This Article Full Text Full Text (PDF) All Versions of this Article: 20/12/3186    most recent tpc.108.064311v3 tpc.108.064311v2 tpc.108.064311v1 Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Web of Science (3) Citing Articles via Google Scholar Google Scholar Articles by Meyers, B. C. Articles by Zhu, J.-K. Search for Related Content PubMed PubMed Citation Articles by Meyers, B. C. Articles by Zhu, J.-K. Agricola Articles by Meyers, B. C. Articles by Zhu, J.-K.

COMMENTARY

Criteria for Annotation of Plant MicroRNAs

^a Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
^b Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
^c Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005
^d Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Whitehead Institute, Cambridge, Massachusetts 02142
^e Plant Sciences Department, Cambridge University, Cambridge CB2 3EA, United Kingdom
^f School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
^g Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
^h Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
ⁱ Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
^j Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
^k Howard Hughes Medical Institute, Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
^l Laboratoire de Biologie Cellulaire, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, 78026 Versailles Cedex, France
^m Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
ⁿ Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
^o National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
^p Institut de Biologie Moleculaire des Plantes du Centre National de la Recherche Scientifique 12, 67084 Strasbourg Cedex, France
^q Department of Life Sciences, University of Tokyo, Meguro, Tokyo 153-8902, Japan
^r Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany

¹ Address correspondence to meyers{at}dbi.udel.edu or mja18{at}psu.edu.

ABSTRACT

MicroRNAs (miRNAs) are 21 nucleotide noncoding RNAs produced by Dicer-catalyzed excision from stem-loop precursors. Many plant miRNAs play critical roles in development, nutrient homeostasis, abiotic stress responses, and pathogen responses via interactions with specific target mRNAs. miRNAs are not the only Dicer-derived small RNAs produced by plants: A substantial amount of the total small RNA abundance and an overwhelming amount of small RNA sequence diversity is contributed by distinct classes of 21- to 24-nucleotide short interfering RNAs. This fact, coupled with the rapidly increasing rate of plant small RNA discovery, demands an increased rigor in miRNA annotations. Herein, we update the specific criteria required for the annotation of plant miRNAs, including experimental and computational data, as well as refinements to standard nomenclature.

This article has been cited by other articles:

				C. Zeng, W. Wang, Y. Zheng, X. Chen, W. Bo, S. Song, W. Zhang, and M. Peng Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants Nucleic Acids Res., January 1, 2010; 38(3): 981 - 995. [Abstract] [Full Text] [PDF]

				L.-C. Hsieh, S.-I. Lin, A. C.-C. Shih, J.-W. Chen, W.-Y. Lin, C.-Y. Tseng, W.-H. Li, and T.-J. Chiou Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing Plant Physiology, December 1, 2009; 151(4): 2120 - 2132. [Abstract] [Full Text] [PDF]

				T. Mourier and E. Willerslev Retrotransposons and non-protein coding RNAs Briefings in Functional Genomics, November 1, 2009; 8(6): 493 - 501. [Abstract] [Full Text] [PDF]

				L. Wu, Q. Zhang, H. Zhou, F. Ni, X. Wu, and Y. Qi Rice MicroRNA Effector Complexes and Targets PLANT CELL, November 1, 2009; 21(11): 3421 - 3435. [Abstract] [Full Text] [PDF]

				S. A. Simon, B. C. Meyers, and D. J. Sherrier MicroRNAs in the Rhizobia Legume Symbiosis Plant Physiology, November 1, 2009; 151(3): 1002 - 1008. [Full Text] [PDF]

				D. S. Horner, G. Pavesi, T. Castrignano, P. D. De Meo, S. Liuni, M. Sammeth, E. Picardi, and G. Pesole Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing Brief Bioinform, October 27, 2009; (2009) bbp046v1. [Abstract] [Full Text] [PDF]

				C. Lelandais-Briere, L. Naya, E. Sallet, F. Calenge, F. Frugier, C. Hartmann, J. Gouzy, and M. Crespi Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules PLANT CELL, September 1, 2009; 21(9): 2780 - 2796. [Abstract] [Full Text] [PDF]

				C. Johnson, A. Kasprzewska, K. Tennessen, J. Fernandes, G.-L. Nan, V. Walbot, V. Sundaresan, V. Vance, and L. H. Bowman Clusters and superclusters of phased small RNAs in the developing inflorescence of rice Genome Res., August 1, 2009; 19(8): 1429 - 1440. [Abstract] [Full Text] [PDF]

				B. D. Pant, M. Musialak-Lange, P. Nuc, P. May, A. Buhtz, J. Kehr, D. Walther, and W.-R. Scheible Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing Plant Physiology, July 1, 2009; 150(3): 1541 - 1555. [Abstract] [Full Text] [PDF]

				N. Fahlgren, C. M. Sullivan, K. D. Kasschau, E. J. Chapman, J. S. Cumbie, T. A. Montgomery, S. D. Gilbert, M. Dasenko, T. W.H. Backman, S. A. Givan, et al. Computational and analytical framework for small RNA profiling by high-throughput sequencing RNA, May 1, 2009; 15(5): 992 - 1002. [Abstract] [Full Text] [PDF]