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MBE Advance Access originally published online on February 22, 2008
Molecular Biology and Evolution 2008 25(5):892-902; doi:10.1093/molbev/msn029
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© 2008 The Authors.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Research Articles

Comparative Analysis of the MIR319a MicroRNA Locus in Arabidopsis and Related Brassicaceae

Norman Warthmann*,2, Sandip Das*,1,2, Christa Lanz{dagger} and Detlef Weigel*

* Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
{dagger} Genome Center, Max Planck Institute for Developmental Biology, Tübingen, Germany

E-mail: weigel{at}weigelworld.org.

Accepted for publication January 30, 2008.

MicroRNAs (miRNAs) are important regulators of gene expression in multicellular organisms. Yet, little is known about their molecular evolution. The 20- to 22-nt long miRNAs are processed in plants from foldbacks that are a few hundred base pairs in size. Often, these foldbacks are embedded in much larger precursor transcripts. To investigate functional constraints on sequence evolution of miRNA precursor genes, we have studied sequence variation in the precursor of miR319a, MIR319a, between species from the Brassicaceae. We compared the genomic context in Arabidopsis thaliana, Arabidopsis halleri, and Capsella rubella, using bacterial artificial chromosome clones, and analyzed precursor sequences obtained by polymerase chain reaction from 13 additional species. Phylogenetic shadowing identifies a conserved motif around the transcription start site, which we demonstrate to be functionally important. We further assessed the functionality of MIR319a orthologs from several Brassicaceae species in A. thaliana. The ortholog from kale (Brassica oleracea var. acephala) was found to be largely inactive, at least partially due to mutations in the miRNA itself, but experimental evidence suggests that loss of miR319a function is compensated by other members of the miR319 family. More broadly, we find that the foldback diverges less rapidly than the remainder of the primary transcript. To understand the molecular evolution of miRNA genes, investigations at different levels of phylogenetic divergence are required.

Key Words: microRNA • miRNA • RNA interference • phylogenetic shadowing • Arabidopsis • Brassicaceae

1 Present address: Department of Biotechnology, Hamdard University, New Delhi, India.

2 These authors contributed equally to this work.

Peter Lockhart, Associate Editor


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