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Plant Cell Advance Online Publication
Published on December 12, 2008; 10.1105/tpc.108.064311

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Criteria for Annotation of Plant MicroRNAs

Blake C. Meyers 1*, Michael J. Axtell 2, Bonnie Bartel 3, David P. Bartel 4, David Baulcombe 5, John L. Bowman 6, Xiaofeng Cao 7, James C. Carrington 8, Xuemei Chen 9, Pamela J. Green 1, Sam Griffiths-Jones 10, Steven E. Jacobsen 11, Allison C. Mallory 12, Robert A. Martienssen 13, R. Scott Poethig 14, Yijun Qi 15, Herve Vaucheret 12, Olivier Voinnet 16, Yuichiro Watanabe 17, Detlef Weigel 18, and Jian-Kang Zhu 9

1 Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
2 Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
3 Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005
4 Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Whitehead Institute, Cambridge, Massachusetts 02142
5 Plant Sciences Department, Cambridge University, Cambridge CB2 3EA, United Kingdom
6 School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
7 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
8 Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
9 Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
10 Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
11 Howard Hughes Medical Institute, Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095
12 Laboratoire de Biologie Cellulaire, Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, 78026 Versailles Cedex, France
13 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
14 Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
15 National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
16 Institut de Biologie Moleculaire des Plantes du Centre National de la Recherche Scientifique 12, 67084 Strasbourg Cedex, France
17 Department of Life Sciences, University of Tokyo, Meguro, Tokyo 153-8902, Japan
18 Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany

* To whom correspondence should be addressed. E-mail: meyers{at}dbi.udel.edu.

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.




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