Skip Navigation



Bioinformatics Advance Access published online on March 29, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti411
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
21/11/2590    most recent
bti411v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Clutterbuck, D. R.
Right arrow Articles by Semple, C. A. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Clutterbuck, D. R.
Right arrow Articles by Semple, C. A. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
M. Barak, E. Y. Levanon, E. Eisenberg, N. Paz, G. Rechavi, G. M. Church, and R. Mehr
Evidence for large diversity in the human transcriptome created by Alu RNA editing
Nucleic Acids Res., November 1, 2009; 37(20): 6905 - 6915.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
J. P. Palavicini, M. A. O'connell, and J. J.C. Rosenthal
An extra double-stranded RNA binding domain confers high activity to a squid RNA editing enzyme
RNA, June 1, 2009; 15(6): 1208 - 1218.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
J. B. Li, E. Y. Levanon, J.-K. Yoon, J. Aach, B. Xie, E. LeProust, K. Zhang, Y. Gao, and G. M. Church
Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing
Science, May 29, 2009; 324(5931): 1210 - 1213.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
R. Schulz, R. B. McCole, K. Woodfine, A. J. Wood, M. Chahal, D. Monk, G. E. Moore, and R. J. Oakey
Transcript- and tissue-specific imprinting of a tumour suppressor gene
Hum. Mol. Genet., January 1, 2009; 18(1): 118 - 127.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
W. M. Gommans, N. E. Tatalias, C. P. Sie, D. Dupuis, N. Vendetti, L. Smith, R. Kaushal, and S. Maas
Screening of human SNP database identifies recoding sites of A-to-I RNA editing
RNA, October 1, 2008; 14(10): 2074 - 2085.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
E. M. Riedmann, S. Schopoff, J. C. Hartner, and M. F. Jantsch
Specificity of ADAR-mediated RNA editing in newly identified targets
RNA, June 1, 2008; 14(6): 1110 - 1118.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
N. Paz, E. Y. Levanon, N. Amariglio, A. B. Heimberger, Z. Ram, S. Constantini, Z. S. Barbash, K. Adamsky, M. Safran, A. Hirschberg, et al.
Altered adenosine-to-inosine RNA editing in human cancer
Genome Res., November 1, 2007; 17(11): 1586 - 1595.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
H. Poulsen, R. Jorgensen, A. Heding, F. C. Nielsen, B. Bonven, and J. Egebjerg
Dimerization of ADAR2 is mediated by the double-stranded RNA binding domain
RNA, July 1, 2006; 12(7): 1350 - 1360.
[Abstract] [Full Text] [PDF]

Home page
 Brief Funct Genomic ProteomicHome page
E. Y. Levanon and E. Eisenberg
Algorithmic approaches for identification of RNA editing sites
Brief Funct Genomic Proteomic, March 1, 2006; 5(1): 43 - 45.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
Y. Feng, C. L. Sansam, M. Singh, and R. B. Emeson
Altered RNA Editing in Mice Lacking ADAR2 Autoregulation
Mol. Cell. Biol., January 15, 2006; 26(2): 480 - 488.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. E. Watkins Jr and J. SantaLucia Jr
Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes
Nucleic Acids Res., November 1, 2005; 33(19): 6258 - 6267.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.