Comprehensive Analyses Of RNA Editing Events In Rat Based On Large High-throughput RNA-Seq Data

RNA editing is the process of changing the genetic information at the mRNA level. It is a post-transcriptional regulation phenomenon. During the gene transcription, since the nucleotide deletion, insertion or substitution, the transcripts may not be complementary to the original gene sequence. So it could not maintain the genome information faithfully. RNA editing could potentially affect RNA translation and regulation. Most transcripts of some genes must be edited for its effectively initiating translation as it could produce the correct open reading frame, which has vital biological significance. RNA editing can not only change the sequence of amino acids, alter the translation initiation codon or termination codon, destroy or re-build alternative splicing signals, but also can affect miRNA precursor processing and mature miRNA targeting capabilities. It plays an important role in diversity of potein, tissue development and differentiation. However, the abnormal RNA editing events may cause some serious diseases, such as:depression, schizophrenia, amyotrophic lateral sclerosis and some other nervous system disorders.Rat(Rattus norvegicus) is a crucial model organism in toxicological, neurological and drug research for its short period and high similarity with human. Compared with the human, mouse, rhesus macaque plutella xylostella and drosophila melanogaster, the study of RNA editing events in rat has yet been scarce. There are few published papers that can offer some reference. Therefore, in order to better understand RNA editing events in rat, the study used RNA-seq datasets, which contains 320 RNA samples derived from eleven organs from both sexes of Fischer 344 rats across four developmental stages (immature, puberty, adult, and aged), to developed a suit of pipeline to predict and annotate the RNA editing sites. The results were verified through the public databases and previously studies by literature mining. It shows that the pipeline in this article demonstrated a high performance and reliability.On the basis of the pipeline, a total of 1,032,006 possible RNA editing sites were predicted from 320 samples. After all redundant sites been removed, there were 51,463 RNA editing sites left. From this number, we can conclude that the overlap degree of RNA editing events was high, which was consistent with previous studies that the same editing site often presents in different individuals, whereas rare SNPs are most likely not. Then the sites that had unique strand orientation according to Ensembl rat gene annotation files were selected. At last,29,576 RNA editing sites were finally obtained for subsequent analysis, which contained ANNOVAR annotation, pathway analysis, evolution of the conservative analysis, biological function analysis of RNA eidting sites that located in 3’UTR and 5’UTR, sequence context analysis, and so on.Through our comprehensive analyses of RNA editing events in rat, this paper found that the major editing types in rat included C-to-T, A-to-G, G-to-A and T-to-C conversions, which was significantly different from primates that the most common type of RNA editing events is A-to-G. The frequency of RNA editing events was closely related to activity of tissues and gene expression. RNA editing events located in protein-coding region might affect protein functions by altering protein spatial structure and RNA secondary structure. A special base preference was depicted in RNA editing loci. Tissue-specific RNA editing events were associated with the corresponding tissue biological functions. Besides, when analyzed a RNA editing site that located in 5’UTR occurring at kozak consensus sequence, it showed that the RNA editing event had a great impact on transcription and translation, which is a totally innovative discovery. A verification site mapping to gene Cog3 showed that the RNA editing events are results of a long evolutionary process. All the results had fully demonstrated that the RNA editing events play an important role in organism’s growth and development across the whole life cycle. This study can not only provide deep insights into the rat editome but also improve our understanding in RNA editing events for leading to a better preclinical model for drug development and translational medicine.