacyanin.

Figure 2

Differential expression of miRNAs in stress response in plants A. miRNAs commonly expressed in Arabidopsis and rice show the opposing expression patterns during heat stress. Expression of miR-156, miR-319, and miR-396 is up-regulated in Arabidopsis, but downregulated in rice, whereas expression of miR-169 was down-regulated in Arabidopsis, but up-regulated in rice. B. miRNAs are commonly involved in response to multiple stresses in Arabidopsis. Expression of miRNAs is either induced/increased (red), inhibited (green), or unaltered (white) under different stress conditions. ABA, abscisic acid; N, nitrogen; Pi, phosphate; S, sulfur; Cu, copper.

Figure 3

Roles of lncRNAs in stress response in plants The major mechanisms underlying the involvement of lncRNAs in stress response include target mimicry, sRNA precursors, NAT pairs, lncR2Epi, and RdDM. NAT pair, the interaction between sense mRNA and antisense lncRNA; lncR2Epi, lncRNA-mediated chromatin modification; RdDM, RNA-directed DNA methylation; FLC, FLOWERING LOCUS C (FLC); PRC2, polycomb repressive complex 2; DRM2, domains rearranged methyltransferase 2; AGO4, argonaute 4; TF, transcription factor; RNAPII, RNA polymerase II.