Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

Abstract

Arabidopsis microRNA expression regulation was studied in a wide array of abiotic stresses such as drought, heat, salinity, copper excess/deficiency, cadmium excess, and sulfur deficiency. A home-built RT-qPCR mirEX platform for the amplification of 289 Arabidopsis microRNA transcripts was used to study their response to abiotic stresses. Small RNA sequencing, Northern hybridization, and TaqMan® microRNA assays were performed to study the abundance of mature microRNAs. A broad response on the level of primary miRNAs (pri-miRNAs) was observed. However, stress response at the level of mature microRNAs was rather confined. The data presented show that in most instances, the level of a particular mature miRNA could not be predicted based on the level of its pri-miRNA. This points to an essential role of posttranscriptional regulation of microRNA expression. New Arabidopsis microRNAs responsive to abiotic stresses were discovered. Four microRNAs: miR319a/b, miR319b.2, and miR400 have been found to be responsive to several abiotic stresses and thus can be regarded as general stress-responsive microRNA species.

Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels

“…The values presented in the charts are the mean 6 SD (n = 3). * t test P value # 0.05; ** t test P value # 0.01. treatment of Arabidopsis seedlings with 250 mM NaCl, the levels of miRNA161 and miR173 did not increase, indicating that the salinity-induced accumulation of miRNA161 and miRNA173 observed is part of the rapid response of plants to this environmental stimulus (Barciszewska-Pacak et al, 2015).…”

“…miRNA161 and miRNA173, the decreased level of primary precursors correlated with a higher accumulation of mature miRNA molecules. It has already been suggested that these negative correlations between the levels of pri-miRNAs and their cognate mature miRNAs result from many different environmental stresses, including salinity (Barciszewska-Pacak et al, 2015); however, the molecular mechanism underlying such nontranscriptional regulation of miRNA expression remains unknown. Interestingly, after a 24-h-long Figure 9.…”

“…Recently, we developed a high-throughput real-time quantitative PCR (RT-qPCR)-based platform, mirEX, which can be applied for the simultaneous examination of the accumulation of all known Arabidopsis miRNA precursors (pri-miRNAs). Our mirEX platform has been demonstrated to be a useful tool for the global profiling of miRNA expression during different developmental stages, mutants, and/or Arabidopsis plants growing under various environmental conditions (Zielezinski et al, 2015;Barciszewska-Pacak et al, 2015). We applied the mirEX panel to investigate the influence of salt stress on MIR gene expression in T87 cells.…”

“…It also includes the control of the level of DCL1 and AGO1 mRNA by specific miRNAs (Meng et al, 2011) in a distinctive feedback mechanism. The final accumulation of miRNA molecules and consequently the final levels of their mRNA targets result from a combined effect of the regulation of MIR genes transcription as well as the processing of miRNA precursors (Kai and Pasquinelli, 2010;Barciszewska-Pacak et al, 2015). The final levels of mature miRNAs can also be regulated by miRNA degradation or stabilization (Meng et al, 2011).…”

“…Particularly in plants, which are sessile organisms, such rapid and effective responses to different environmental stimuli are crucial for the proper acclimatization to new conditions. Many miRNAs have been ascribed to different biotic and abiotic stresses (Kruszka et al, 2012;Barciszewska-Pacak et al, 2015); however, only in very few examples is the mechanism underlying the regulation of such miRNA expression understood. Therefore, to understand the mechanisms underlying the regulation of miRNA expression in plants, we investigated the influence of salinity stress on the miRNA Arabidopsis transcriptome by applying the qPCR-based platform mirEX that was recently developed in our laboratory and allows us to monitor the levels of all known Arabidopsis pri-miRNAs Zielezinski et al, 2015).…”