MBE Advance Access published online on February 22, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn029
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Research Article |
Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae
1 Department of Molecular Biology
2 Department of Molecular Biology, Genome Center, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
Contact information for corresponding author: Detlef Weigel, Dept. of Molecular Biology, MPI for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany; email: weigel{at}weigelworld.org; fax +49-7071 601 1412
Received for publication August 16, 2007. Revision received December 27, 2007. Revision received January 29, 2008. 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 nucleotide 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, A. halleri and Capsella rubella, using bacterial artificial chromosome (BAC) 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 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
* Present address: Department of Biotechnology, Hamdard University, New Delhi-110062, India
These authors contributed equally to this work
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