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Nucleic Acids Research Advance Access published online on August 6, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn479
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© 2008 The Author(s)
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.

RNA

Frequency and fate of microRNA editing in human brain

Yukio Kawahara1, Molly Megraw2, Edward Kreider1, Hisashi Iizasa1, Louis Valente1, Artemis G. Hatzigeorgiou2,3,4 and Kazuko Nishikura1,*

1The Wistar Institute, 3601 Spruce Street, 2Department of Genetics, School of Medicine, University of Pennsylvania, 3Department of Computer and Information Science, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA and 4Institute of Molecular Oncology, BSRC "Alexander Fleming", Vari-Athens, Greece

*To whom correspondence should be addressed. Tel: +1 215 898 3828; Fax: +1 215 898 3911; Email: kazuko{at}wistar.org

Received May 25, 2008. Revised July 8, 2008. Accepted July 9, 2008.

Primary transcripts of certain microRNA (miRNA) genes (pri-miRNAs) are subject to RNA editing that converts adenosine to inosine (A->I RNA editing). However, the frequency of the pri-miRNA editing and the fate of edited pri-miRNAs remain largely to be determined. Examination of already known pri-miRNA editing sites indicated that adenosine residues of the UAG triplet sequence might be edited more frequently. In the present study, therefore, we conducted a large-scale survey of human pri-miRNAs containing the UAG triplet sequence. By direct sequencing of RT–PCR products corresponding to pri-miRNAs, we examined 209 pri-miRNAs and identified 43 UAG and also 43 non-UAG editing sites in 47 pri-miRNAs, which were highly edited in human brain. In vitro miRNA processing assay using recombinant Drosha-DGCR8 and Dicer-TRBP (the human immuno deficiency virus transactivating response RNA-binding protein) complexes revealed that a majority of pri-miRNA editing is likely to interfere with the miRNA processing steps. In addition, four new edited miRNAs with altered seed sequences were identified by targeted cloning and sequencing of the miRNAs that would be processed from edited pri-miRNAs. Our studies predict that ~16% of human pri-miRNAs are subject to A->I editing and, thus, miRNA editing could have a large impact on the miRNA-mediated gene silencing.


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