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Bioinformatics Advance Access published online on March 29, 2005
Bioinformatics, 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@oupjournals.org
Received January 18, 2005
Revised March 21, 2005
Accepted March 24, 2005

Article

A bioinformatic screen for novel A-I RNA editing sites reveals re-coding editing in BC10

D. R. Clutterbuck 1*, A. Leroy 1, M. A. O'Connell 1, and C. A. M. Semple 1

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

* To whom correspondence should be addressed.
D. R. Clutterbuck, E-mail: daniel.clutterbuck{at}hgu.mrc.ac.uk


  Abstract

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 prioritised 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.

Supplementary Information: On journal website.


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