MicroRNA-guided regulation of heat stress response in wheat

Abstract

Background: With rising global temperature, understanding plants' adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the posttranscriptional level. In this study, small RNAs and the degradome (parallel analysis of RNA ends) of leaf tissues collected from control and heat-stressed wheat plants immediately at the end of the stress period and 1 and 4 days later were analysed. Results: Sequencing of 24 small RNA libraries produced 55.2 M reads while 404 M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeatcontaining proteins and mitochondrial transcription termination factor-like proteins. Conclusion: The interlaced data set generated in this study identified and validated heat stress regulated miRNAs and their target genes associated with thermotolerance. Such accurate identification and validation of miRNAs and their target genes are essential to develop novel regulatory gene-based breeding strategies.

Insight into the Role of Epigenetic Processes in Abiotic and Biotic Stress Response in Wheat and Barley

“…In eukaryotic cells, miRNAs coding genes are transcribed to generate primary miRNAs (pri-miRNAs), which are then cleaved and processed into mature miRNAs under the action of DICER-LIKE proteins (DCLs). In Arabidopsis, ARGONAUTE (AGO) family proteins such as AGO1 then bind the nascent mature miRNAs and guide the target-specific post-transcriptional gene silencing (PTGS) [97]. Unlike microRNA, short/small interfering RNAs (siRNAs) are generated from long linear double-stranded RNAs with 20-24 nt length and are transcribed by RNA polymerase IV (RNAPIV) from transposons and repetitive regions.…”

“…Increasing evidence from Arabidopsis studies revealed that ncRNAs such as siRNAs and lncRNAs regulate plant stress-responsive gene expression through multiple epigenetic mechanisms, including DNA methylation, histone modification and genome topology changes [97]. For instance, siRNAs and lncRNAs both participate into the DNA de novo cytosine methylation via the RNA-directed DNA methylation (RdDM) pathway in Arabidopsis [105].…”

Different MicroRNA Families Involved in Regulating High Temperature Stress Response during Cotton (Gossypium hirsutum L.) Anther Development

“…The identified miRNA families and their diverse expression patterns at different stages implicated the complexity of miRNAs involved in the regulation of the response of anthers to heat stress. Usually, the miRNAs with high abundance are considered the dominant and functional products that respond to stresses, such as HT [28,29]. In our study, seven miRNA families (miR2949, miR167, and miR160 at the SCP stage; miR156 and miR172 at the MP stage; miR156 at the MRP stage; and miR393 and miR3476 at the PM stage) with expression abundance of more than 10% of the total expression abundance served as the main regulators that respond to HT stress with positive or negative regulation patterns (Figure 4a).…”

“…The miRNAs within the same family have a similar function attributable to their conserved sequence and structural configuration [6,23]. High-and low-abundance miRNAs may play major and minor regulatory roles, respectively [28,29]. The coordinated regulation of these two types of abundance of miRNAs ultimately leads to the regulation of heat stress response [28].…”

Identification and Characterization of Heat-Responsive miRNAs and their Regulatory Network in Maize

“…Thus, improving the adaptability to high temperature has become a new focus in the process of crop molecular breeding. Plant has developed elaborate regulatory mechanisms at morphological, physiological and molecular levels to cope with heat stress [34,35], and many studies have paid more attention on gene expression and its roles in response to abiotic stresses [36][37][38][39]. MiRNAs are a group of non-coding sRNAs that play essential roles in plant growth, development, and stress responses [20-23, 40, 41].…”