Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MiRNA-mediated post-transcriptional regulation of gene expression in ABR17 transgenic Arabidopsis thaliana under salt stress

ABSTRACT: Micro RNAs (miRNAs) are a class of small endogenous RNAs conserved in eukaryotic organisms including plants. They suppress gene expression post-transcriptionally in many different biological processes. Previously, we reported salinity-induced changes in gene expression in transgenic Arabidopsis thaliana plants that constitutively expressed a pea abscisic acid-responsive (ABR17) gene. In the current study, we used a microarray to investigate the role of miRNA-mediated post-transcriptional gene regulation in these same transgenic plants in the presence and absence of salinity stress. We identified nine miRNAs that were significantly modulated due to ABR17 gene expression, and seven miRNAs that were modulated in response to salt stress. The target genes regulated by these miRNAs were identified using starBase (sRNA target Base) Degradome analysis and through 5' RNA Ligase Mediated-Rapid Amplification of cDNA Ends (RLM-RACE). Our findings revealed miRNA:mRNA interactions comprising regulatory networks of Auxin Response Factor (ARF), ARGONAUTE 1, (AGO1), Dicer-like proteins 1 (DCL1), Squamosa Promoter Binding (SPB), NAC, APETALA 2 (AP2), Nuclear Factor-Y (NFY), RNA binding proteins, Arabidopsis thaliana vacuolar phyrophosphate 1 (AVP1) and Pentatricopetide repeat (PPR) in ABR17 transgenic A. thaliana, which control physiological, biochemical and stress signalling cascades due to the imposition of salt stress. Our results are discussed within the context of the effect of the transgene, ABR17, and the roles miRNA expression may play in mediating plant responses to salinity. In this miRNA-microarray experiment, a total of 4 samples were analyzed with their 3 biological replicates. Two samples, WT and ABR17 control (without salt treatment), were used as reference controls.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Shiv Verma

PROVIDER: E-GEOD-53783 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: There is a limited capacity to repair damage in the mammalian heart after birth, which is primarily due to the inability of cardiomyocytes to proliferate after birth. This is in contrast to zebrafish and salamander, in which cardiomyocytes retain the ability to proliferate throughout life and can regenerate their heart after significant damage. Recent studies in zebrafish and rodents implicate microRNAs (miRNAs) in the regulation of genes responsible for cardiac cell cycle progression and regeneration, in particular, miR-133a, the miR-15 family, miR-199a and miR-590. However, the significance of these miRNAs and miRNA in general in the regulation of cardiomyocyte proliferation in large mammals, including humans, where the timing of heart development relative to birth is very different than in rodents, is unclear. To determine the involvement of miRNAs in the down-regulation of cardiomyocyte proliferation occurring before birth in large mammals, we investigated miRNA and target gene expression in sheep hearts before and after birth. The experimental approach included targeted transcriptional profiling of miRNA and target mRNA previously identified in rodent studies as well as genome-wide miRNA profiling using microarrays. Results: The cardiac expression of miR-133a increased and its target gene IGF1R decreased with increasing age, reaching their respective maximum and minimum abundance when the majority of ovine cardiomyocytes were quiescent. The expression of the miR-15 family members was variable with age, however, four of their target genes decreased with age. These latter profiles are inconsistent with the direct involvement of this family of miRNA in cardiomyocyte quiescence in late gestation sheep. The expression patterns of ‘pro-proliferative’ miR-199a and miR-590 were also inconsistent with their involvement in cardiomyocyte quiescence. Consequently, miRNA microarray analysis was undertaken, which identified six discrete clusters of miRNA with characteristic developmental profiles. The functions of predicted target genes for the miRNA in four of the six clusters were enriched for aspects of cell division and regulation of cell proliferation suggesting a potential role of these miRNA in regulating cardiomyocyte proliferation. Conclusion: The results of this study show that the expression of miR-133a and one of its target genes is consistent with it being involved in the suppression of cardiomyocyte proliferation, which occurs across the last third of gestation in sheep. The expression patterns of the miR-15 family, miR-199a and miR-590 were inconsistent with direct involvement in the regulation cardiomyocyte proliferation in sheep, despite studies in rodents demonstrating that their manipulation can influence the degree of cardiomyocyte proliferation. miRNA microarray analysis suggests a coordinated and potentially more complex role of multiple miRNA in the regulation of cardiomyocyte quiescence and highlights significant differences between species that may reflect their substantial differences in the timing of this developmental process. RNA, (2 µg) from three heart samples from each of the 91 d (fetus), 141 d (fetus), 5 d (postnatal) and 173 d (postnatal) groups, was used for analysis according to standard procedures. The experimental design included three biological replicates from each of the four normal developmental ages in sheep and thus a total of 12 samples was analyzed.

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MiRNA-mediated post-transcriptional regulation of gene expression in ABR17 transgenic Arabidopsis thaliana under salt stress

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