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MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors [degradome]

ABSTRACT: Elicitor-responsive miRNAs and their targets in rice

ORGANISM(S): Oryza sativa

PROVIDER: GSE66610 | GEO | 2016/03/06

SECONDARY ACCESSION(S): PRJNA277443

REPOSITORIES: GEO

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MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors [miRNA-Seq]

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Project description:MicroRNAs (miRNAs) are small non-coding RNAs that have important regulatory functions in plant growth, development, and response to abiotic stress. Increasing evidence also supports that plant miRNAs contribute to immune responses to pathogens. Here, we used deep sequencing of small RNA libraries for global identification of rice miRNAs that are regulated by fungal elicitors. We also describe 9 previously uncharacterized miRNAs in rice. Combined small RNA and degradome analyses revealed regulatory networks enriched in elicitor-regulated miRNAs supported by the identification of their corresponding target genes. Specifically, we identified an important number of miRNA/target gene pairs involved in small RNA pathways, including miRNA, heterochromatic and trans-acting siRNA pathways. We present evidence for miRNA/target gene pairs implicated in hormone signaling and cross-talk among hormone pathways having great potential in regulating rice immunity. Furthermore, we describe miRNA-mediated regulation of Conserved-Peptide upstream Open Reading Frame (CPuORF)-containing genes in rice, which suggests the existence of a novel regulatory network that integrates miRNA and CPuORF functions in plants. The knowledge gained in this study will help in understanding the underlying regulatory mechanisms of miRNAs in rice immunity and develop appropriate strategies for rice protection.

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Expression data from rice leaves treated or not with fungal elicitors and high-throughput pyrosequencing of endogenous small RNAs from Oryza sativa

Project description:High-throughput sequencing of small RNAs from rice was used to identify distinct miRNAs that are responsive to elicitors from the fungal pathogen Magnaporthe oryzae. [Expression profiling by array] We used microarrays to determine the expression behaviour of target genes for elicitor-regulated miRNAs. [High throughput sequencing] High-throughput sequencing of rice small RNAs was performed in two different tissues, leaves and roots, and two different time point of elicitor treatment, 30' and 2h Amplicons were prepared by 5M-BM-4and 3M-BM-4adaptor ligation in which the 5'-adaptor contained a 'barcode' consisting of a 4-nucleotide identifier sequence for each sample. The libraries containing unique barcodes were combined and subjected to pyrosequencing (454 Life SciencesTM, Roche) [Expression profiling by array] Leaves from rice plants were harvested at two time points after the onset of treatment (30' and 2h) with elicitors of Magnaporthe oryzae 18.1 and used for RNA extraction and hybridization on Affymetrix microarrays. Mock inoculations were performed with sterile water for control experiments. Three biological replicates were analyzed. Each sample represented a pool of approximately 150 rice plants. [High throughput sequencing] 8 samples examined: leaves and roots, treated or not with elicitors at two different time points, 30' and 2h (2x2x2)

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MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-03-06 | GSE66611 | GEO

MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors

Project description:MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors

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