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Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon Public Deposited

https://ir.library.oregonstate.edu/concern/articles/q811km50c

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  • BACKGROUND: The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using parallel analysis of RNA ends (PARE) data is lacking in B. distachyon. RESULTS: B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset for analyzing small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner. CONCLUSIONS: B. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants.
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  • Jeong, D. H., Schmidt, S. A., Rymarquis, L. A., Park, S., Ganssmann, M., German, M. A., ... & Green, P. J. (2013). Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biology, 14(12), R145. doi:10.1186/gb-2013-14-12-r145
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  • This research was supported primarily by the Office of Biological and Environmental Research of the Department of Energy under Plant Feedstock Genomics for Bioenergy award number DE-FG02-07ER64450 to PJG, with additional support from the National Science Foundation, award number MCB-1231726 and the National Institutes of Health, award number AI043288 to JCC. NF was supported, in part, by a USDA-NIFA postdoctoral fellowship.
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  • description.provenance : Made available in DSpace on 2014-04-21T16:56:09Z (GMT). No. of bitstreams: 4 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) FoxSamuelBotanyPlantPathologyParallelAnalysisRNA.pdf: 1139059 bytes, checksum: 7e562d2b5366ff9d6d20755b7c39b2d7 (MD5) FoxSamuelBotanyPlantPathologyParallelAnalysisRNA_FigureS1.pdf: 734628 bytes, checksum: 074081bc23280fc0fd9e6e763ff5209e (MD5) FoxSamuelBotanyPlantPathologyParallelAnalysisRNA_TableS1.pdf: 350880 bytes, checksum: 9799d9dd2ab947fb9d5ba0122d7b85df (MD5) Previous issue date: 2013-12-24
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  • description.provenance : Submitted by Erin Clark (erin.clark@oregonstate.edu) on 2014-04-21T16:55:54Z No. of bitstreams: 4 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) FoxSamuelBotanyPlantPathologyParallelAnalysisRNA.pdf: 1139059 bytes, checksum: 7e562d2b5366ff9d6d20755b7c39b2d7 (MD5) FoxSamuelBotanyPlantPathologyParallelAnalysisRNA_FigureS1.pdf: 734628 bytes, checksum: 074081bc23280fc0fd9e6e763ff5209e (MD5) FoxSamuelBotanyPlantPathologyParallelAnalysisRNA_TableS1.pdf: 350880 bytes, checksum: 9799d9dd2ab947fb9d5ba0122d7b85df (MD5)

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