Genome-wide identification and analysis of A-to-I RNA editing events in bovine by transcriptome sequencing

Abstract

RNA editing increases the diversity of the transcriptome and proteome. Adenosine-to-inosine (A-to-I) editing is the predominant type of RNA editing in mammals and it is catalyzed by the adenosine deaminases acting on RNA (ADARs) family. Here, we used a largescale computational analysis of transcriptomic data from brain, heart, colon, lung, spleen, kidney, testes, skeletal muscle and liver, from three adult animals in order to identify RNA editing sites in bovine. We developed a computational pipeline and used a rigorous strategy to identify novel editing sites from RNA-Seq data in the absence of corresponding DNA sequence information. Our methods take into account sequencing errors, mapping bias, as well as biological replication to reduce the probability of obtaining a false-positive result. We conducted a detailed characterization of sequence and structural features related to novel candidate sites and found 1,600 novel canonical A-to-I editing sites in the nine bovine tissues analyzed. Results show that these sites 1) occur frequently in clusters and short interspersed nuclear elements (SINE) repeats, 2) have a preference for guanines depletion/enrichment in the flanking 5′/3′ nucleotide, 3) occur less often in coding sequences than other regions of the genome, and 4) have low evolutionary conservation. Further, we found that a positive correlation exists between expression of ADAR family members and tissue-specific RNA editing. Most of the genes with predicted A-to-I editing in each tissue were significantly enriched in biological terms relevant to the function of the corresponding tissue. Lastly, the results highlight the importance of the RNA editome in nervous system regulation. The present study extends the list of RNA editing sites in bovine and provides pipelines that may be used to investigate the editome in other organisms.

Large-scale RNA editing profiling in different adult chicken tissues

“…Among all 68 the A-to-G editing sites, 42% had editing ratio <30%, whereas 17% had editing ratio >60%. In agreement with our previous study (Bakhtiarizadeh et al, 2018) in bovine, no significant difference was observed (using unpaired t-test and adjusted P-value <0.05) in the average editing ratio between different tissues. The average level of editing ratio was 0.38, 0.38 0.6, 0.40, 0.53, 0.37, 0.36 and 0.36 in brain, colon, heart, kidney, liver, lung, spleen and testes, respectively (Figure 4, Supplementary File S3).…”

“…The second and third type of the identified events were T-to-C and G-to-A mismatches. Interestingly, similar results are reported in human (Ramaswami et al, 2013, Franzén et al, 2018 and bovine (Bakhtiarizadeh et al, 2018), which used strand-specific RNA-Seq data for RNA editing detection. On the other hand, we can use the ratio of G-to-A to Ato-G mismatches as a criterion for evaluating the specificity of the RNA editing detection, as have been used in previous studies (Levanon et al, 2004, Bahn et al, 2012, Liscovitch-Brauer et al, 2017.…”

“…Although the mechanisms of target recognition by ADAR enzymes are not well understood, it has been shown that under-and over-represented nucleotide in the 5′ -1 and the 3′ +1 of A-to-G editing sites is guanine in mammals (Danecek et al, 2012, Bazak et al, 2014, Picardi et al, 2015. Here, when the flanking sequences of all A-to-G editing sites were analyzed, a similar sequence-preference between chicken and mammals was observed (Bazak et al, 2014, Picardi et al, 2015, Huntley et al, 2016, Bakhtiarizadeh et al, 2018, suggesting similar ADAR preference among mammals and birds (Bazak et al, 2014, Picardi et al, 2015. Interestingly, under-representation of A nucleotide in regions upstream and downstream editing sites is consistent with other studies in human (Picardi et al, 2015) and rhesus macaque .…”

“…Expression of these genes varied across the tissues, as ADARB1 was uniformly expressed in all tissues (the highest expression observed in brain). As with mammals (Picardi et al, 2015, Bakhtiarizadeh et al, 2018, ADARB2 was exclusively expressed in brain (Figure 8). In spite of the questionable editing activity of ADARB2 (CHEN et al, 2000), this result has raised the suspicion that the expression pattern of this gene can explain why more A-to-G editing sites occurred in the brain than the other tissues.…”

“…The development of high-throughput sequencing technology such as RNA-Seq method and the open access data sharing in genomic research have facilitated the discovery of RNA editing events and its functional mechanisms in different organisms. Hence, many genome-wide characterizations of RNA editing studies have been performed in primate such as human (Bahn et al, 2012, Li and Church, 2013, Bazak et al, 2014, Mo et al, 2014, Picardi et al, 2015, mouse (Danecek et al, 2012, Gu et al, 2012, Lagarrigue et al, 2013, Huntley et al, 2016, cattle (Pinto et al, 2014, Bakhtiarizadeh et al, 2018, pig (Larsen et al, 2016), chicken (Frésard et al, 2015, Roux et al, 2016 using this method, that has expedited the exploration of a large number of RNA editing sites (Picardi et al, 2015). The importance of chickens in evolutionary biology is quite obvious, as they are known as an ideal organism for filling the evolution gap between mammals and other vertebrates (Roux et al, 2016).…”