RNA Editing detection using High-Through Sequencing

The central dogma of biology indicates DNA sequence gets transcribed to RNA sequence and then RNA sequence gets translated to protein. Thus, for long time it was known fact that each base of RNA sequence corresponds to an exact base in DNA sequence. However, Mahendran et al. (10.1038/349434a0) discovered for the first time this one to one relation is not necessary true. The phenomena where RNA sequences and DNA sequences are different is known as RNA editing(RNA DNA Difference). Although the underlying cause for RNA editing is still unknown, it is known A to I editing is the most common. A-I editing occurs when adenine (A) DNA base converts to guanine (G) base. On the other hand other sorts of RNA editing in mammalian genomes was known to be rare until recently where Li et al. (10.1126/science.1207018) reported 10,000 cites of RNA editing in human cancer cell lines where a significant number of them are not A-I editing. This study was the first that use the high-through sequencing (HTS) technologies to detect the RNA editing in whole genome scale. Following this study series of works supported the Li et al. (10.1126/science.1207018) results as the RNA editing is more common as was known before HTS era. On the orthogonal direction series of works (10.1371/journal.pone.0025842), (10.1126/science.1209658), (10.1126/science.1210484), and (10.1126/science.1210624) indicate vast majority of RNA editing observed in the HTS data is due to systematic error in sequencing process.

We use mouse as a model organism to study the RNA editing in mammalian genomes. We use the F1 cross of C57BL/6 and DBA. Leveraging the power of F1 mice and the fact both strains where deeply sequenced by Sanger institute (10.1038/nature10413) provide us with an ease framework to study RNA editing in mammalian genomes. Furthermore, to remove any technical artifacts we use biological replicate of the same F1 cross and we consider the mRNA of both liver and adipose tissues. In our paper (10.1534/genetics.112.149054) we used a set of stringent conditions to make sure our results contain no possible sequencing artifacts. Although, our stringent conditions may remove some true positive, our goal is to illustrate the existing of sequencing artifacts and further indicates the RNA editing beside the A-I exists but not as common as A-I editing. We found 63 sites in liver and 216 sites in adipose which are RNA editing.