Comment[ArrayExpressAccession] E-GEOD-17741 Public Release Date 2009-12-01 Investigation Title Uncovering small RNA-mediated responses to phosphate-deficiency in Arabidopsis by deep sequencing Comment[Submitted Name] Uncovering small RNA-mediated responses to phosphate-deficiency in Arabidopsis by deep sequencing Experiment Description 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 Date of Experiment Term Source Name EFO Term Source Version Term Source File http://www.ebi.ac.uk/efo/efo.owl Person Last Name Hsieh Chiou Li Hsieh Lin Shih Chen Lin Person First Name Li-Ching Tzyy-Jen Wen-Hsiung Li-Ching Shu-I Arthur June-Wei Wei-Yi Person Mid Initials C Person Email geo@ncbi.nlm.nih.gov Person Affiliation Academia Sinica Person Phone Person Fax Person Address Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei, Taiwan Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Experimental Design Experimental Design Term Accession Number Experimental Design Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF Protocol Name P-GSE17741-1 P-GSE17741-2 P-GSE17741-4 P-GSE17741-3 P-GSE17741-5 Protocol Description SEQUENCE =
COUNT = Seventeen-day-old seedlings were subjected for phosphate starvation treatment by transferring them from 250 μM KH2PO4 (+Pi) into 0 μM KH2PO4 (-Pi) nutrient solution. Control samples were maintained under 250 μM KH2PO4 (+Pi) nutrient solution. Roots and shoots were collected separately after 5-day treatment. Total RNA was isolated with the use of TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer's instructions. Nine-day-old Arabidopsis seedlings grown on half-strength modified Hoagland nutrient solution containing 250 μM KH2PO4 (+Pi) and 1% sucrose were transferred to a hydroponic culture system with half-strength modified Hoagland nutrient solution containing 250 μM KH2PO4 for additional growth of 8 days. All plants were grown at 22oC under a 16-hr photoperiod with cool fluorescent light at 100 to 150 μE. Processed data files contain the perfectly mapped reads with 5' and 3' adapters removed (reads were mapped on the TAIR8 genome). Same reads are sorted together and the numbers of repetitivity are indicated Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation specified_biomaterial_action nucleic_acid_extraction grow feature_extraction Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name Experimental Factor Type Experimental Factor Term Source REF Experimental Factor Term Accession Number Publication Title Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. Publication Author List Hsieh LC, Lin SI, Shih AC, Chen JW, Lin WY, Tseng CY, Li WH, Chiou TJ PubMed ID 19854858 Publication DOI 10.1104/pp.109.147280 Publication Status Publication Status Term Source REF Publication Status Term Accession Number Comment[SecondaryAccession] GSE17741 SRP001557 Comment[GEOLastUpdateDate] 2012-05-08 Comment[AEExperimentType] RNA-seq of non coding RNA Comment[GEOReleaseDate] 2009-12-01 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR032112-SRR032115 Comment[ArrayExpressSubmissionDate] 2009-08-19 SDRF File E-GEOD-17741.sdrf.txt