Identifying mRNA Editing Deaminase Targets by RNA-Seq
RNA editing deaminases act on a variety of targets in different organisms. A number of such enzymes have been shown to act on mRNA, with the resultant nucleotide changes modifying a transcript’s information content. Though the deaminase activity of mRNA editing enzymes is readily demonstratedin vitro, identifying their physiological targets has proved challenging. Recent advances in ultra high-throughput sequencing technologies have allowed for whole transcriptome sequencing and expression profiling (RNA-Seq). We have developed a system to identify novel mRNA editing deamination targets based on comparative analysis of RNA-Seq data. The efficacy and utility of this approach is demonstrated for APOBEC1, a cytidine deaminase with a known and well-characterized mRNA editing target in the mammalian small intestine.
Key wordsRNA editing Cytidine deaminase Adenosine deaminase APOBEC1 RNA-Seq
- 5.Hirano, K., Young, S. G., Farese, R. V., Ng, J., Sande, E., Warburton, C., Powell-Braxton, L. M., and Davidson, N. O. (1996) Targeted disruption of the mouse apobec-1 gene abolishes apolipoprotein B mRNA editing and eliminates apolipoprotein B48, J Biol Chem 271, 9887–9890.PubMedCrossRefGoogle Scholar
- 7.Illumina. (2008) Using the Single-Read Cluster Generation Kit v2 on the Cluster Station, San Diego, CA.Google Scholar
- 8.Illumina. (2008) Using SBS Sequencing Kit v3 on the Genome Analyzer, San Diego, CA.Google Scholar