Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods

Abstract

To survive under abiotic stresses in the environment, plants trigger a reprogramming of gene expression, by transcriptional regulation or translational regulation, to turn on protective mechanisms. The current focus of research on how plants cope with abiotic stresses has transitioned from transcriptomic analyses to small RNA investigations. In this review, we have summarized and evaluated the current methodologies used in the identification and validation of small RNAs and their targets, in the context of plant responses to abiotic stresses.

Keywords: abiotic stress; bioinformatics; microRNA; small RNA; transcriptional regulation.

Figure 1

A simplified representation to illustrate the central role of gene expression reprogramming in triggering the adaption to abiotic stresses. Upon abiotic stresses, cellular homeostasis is disrupted. The signal is sensed and transduced by signaling molecules. This brings forth the reprogramming of gene expression which involves transcriptional factors and sRNAs, resulting in the up-regulation of positive regulators and down-regulation of negative regulators.

Figure 2

hc-siRNAs are transcribed at the heterochromatic regions where they act in cis to trigger the methylation of cytosine in these sequence contexts: CG, CHG and CHH [17,18,19], resulting in transcriptional silencing.

Figure 3

The roles of miRNA and siRNA in PTGS (post-transcriptional gene silencing). (A) The precursor of miRNA is a self-complementary RNA which forms a hair-pin structure while the precursor of siRNA is a dsRNA. The precursors are diced to form mature miRNA or siRNA [7,28,29]; (B) The mature miRNA or siRNA interacts with the AGO (argonaute) protein to form RISC (RNA-induced silencing complexes), which causes the silencing of the target gene by transcript cleavage or translational inhibition [7,28,29].

Figure 3

The roles of miRNA and siRNA in PTGS (post-transcriptional gene silencing). (A) The precursor of miRNA is a self-complementary RNA which forms a hair-pin structure while the precursor of siRNA is a dsRNA. The precursors are diced to form mature miRNA or siRNA [7,28,29]; (B) The mature miRNA or siRNA interacts with the AGO (argonaute) protein to form RISC (RNA-induced silencing complexes), which causes the silencing of the target gene by transcript cleavage or translational inhibition [7,28,29].

Figure 4

A flowchart for miRNA gene prediction. This flowchart summarized how computational tools predict miRNAs with different approaches. Purely ab initio miRNA prediction programs (pink boxes) use the reference genome of interest as the only starting material to generate miRNA precursor candidates, followed by classifying/filtering with known miRNA properties. In contrast, comparative genomics miRNA prediction programs (green boxes) start with identifying conserved regions between two or more genomes to generate miRNA precursor candidates, followed by the same classifying/filtering step of purely ab initio prediction programs (orange boxes). The sequencing read-based prediction programs (purple boxes) use miRNA expression data to locate possible mature miRNAs. Subsequently, flanking genomic regions of mapped reads are extracted and evaluated whether they pass the criteria of miRNA annotation, using various scoring/classifying algorithms.