A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10.
Bioinformatics
; 21(11): 2590-5, 2005 Jun 01.
Article
in En
| MEDLINE
| ID: mdl-15797904
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 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.
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Collection:
01-internacional
Database:
MEDLINE
Main subject:
Algorithms
/
Sequence Alignment
/
Chromosome Mapping
/
Sequence Analysis, RNA
/
RNA Editing
/
Neoplasm Proteins
Type of study:
Evaluation_studies
Limits:
Animals
/
Humans
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2005
Document type:
Article
Affiliation country:
Reino Unido