Abstract
Massive transcriptome sequencing through the RNAseq technology has enabled quantitative transcriptome-wide investigation of co-/post-transcriptional mechanisms such as alternative splicing and RNA editing. The latter is abundant in human transcriptomes in which million adenosines are deaminated into inosines by the ADAR enzymes. RNA editing modulates the innate immune response and its deregulation has been associated with different human diseases including autoimmune and inflammatory pathologies, neurodegenerative and psychiatric disorders, and tumors. Accurate profiling of RNA editing using deep transcriptome data is still a challenge, and the results depend strongly on processing and alignment steps taken. Accurate calling of the inosinome repertoire, however, is required to reliably quantify RNA editing and, in turn, investigate its biological and functional role across multiple samples. Using real RNAseq data, we demonstrate the impact of different bioinformatics steps on RNA editing detection and describe the main metrics to quantify its level of activity.
Highlights
Eukaryotic organisms exhibit quite complex and dynamic transcriptomes whose regulation is essential for all cellular processes and for maintaining the homeostatic state (Mele et al, 2015)
SNPs and somatic mutations may be partly filtered out using genomic reads from matched whole genome sequencing (WGS) or whole exome sequencing (WXS) experiments, as well as tables of known SNPs from public databases
The number of detected sites varied depending on the processing steps, suggesting that the trimming procedure as well as the aligner type affect the detection of RNA editing
Summary
Eukaryotic organisms exhibit quite complex and dynamic transcriptomes whose regulation is essential for all cellular processes and for maintaining the homeostatic state (Mele et al, 2015). The complexity and dynamicity of transcriptomes depends on highly controlled and modulated post-transcriptional mechanisms such as alternative splicing and RNA modifications (Pan et al, 2008; Meyer and Jaffrey, 2014; Roundtree et al, 2017). The latter are emerging as key players in promoting transcriptome diversity and fine tuning gene expression (Helm and Motorin, 2017; Roundtree et al, 2017). The most common RNA editing event involves the deamination of adenosine (A) into inosine (I), carried out by members of the ADAR family of enzymes acting on double stranded RNA (dsRNA) (Nishikura, 2016; Eisenberg and Levanon, 2018)
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