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Bioinformatics Advance Access published online on August 10, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl437
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 7, 2006
Revised August 3, 2006
Accepted August 8, 2006

Discovery note

Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs

Yu Wang 1, Tobias Hindemitt 1, and Klaus F. X. Mayer 1 *

1 MIPS/Institute for Bioinformatics, GSF Research Centre for Environment and Health, Ingolstaedter Landstr. 1 85758 Neuherberg, Germany

* To whom correspondence should be addressed.
Klaus F. X. Mayer, E-mail: Kmayer{at}gsf.de


  Abstract

Some plant microRNAs have been shown to be de novo generated by inverted duplication from their target genes. Subsequent duplication events potentially generate multigene microRNA families. Within this paper we provide supportive evidence for the inverted duplication model of plant microRNA evolution. Firstly, we report that the precursors of four Arabidopsis thaliana microRNA families, miR157, miR158, miR405 and miR447 share nearly identical nucleotide sequences throughout the whole miRNA precursor between the family members. The extent and degree of sequence conservation is suggestive of recent evolutionary duplication events. Furthermore we found that sequence similarities are not restricted to the transcribed part but extend into the promoter regions. Thus the duplication event most likely included the promoter regions as well. Conserved elements in upstream regions of miR163 and its targets were also detected. This implies that the inverted duplication of target genes, at least in certain cases, had included the promoters of the target genes. Sequence conservation within promoters of miRNA families as well as between miRNA and its potential progenitor gene can be exploited for understanding the regulation of microRNA genes.

Supplementary Material: Web supplementary information is available on http://mips.gsf.de/proj/regulomips/microRNA/. Further supplementary material is available on Bioinformatics online.

Associate Editor: Alfonso Valencia
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