אסיף מאגר המחקר החקלאי

Parallel analysis of rna ends enhances global investigation of micrornas and target rnas of brachypodium distachyon

Year:

2013

Source of publication :

Authors :

Volume :

14

Co-Authors:

Jeong, D.-H., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
Schmidt, S.A., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
Rymarquis, L.A., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States, Monsanto Company, Chesterfield, MO, United States
Park, S., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
Ganssmann, M., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States, IBACON GmbH, Rossdorf, Germany
German, M.A., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States, Dow AgroSciences LLC, Portland, OR, United States
Accerbi, M., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
Zhai, J., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
Fahlgren, N., Donald Danforth Plant Science Center, St Louis, MO, United States
Fox, S.E., Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States, Linfield College, McMinnville, OR, United States
Garvin, D.F., USDA-ARS Plant Science Research Unit, University of Minnesota, St Paul, MN, United States
Mockler, T.C., Donald Danforth Plant Science Center, St Louis, MO, United States
Carrington, J.C., Donald Danforth Plant Science Center, St Louis, MO, United States
Meyers, B.C., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States
Green, P.J., Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE, United States

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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. © 2013 Jeong et al.

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