RNA Editing in the Bovine Transcriptome

RNA editing is a post-transcriptional process that results in altered transcript sequences due to the modification of nucleotides. Of the known types of RNA editing, the most common is the deamination of adenosine to inosine (A-to-I), catalyzed by adenosine deaminase acting on RNA (ADAR). These nucleotide substitutions occur in a site-specific and tissue dependent manner and can lead to increased protein sequence diversity and altered UTR binding sites. A-to-I editing can be observed as an adenosine to guanine (A-to-G) substitution in RNA with respect to the DNA.  We searched for putative RNA editing sites in Bos taurus using high throughput RNAseq data of 48 tissues harvested from L1 Dominette 01449, the bovine reference genome individual.  RNAseq reads (Illumina,100 bp single-end) were aligned to the bovine UMD3.1 genome assembly using BWA and Hisat.  Reads with high quality bases were used to identify variants; then RNAseq variants were filtered for single nucleotide polymorphisms (SNP) using dbSNP and SNPs called from the alignment of ~60x Dominette genomic sequencing data.  A variant was predicted if it was represented in at least ten reads and greater than 10 percent of the reads supported the alternate allele.  Our analysis revealed hundreds of A-to-I RNA editing sites in the bovine transcriptome. We predicted the effects of edits within protein coding regions, and whether editing in UTR impact miRNA binding sites.