A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.
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.
Ensterö
Mats
M
Department of Molecular Biology and Functional Genomics, Stockholm University, Svante Arrheniusväg 20C, SE-10691 Stockholm, Sweden.
Akerborg
Orjan
O
Lundin
Daniel
D
Wang
Bei
B
Furey
Terrence S
TS
Ohman
Marie
M
Lagergren
Jens
J
D000241:Adenosine / Q000235:genetics* / Q000378:metabolism; D020087:Alu Elements / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D016678:Genome; D007288:Inosine / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D009474:Neurons / Q000378:metabolism*; D010802:Phylogeny; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D017393:RNA Editing; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA
D016601:RNA-Binding Proteins; D007288:Inosine; D012313:RNA; D000241:Adenosine