E-GEOD-17741 - Uncovering small RNA-mediated responses to phosphate-deficiency in Arabidopsis by deep sequencing

Released on 1 December 2009, last updated on 27 June 2012
Arabidopsis thaliana
Samples (4)
Protocols (5)
Deep sequencing of Arabidopsis thaliana small RNAs was conducted to reveal microRNAs (miRNAs) and other small RNAs that were differentially expressed in response to phosphate (Pi) deficiency. About 3.5 million sequence reads corresponding to 0.6-1.2 million unique sequence tags from each Pi-sufficient or -deficient root or shoot sample were mapped to the Arabidopsis genome. We showed that upon Pi deprivation, the expression of miR156, miR399, miR778 and miR827 was induced, whereas the expression of miR169, miR395 and miR398 was repressed. We found crosstalks coordinated by these miRNAs under different nutrient deficiencies. Moreover, we found a new miRNA family upregulated specifically by Pi deficiency. In addition to miRNAs, we identified one Pi starvation-induced DCL1-dependent small RNA derived from the long terminal repeat of a retrotransposon and a group of 19-nucleotide small RNAs corresponding to the 5' end of tRNA and expressed at a high level in Pi-starved roots. Interestingly, we observed an increased abundance of TAS4-derived trans-acting siRNAs (ta-siRNAs) in Pi-deficient shoots and uncovered an autoregulatory mechanism of PAP1/MYB75 via miR828 and TAS4-siR81(-) that regulates the biosynthesis of anthocyanin. This finding sheds light on the regulatory network between miRNA/ta-siRNA and its target gene. Of note, a substantial amount of miR399* accumulated under Pi deficiency. Like miR399, miR399* can move across the graft junction, implying a potential biological role for miR399*. This study represents a comprehensive expression profiling of Pi-responsive small RNAs and advances our understanding of the regulation of Pi homeostasis mediated by small RNAs. Keywords: Transcriptome analysis Examination of 4 samples from root and shoot tissues of Arabidopsis in either phosphate-sufficient or phosphate-deficient condition
Experiment type
RNA-seq of non coding RNA 
Arthur C Shih, June-Wei Chen, Li-Ching Hsieh, Shu-I Lin, Tzyy-Jen Chiou, Wei-Yi Lin, Wen-Hsiung Li
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-17741.idf.txt
Sample and data relationshipE-GEOD-17741.sdrf.txt
Processed data (1)E-GEOD-17741.processed.1.zip