Article
 

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

Public Deposited

Downloadable Content

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

Descriptions

Attribute NameValues
Creator
Abstract
  • 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.
  • This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by BioMed Central Ltd. The published article can be found at: http://genomebiology.com/.
Resource Type
DOI
Date Available
Date Issued
Citation
  • 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
Journal Title
Journal Volume
  • 14
Journal Issue/Number
  • 12
Rights Statement
Funding Statement (additional comments about funding)
  • This research was supported primarily by the Office ofBiological and Environmental Research of the Department of Energy underPlant Feedstock Genomics for Bioenergy award number DE-FG02-07ER64450to PJG, with additional support from the National Science Foundation,award number MCB-1231726 and the National Institutes of Health, awardnumber AI043288 to JCC. NF was supported, in part, by a USDA-NIFApostdoctoral fellowship.
Publisher
Peer Reviewed
Language
Replaces

Relationships

Parents:

This work has no parents.

Items

Thumbnail Title Date Uploaded Visibility Actions
file details FoxSamuelBotanyPlantPathologyParallelAnalysisRNA_FigureS1.pdf 07/26/2017 Public
file details FoxSamuelBotanyPlantPathologyParallelAnalysisRNA_TableS1.pdf 07/26/2017 Public
file details FoxSamuelBotanyPlantPathologyParallelAnalysisRNA.pdf 07/26/2017 Public