Show simple item record Furey, Terry en_US 2011-06-21T17:29:30Z 2011-06-21T17:29:30Z 2010 en_US
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. en_US
dc.identifier.issn 1471-2105 en_US
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. en_US
dc.language.iso en_US en_US
dc.publisher BIOMED CENTRAL LTD en_US
dc.relation.isversionof doi:10.1186/1471-2105-11-6 en_US
dc.subject double-stranded-rna en_US
dc.subject pre-messenger-rna en_US
dc.subject adenosine deamination en_US
dc.subject snp en_US
dc.subject database en_US
dc.subject identification en_US
dc.subject adar1 en_US
dc.subject gene en_US
dc.subject sequences en_US
dc.subject mouse en_US
dc.subject information en_US
dc.subject biochemical research methods en_US
dc.subject biotechnology & applied microbiology en_US
dc.subject mathematical & computational biology en_US
dc.title A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins en_US
dc.title.alternative en_US
dc.description.version Version of Record en_US 2010-1-4 en_US
duke.description.endpage 6 en_US
duke.description.issue en_US
duke.description.startpage 6 en_US
duke.description.volume 11 en_US
dc.relation.journal Bmc Bioinformatics en_US

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