BIOMAT Database Logo BIOMAT Database Logo

Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing. 2009

Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.

Recent studies have demonstrated the important role of plant microRNAs (miRNAs) under nutrient deficiencies. In this study, deep sequencing of Arabidopsis (Arabidopsis thaliana) small RNAs was conducted to reveal 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 to 1.2 million unique sequence tags from each Pi-sufficient or Pi-deficient root or shoot sample were mapped to the Arabidopsis genome. We showed that upon Pi deprivation, the expression of miR156, miR399, miR778, miR827, and miR2111 was induced, whereas the expression of miR169, miR395, and miR398 was repressed. We found cross talk coordinated by these miRNAs under different nutrient deficiencies. In addition to miRNAs, we identified one Pi starvation-induced DICER-LIKE1-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. Importantly, we observed an increased abundance of TAS4-derived trans-acting small interfering RNAs (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.

UI MeSH Term Description Entries
D010710 Phosphates Inorganic salts of phosphoric acid. Inorganic Phosphate,Phosphates, Inorganic,Inorganic Phosphates,Orthophosphate,Phosphate,Phosphate, Inorganic
D006706 Homeostasis The processes whereby the internal environment of an organism tends to remain balanced and stable. Autoregulation
D000073718 Pancreatitis-Associated Proteins C-type lectins that restrict growth of bacteria in the intestinal epithelia and have bactericidal activity against gram-positive and gram-negative bacteria. They also regulate proliferation and differentiation of KERATINOCYTES following injury. Human pancreatitis-associated protein-1 (Reg3a) is overexpressed by pancreatic ACINAR CELLS in patients with CHRONIC PANCREATITIS. It is also highly expressed by pancreatic, bladder, and gastrointestinal cancer cells and may serve as a diagnostic biomarker. Regenerating Islet-Derived Protein,Pancreatitis-Associated Protein,Pancreatitis-Associated Protein-1,Regenerating Islet-Derived Protein 3,Regenerating Islet-Derived Proteins,Islet-Derived Protein, Regenerating,Pancreatitis Associated Protein,Pancreatitis Associated Protein 1,Pancreatitis Associated Proteins,Protein, Pancreatitis-Associated,Protein, Regenerating Islet-Derived,Regenerating Islet Derived Protein,Regenerating Islet Derived Protein 3,Regenerating Islet Derived Proteins
D012343 RNA, Transfer The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains. Suppressor Transfer RNA,Transfer RNA,tRNA,RNA, Transfer, Suppressor,Transfer RNA, Suppressor,RNA, Suppressor Transfer
D015203 Reproducibility of Results The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results. Reliability and Validity,Reliability of Result,Reproducibility Of Result,Reproducibility of Finding,Validity of Result,Validity of Results,Face Validity,Reliability (Epidemiology),Reliability of Results,Reproducibility of Findings,Test-Retest Reliability,Validity (Epidemiology),Finding Reproducibilities,Finding Reproducibility,Of Result, Reproducibility,Of Results, Reproducibility,Reliabilities, Test-Retest,Reliability, Test-Retest,Result Reliabilities,Result Reliability,Result Validities,Result Validity,Result, Reproducibility Of,Results, Reproducibility Of,Test Retest Reliability,Validity and Reliability,Validity, Face
D015854 Up-Regulation A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins. Receptor Up-Regulation,Upregulation,Up-Regulation (Physiology),Up Regulation
D017360 Arabidopsis A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development. Arabidopsis thaliana,Cress, Mouse-ear,A. thaliana,A. thalianas,Arabidopses,Arabidopsis thalianas,Cress, Mouse ear,Cresses, Mouse-ear,Mouse-ear Cress,Mouse-ear Cresses,thaliana, A.,thaliana, Arabidopsis,thalianas, A.
D017423 Sequence Analysis, RNA A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE. RNA Sequence Analysis,Sequence Determination, RNA,Analysis, RNA Sequence,Determination, RNA Sequence,Determinations, RNA Sequence,RNA Sequence Determination,RNA Sequence Determinations,RNA Sequencing,Sequence Determinations, RNA,Analyses, RNA Sequence,RNA Sequence Analyses,Sequence Analyses, RNA,Sequencing, RNA
D018506 Gene Expression Regulation, Plant Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants. Plant Gene Expression Regulation,Regulation of Gene Expression, Plant,Regulation, Gene Expression, Plant
D018517 Plant Roots The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990) Plant Bulbs,Plant Root,Bulb, Plant,Bulbs, Plant,Plant Bulb,Root, Plant,Roots, Plant

Related Publications

Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male-sterile line by deep sequencing.
June 2012, Plant physiology,
Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Uncovering microRNA-mediated response to SO2 stress in Arabidopsis thaliana by deep sequencing.
October 2016, Journal of hazardous materials,
Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis.
January 2009, PloS one,
Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Phosphate starvation responses are mediated by sugar signaling in Arabidopsis.
March 2007, Planta,
Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Biases in small RNA deep sequencing data.
February 2014, Nucleic acids research,
Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
DSAP: deep-sequencing small RNA analysis pipeline.
July 2010, Nucleic acids research,
Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Identification of adenovirus-encoded small RNAs by deep RNA sequencing.
August 2013, Virology,
Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Identification of Intronic Lariat-Derived Circular RNAs in Arabidopsis by RNA Deep Sequencing.
January 2021, Methods in molecular biology (Clifton, N.J.),
Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots.
September 2021, Life (Basel, Switzerland),
Li-Ching Hsieh, and Shu-I Lin, and Arthur Chun-Chieh Shih, and June-Wei Chen, and Wei-Yi Lin, and Ching-Ying Tseng, and Wen-Hsiung Li, and Tzyy-Jen Chiou
Using Small RNA Deep Sequencing Data to Detect Human Viruses.
January 2016, BioMed research international,
Copied contents to your clipboard!