Characterization of microRNAs and their target genes associated with transcriptomic changes in gamma-irradiated Arabidopsis

Abstract

ABSTRACT. MicroRNAs (miRNAs) regulate gene expression in response to biotic and abiotic stress in plants. We investigated gammaray-responsive miRNAs in Arabidopsis wild-type and cmt3-11t mutant plants using miRNA microarray analysis. miRNA expression was differentiated between the wild-type and cmt3-11t mutants. miR164a, miR169d, miR169h, miR172b*, and miR403 were identified as repressible in the wild-type and/or cmt3-11t mutant in response to gamma irradiation, while miR827, miR840, and miR850 were strongly inducible. These eight miRNA genes contain UV-B-responsive ciselements, including G-box, I-box core, ARE, and/or MBS in the putative promoter regions. Moreover, Box 4, MBS, TCA-element, and Unnamed_4, as well as CAAT-and TATA-box, were identified in these eight miRNA genes. However, a positive correlation between the transcriptions of miRNAs and their putative target genes was only observed between miR169d and At1g30560 in the wild-type, and between miR827 and At1g70700 in the cmt3-11t mutant. Quantitative RT-PCR analysis confirmed that the transcription of miR164a, miR169d, miR169h, miR172b*, miR403, and miR827 differed after gamma irradiation depending on the genotype (wild-type, cmt3-11t, drm2, drd1-6, and ddm1-2) and developmental stage (14 or 28 days after sowing). In contrast, high transcriptional induction of miR840 and miR850 was observed in these six genotypes regardless of the developmental stage. Although the actual target genes and functions of miR840 and miR850 remain to be determined, our results indicate that these two miRNAs may be strongly induced and reproducible genetic markers in Arabidopsis plants exposed to gamma rays.

Exploring microRNA Signatures of DNA Damage Response Using an Innovative System of Genotoxic Stress in Medicago truncatula Seedlings

“…The presence of DNA lesions influences miRNA degradation as well as their expression. In both plants and animals, it has been demonstrated that miRNAs are responsive to irradiation (IR)-induced oxidative stress and may be responsible for the post-transcriptional regulation of some DDR genes (Joly-Tonetti and Lamartine, 2012; Kim et al, 2016). Plant specific miRNAs responsive to genotoxic stress include the IR-induced Arabidopsis miR840 and miR850, which remain to be further characterized in terms of their roles in DDR and DNA repair (Kim et al, 2016).…”

“…In both plants and animals, it has been demonstrated that miRNAs are responsive to irradiation (IR)-induced oxidative stress and may be responsible for the post-transcriptional regulation of some DDR genes (Joly-Tonetti and Lamartine, 2012; Kim et al, 2016). Plant specific miRNAs responsive to genotoxic stress include the IR-induced Arabidopsis miR840 and miR850, which remain to be further characterized in terms of their roles in DDR and DNA repair (Kim et al, 2016). Few rice miRNAs (osa-miR414, osa-miR164e, and osa-miR408) demonstrated to target specific helicases (Macovei and Tuteja, 2012) were also found to be responsive to γ-irradiation (Macovei and Tuteja, 2013).…”

Chromatin Remodeling and Epigenetic Regulation in Plant DNA Damage Repair

“…Histone trimethyltransferases and/or acetyltransferases may induce histone modifications associated with the transcription of some DDR genes in Arabidopsis after γ-irradiation [78]. In addition, small noncoding microRNAs (miRNAs) in plant and animal genomes are responsive to IR-induced oxidative stress and may be responsible for the epigenetic regulation of some DDR genes [79,80]. The specific roles of plant epigenetic modifiers in DNA damage signaling and repair are detailed in Section 5.2, Section 5.3 and Section 5.4.…”

“…However, there is no direct evidence supporting a correlation between miRNAs and DDR/DNA repair in plants. Plant specific and genotoxic stress-responsive miRNAs including the IR-induced Arabidopsis miR840 and miR850 remain to be further characterized in terms of their functions in DDR and DNA repair [80].…”