Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica)
Open Access
- 27 November 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 39 (7), 2821-2833
- https://doi.org/10.1093/nar/gkq1047
Abstract
Plant microRNAs (miRNAs) have been shown to play critical roles in regulating gene expression at the post-transcriptional level. In this study, we employed high throughput sequencing combined with computational analysis to survey miRNAomes from the seedlings of rice under normal conditions and treatments of H2O2 that result in oxidative stress. Comparison of the miRNAomes and subsequent northern blot analysis identified seven miRNA families differentially expressed under H2O2 stress. Predicted and experimentally validated targets of these H2O2-responsive miRNAs are involved in different cellular responses and metabolic processes including transcriptional regulation, nutrient transport, auxin homeostasis, cell proliferation and programmed cell death. This indicates that diverse miRNAs form a complex regulatory network to coordinate plants’ responses under oxidative stress. In addition, we also discovered 32 new miRNAs in the seedlings of rice. Interestingly, of these new miRNAs, miR3981 was originally found to be a putative exonic miRNA located in the exon of AK106348, suggesting that plants may also use some exons as an miRNA source. This study is the first genome-wide investigation of H2O2-regulated miRNAs in plants and broadens our perspectives on the important regulatory roles of miRNAs in plant oxidative stress and physiological adaption.Keywords
This publication has 67 references indexed in Scilit:
- Transcriptional Control of Gene Expression by MicroRNAsCell, 2010
- Biogenesis of small RNAs in animalsNature Reviews Molecular Cell Biology, 2009
- Origin, Biogenesis, and Activity of Plant MicroRNAsCell, 2009
- Posttranscriptional Crossregulation between Drosha and DGCR8Cell, 2009
- Comparative Proteomics Analysis Reveals an Intimate Protein Network Provoked by Hydrogen Peroxide Stress in Rice Seedling LeavesMolecular & Cellular Proteomics, 2008
- Global identification of microRNA–target RNA pairs by parallel analysis of RNA endsNature Biotechnology, 2008
- MicroRNA-mediated Systemic Down-regulation of Copper Protein Expression in Response to Low Copper Availability in ArabidopsisJournal of Biological Chemistry, 2008
- Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)Proceedings of the National Academy of Sciences, 2008
- UV‐B responsive microRNA genes in Arabidopsis thalianaMolecular Systems Biology, 2007
- Specific Effects of MicroRNAs on the Plant TranscriptomeDevelopmental Cell, 2005