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Endogenous small RNAs of meristematic and a terminally differentiated tissue of rice.

ABSTRACT: To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from root apices (RoApx), shoot apices (ShApx), developing inflorescence (Infl) and mature leaf (Leaf). These tissues were chosen because they are expected to be rich in small RNAs and display different patterns of small RNA expression. The RoApx, ShApx, and Infl samples are expected to be enriched for meristematic tissues each of which have different fates. The Infl sample would also be expected to contain developing female gametes. In contrast, the Leaf sample is terminally differentiated and may be expected to be more transcriptionally repressed. These small RNAs comprise a total of 781,885 distinct sequences, and all of these map to at least one locus of the rice genome TIGR version 5.

ORGANISM(S): Oryza sativa

PROVIDER: GSE16350 | GEO | 2009/06/08

SECONDARY ACCESSION(S): PRJNA115305

REPOSITORIES: GEO

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Endogenous small RNAs of meristematic and a terminally differentiated tissue of rice.

Project description:To address the role of small regulatory RNAs in rice development, we generated a large data set of small RNAs from root apices (RoApx), shoot apices (ShApx), developing inflorescence (Infl) and mature leaf (Leaf). These tissues were chosen because they are expected to be rich in small RNAs and display different patterns of small RNA expression. The RoApx, ShApx, and Infl samples are expected to be enriched for meristematic tissues each of which have different fates. The Infl sample would also be expected to contain developing female gametes. In contrast, the Leaf sample is terminally differentiated and may be expected to be more transcriptionally repressed. These small RNAs comprise a total of 781,885 distinct sequences, and all of these map to at least one locus of the rice genome TIGR version 5. Total RNA was extracted from root apices, shoot apices, developing inflorescence and mature leaf. Three samples from each tissue were taken to represent replicates and small RNAs from these were ligated to a common 5' RNA adapter and a replicate-specific 3' adapter. These replicate samples were then identified from within single 454 data sets using the 3' adapter sequence. It should be noted that there was a strong frequency bias observed between the RNA sequence and the particular 3' adapter used in the sequencing. This resulted in both increased or decreased read counts for the known miRNA sequences in a 3' adapter dependent fashion. Use of the three samples for each tissue as replicates is therefore problematic.

2009-06-07 | E-GEOD-16350 | biostudies-arrayexpress

miRNA profiling of rice developing leaves in response to elevated CO2

Project description:Elevated CO2 (eCO2) has an influence on developing leaf growth of rice (Oryza sativa cv. Nipponbare), specifically lower growth stage than P4 (plastochron number), resulting in decrease in leaf size compared with that in ambient CO2 (aCO2). Since several micro RNAs are associated with the regulation of plant leaf development, in order to clarify which micro RNAs are involved in the decrease of leaf blade size at eCO2, we carried out high-throughput small RNA sequencing analysis and compared the amount of identified miRNAs in developing rice leaf blade grown between aCO2 and eCO2 condition.

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Preliminary exploration of Oryza sativa small RNAs - Run 1 and 2

Project description:The small RNAs presented here were produced as a preliminary exploration of small RNAs in rice, and as such, various tissues and stress conditions were sampled. Small RNAs present in these samples were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682. The datasets contain Oryza sativa var Nipponbar endogenous small RNA sequences in the size range 18 to 34 nt. Plants were grown in a Conviron Environmental Chamber at high light intensity using both high pressure sodium and metal halide lamps for 10.5 hr at 28 degrees C and for 13.5 hr at 26 degrees C in the dark. RNA was extracted from rice tissues at various stages of development and under different abiotic and biotic stresses. The small RNAs presented here were all mapped to the rice genome TIGR version 5. The total number of distinct mapped sequences are 12879 for Run 1 and 88508 for Run 2. The total number of sequence reads were respectively 70406 and 191682.

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PLETHORA transcription factors promote early embryo development through induction of meristematic potential

Project description:Given that PLTs are key transcription factors in meristems, we hypothesized that loss of activity fails to confer meristematic properties or 'stemness' to the first embryonic cells, leading to developmental arrest. We asked to what degree downstream PLT targets in meristems overlap with those in early embryos. We selected direct PLT target genes by overlaying existing PLT ChIP-seq and DAP-seq datasets. We extended this set with an additional PLT3-DAP experiment on young roots, because previous PLT-DAP data have only low read counts and used leaf material in which PLTs are typically not strongly expressed.

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Next Generation Sequencing Facilitates Small RNA Mediated Rice Resistance to Xoo

Project description:Purpose: The goal of this study is to identify small non-conding RNAs which are involved in rice resistance to Xoo. Methods: Rice leaves were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation). And then, total RNA was extracted to be sequenced using Illumina GAIIx. Results: Using an optimized data analysis workflow to count the expression level of small ncRNA, we found several differentially expressed small ncRNA which may be participated in the interaction between rice and Xoo. Conclusions: Small ncRNA have be found to function in a variety of biological processes. Our study here has showed that several candidate miRNA or siRNA may play a significant role in rice immunity.

2016-02-25 | GSE69242 | GEO

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2011-03-21 | GSE24464 | GEO

Oryza sativa

Project description:Endogenous small RNAs of meristematic and a terminally differentiated tissue of rice.

| PRJNA115305 | ENA

H3K27 tri-methylation analysis of meristematic tissue (Me) and young leaves (Le) isolated by manual dissection of clv3-9 plants

Project description:For the histone methylation analysis of undifferentiated and differentiated tissues a meristem enriched fraction and young leaves (up to 3 mm leaf blade length) were isolated from clavata3-9 plants. Clavata3-9 mutants harbour larger shoot apical meristems than wild type plants enabling the preparation of meristematic tissue by manual dissection. Samples from both tissues were used for expression and histone H3 lysine 27 trimethylation (H3K27me3) analysis. Tissues for expression and H3K27me3 ChIP-chip analyses were simultaneously harvested.

2011-03-21 | GSE24474 | GEO

Gene expression profiling of rice developing leaves in response to elevated CO2

Project description:Elevated CO2 (eCO2) condition has influence on developing leaf growth of rice (Oryza sativa cv. Nipponbare), specifically lower than P4 (plastochron number) stage, resulting in decrease in leaf size compared with that grown at ambient CO2 (aCO2). In this case, decrease in leaf size seems to be one of acclimation process at CO2 replete environment despite of the fact that number of tiller increase during CO2 replete periods; however, it is not yet elucidated which endogenous signal play a precise role in depression of developing leaf growth in those process. In this context, to elucidate precise signal interaction between mature and developing leaf of rice at eCO2 environment, we profiled gene expressions of developing rice leaf (P4) using oligo DNA microarray 4X44K RAP-DB (Agilent Technologies, Santa clara, CA).

2020-10-10 | GSE121054 | GEO

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