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

Dong-Hoon Jeong1, Skye A Schmidt1, Linda A Rymarquis15, Sunhee Park1, Matthias Ganssmann16, Marcelo A German17, Monica Accerbi1, Jixian Zhai1, Noah Fahlgren2, Samuel E Fox38, David F Garvin4, Todd C Mockler2, James C Carrington2, Blake C Meyers1 and Pamela J Green1*

Author Affiliations

1 Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA

2 Donald Danforth Plant Science Center, St Louis, MO 63132, USA

3 Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97322, USA

4 USDA-ARS Plant Science Research Unit, University of Minnesota, St Paul, MN 55108, USA

5 Current address: Monsanto Company, Chesterfield, MO 63017, USA

6 Current address: IBACON GmbH, Rossdorf, Germany

7 Current address: Dow AgroSciences LLC, Portland, OR 97224, USA

8 Current address: Linfield College, McMinnville, OR 97128, USA

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Genome Biology 2013, 14:R145  doi:10.1186/gb-2013-14-12-r145

Published: 24 December 2013



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.


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.


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.