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Plant Cell Advance Online Publication
Published on April 22, 2005; 10.1105/tpc.105.032185

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Received February 24, 2005
Returned for revision March 25, 2005
Accepted March 25, 2005

Antiquity of MicroRNAs and Their Targets in Land Plants

Michael J. Axtell 1 and David P. Bartel 2*

1 Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
2 Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139

* To whom correspondence should be addressed. E-mail: dbartel{at}wi.mit.edu.

MicroRNAs (miRNAs) affect the morphology of flowering plants by the posttranscriptional regulation of genes involved in critical developmental events. Understanding the spatial and temporal dynamics of miRNA activity during development is therefore central for understanding miRNA functions. We describe a microarray suitable for detection of plant miRNAs. Profiling of Arabidopsis thaliana miRNAs during normal development extends previous expression analyses, highlighting differential expression of miRNA families within specific organs and tissue types. Comparison of our miRNA expression data with existing mRNA microarray data provided a global intersection of plant miRNA and mRNA expression profiles and revealed that tissues in which a given miRNA is highly expressed are unlikely to also show high expression of the corresponding targets. Expression profiling was also used in a phylogenetic survey to test the depth of plant miRNA conservation. Of the 23 families of miRNAs tested, expression of 11 was detected in a gymnosperm and eight in a fern, directly demonstrating that many plant miRNAs have remained essentially unchanged since before the emergence of flowering plants. We also describe an empirical strategy for detecting miRNA target genes from unsequenced transcriptomes and show that targets in nonflowering plants as deeply branching as ferns and mosses are homologous to the targets in Arabidopsis. Therefore, several individual miRNA regulatory circuits have ancient origins and have remained intact throughout the evolution and diversification of plants.




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