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Bioinformatics Advance Access originally published online on March 29, 2005
Bioinformatics 2005 21(11):2590-2595; doi:10.1093/bioinformatics/bti411
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

A bioinformatic screen for novel A–I RNA editing sites reveals recoding editing in BC10

D. R. Clutterbuck *, A. Leroy , M. A. O'Connell and C. A. M. Semple

MRC Human Genetics Unit, Western General Hospital Crewe Road, Edinburgh, EH4 2XU, UK

*To whom correspondence should be addressed.

Motivation: Recent studies have demonstrated widespread adenosine–inosine RNA editing in non-coding sequence. However, the extent of editing in coding sequences has remained unknown. For many of the known sites, editing can be observed in multiple species and often occurs in well-conserved sequences. In addition, they often occur within imperfect inverted repeats and in clusters. Here we present a bioinformatic approach to identify novel sites based on these shared features. Mismatches between genomic and expressed sequences were filtered to remove the main sources of false positives, and then prioritized based on these features. This protocol is tailored to identifying specific recoding editing sites, rather than sites in non-coding repeat sequences.

Results: Our protocol is more sensitive for identifying known coding editing sites than any previously published mammalian screen. A novel multiply edited transcript, BC10, was identified and experimentally verified. BC10 is highly conserved across a range of metazoa and has been implicated in two forms of cancer.

Contact: daniel.clutterbuck{at}hgu.mrc.ac.uk

Supplementary information: On journal website.


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