Investigating the extent and function of RNA editing in animal transcriptomes

RNA editing is a post-transcriptional process in which certain nucleotides in RNA become modified to change the sequence of the RNA. The two types of RNA editing involve the deamination of adenosine to inosine (A-to-I) and the deamination of cytosine to uracil (C-to-U) that are mediated respectively by the ADAR family of enzymes and APOBEC1. Although there are many examples of RNA editing altering the coding sequence of specific genes, the extent of RNA editing within metazoans has remained an open problem. Here, I investigate the extent and function of RNA editing in human cell lines, mice, and flies using RNA-seq as well as a new method called ICE-seq. I first assessed the extent of RNA editing as part of the ENCODE project. RNA-seq datasets from fourteen human cell lines were mined for RNA editing events using a novel method that relies on ENCODE ChIP-seq datasets to filter out genomic SNPs. I separately identified new C-to-U RNA editing targets within mouse livers and intestinal enterocytes by comparing wild-type and Apobec1 knockout mice RNA-seq data. I identified 56 Apobec1 RNA editing targets and found that a subset of the targets have altered mRNA and protein levels. Finally, I used ICE-seq to study RNA editing within two species of Drosophila. ICE-seq is a method that includes an acrylonitrile treatment of RNA prior to reverse-transcription. The acrylonitrile specifically reacts with inosine to block reverse transcription. By comparing ICE-seq and RNA-seq samples, RNA editing events were called from Drosophila melanogaster and Drosophila yakuba. I found that there is a core set of RNA editing targets that are shared between the two species and a set of targets with distinct functional enrichments that are species-specific, which suggests that the biological function of RNA editing in these two Drosophila species is still evolving