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A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins

dc.contributor.author Ensterö, Mats
dc.contributor.author Akerborg, Orjan
dc.contributor.author Lundin, Daniel
dc.contributor.author Wang, Bei
dc.contributor.author Furey, Terrence S
dc.contributor.author Ohman, Marie
dc.contributor.author Lagergren, Jens
dc.date.accessioned 2011-06-21T17:29:30Z
dc.date.available 2011-06-21T17:29:30Z
dc.date.issued 2010
dc.identifier.citation Enstero,Mats;Akerborg,Orjan;Lundin,Daniel;Wang,Bei;Furey,Terrence S.;Ohman,Marie;Lagergren,Jens. 2010. A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. Bmc Bioinformatics 11( ): 6-6.
dc.identifier.issn 1471-2105
dc.identifier.uri https://hdl.handle.net/10161/4337
dc.description.abstract Background: Several bioinformatic approaches have previously been used to find novel sites of ADAR mediated A-to-I RNA editing in human. These studies have discovered thousands of genes that are hyper-edited in their non-coding intronic regions, especially in alu retrotransposable elements, but very few substrates that are site-selectively edited in coding regions. Known RNA edited substrates suggest, however, that site selective A-to-I editing is particularly important for normal brain development in mammals. Results: We have compiled a screen that enables the identification of new sites of site-selective editing, primarily in coding sequences. To avoid hyper-edited repeat regions, we applied our screen to the alu-free mouse genome. Focusing on the mouse also facilitated better experimental verification. To identify candidate sites of RNA editing, we first performed an explorative screen based on RNA structure and genomic sequence conservation. We further evaluated the results of the explorative screen by determining which transcripts were enriched for A-G mismatches between the genomic template and the expressed sequence since the editing product, inosine (I), is read as guanosine (G) by the translational machinery. For expressed sequences, we only considered coding regions to focus entirely on re-coding events. Lastly, we refined the results from the explorative screen using a novel scoring scheme based on characteristics for known A-to-I edited sites. The extent of editing in the final candidate genes was verified using total RNA from mouse brain and 454 sequencing. Conclusions: Using this method, we identified and confirmed efficient editing at one site in the Gabra3 gene. Editing was also verified at several other novel sites within candidates predicted to be edited. Five of these sites are situated in genes coding for the neuron-specific RNA binding proteins HuB and HuD.
dc.language.iso en_US
dc.publisher Springer Science and Business Media LLC
dc.relation.isversionof 10.1186/1471-2105-11-6
dc.subject double-stranded-rna
dc.subject pre-messenger-rna
dc.subject adenosine deamination
dc.subject snp
dc.subject database
dc.subject identification
dc.subject adar1
dc.subject gene
dc.subject sequences
dc.subject mouse
dc.subject information
dc.subject biochemical research methods
dc.subject biotechnology & applied microbiology
dc.subject mathematical & computational biology
dc.title A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins
dc.title.alternative
dc.type Other article
dc.description.version Version of Record
duke.date.pubdate 2010-1-4
duke.description.issue
duke.description.volume 11
dc.relation.journal Bmc Bioinformatics
pubs.begin-page 6
pubs.declined 2017-11-21T16:41:12.166-0500


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