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Published on May 22, 2009; 10.1104/pp.109.139139

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Received March 27, 2009
Accepted May 18, 2009

Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time PCR profiling and small RNA sequencing

Bikram Datt Pant , Magdalena Musialak-Lange , Przemyslaw Nuc , Patrick May , Dirk Walther , and Wolf-Rudiger Scheible *

Max-Planck Institute of Molecular Plant Physiology, Science Park Golm, Am Muhlenberg 1, 14476 Potsdam, Germany

* Corresponding author; email: scheible{at}mpimp-golm.mpg.de.

Comprehensive expression profiles of Arabidopsis (Arabidopsis thaliana) MIRNA genes and mature microRNAs (miRs) are currently not available. We established a quantitative real-time PCR (qRT-PCR) 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 169 family pri-miRs as well as pri-miR398a were found to be repressed during N-limitation, whereas during P-limitation pri-miR778, 827 and 399s were induced and pri-miR398a was repressed. The corresponding responses of the biologically active, mature miRs were confirmed using specific stem-loop RT primer qPCR assays and small RNA sequencing. Interestingly, the latter approach also revealed high abundance of some miR star strands (miR*). Bioinformatic analysis of small RNA sequences with a modified miRDeep algorithm led to the identification of the novel P-limitation induced miR144, which is encoded by two loci in the Arabidopsis genome. Furthermore, miR144, miR169, a miR827-like sequence and the abundances of several miR*s 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, the results reveal the existence of complex small RNA-based regulatory networks mediating plant adaptation to mineral nutrient availability.




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