Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing
Open Access
- 22 May 2009
- journal article
- Published by Oxford University Press (OUP) in Plant Physiology
- Vol. 150 (3), 1541-1555
- https://doi.org/10.1104/pp.109.139139
Abstract
Comprehensive expression profiles of Arabidopsis (Arabidopsis thaliana) MIRNA genes and mature microRNAs (miRs) are currently not available. We established a quantitative real-time polymerase chain reaction platform that allows rapid and sensitive quantification of 177 Arabidopsis primary miR transcripts (pri-miRs). The platform was used to detect phosphorus (P) or nitrogen (N) status-responsive pri-miR species. Several pri-miR169 species as well as pri-miR398a were found to be repressed during N limitation, whereas during P limitation, pri-miR778, pri-miR827, and pri-miR399 species were induced and pri-miR398a was repressed. The corresponding responses of the biologically active, mature miRs were confirmed using specific stem-loop reverse transcription primer quantitative polymerase chain reaction assays and small RNA sequencing. Interestingly, the latter approach also revealed high abundance of some miR star strands. Bioinformatic analysis of small RNA sequences with a modified miRDeep algorithm led to the identification of the novel P limitation-induced miR2111, which is encoded by two loci in the Arabidopsis genome. Furthermore, miR2111, miR169, a miR827-like sequence, and the abundances of several miR star strands were found to be strongly dependent on P or N status in rapeseed (Brassica napus) phloem sap, flagging them as candidate systemic signals. Taken together, these results reveal the existence of complex small RNA-based regulatory networks mediating plant adaptation to mineral nutrient availability.Keywords
This publication has 90 references indexed in Scilit:
- Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis DegradomeCurrent Biology, 2008
- Cell-specific nitrogen responses mediate developmental plasticityProceedings of the National Academy of Sciences of the United States of America, 2008
- Construction of small RNA cDNA libraries for deep sequencingMethods, 2007
- Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLAPlant Molecular Biology, 2007
- Small RNAs as big players in plant abiotic stress responses and nutrient deprivationTrends in Plant Science, 2007
- Temporal regulation of shoot development inArabidopsis thalianabymiR156and its targetSPL3Development, 2006
- Posttranscriptional Induction of Two Cu/Zn Superoxide Dismutase Genes in Arabidopsis Is Mediated by Downregulation of miR398 and Important for Oxidative Stress ToleranceTHE PLANT CELL ONLINE, 2006
- MicroRNA genes are transcribed by RNA polymerase IIThe EMBO Journal, 2004
- Radial Patterning of Arabidopsis Shoots by Class III HD-ZIP and KANADI GenesCurrent Biology, 2003
- Comparison of drought tolerance in nitrogen-fixing and inorganic nitrogen-grown common beansPlant Science, 2000