Global analysis of A-to-I RNA editing reveals association with common disease variants

Franzén, Oscar; Ermel, Raili; Sukhavasi, Katyayani; Jain, Rajeev; Jain, Anamika; Betsholtz, Christer; Giannarelli, Chiara; Kovacic, Jason C.; Ruusalepp, Arno; Skogsberg, Josefin; Hao, Ke; Schadt, Eric E.; Björkegren, Johan

doi:10.7717/peerj.4466

Cited by 21 publications

(22 citation statements)

References 80 publications

(105 reference statements)

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“…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.…”

Section: Discussionsupporting

confidence: 79%

“…We also observed low overlap among the three studies in chicken (Supplementary File S7). The limited overlap can be attributed in large part to differences in computational strategy, experimental design, read length and variability in the sequencing type (single/paired-end or stranded/non-stranded) as well as sequencing depth of samples, whereas the importance of these factors is highlighted in previous studies (Diroma et al, 2017, Franzén et al, 2018. For example, Hung et.…”

Section: )mentioning

confidence: 99%

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Large-scale RNA editing profiling in different adult chicken tissues

Shafiei

Salehi

2018

Preprint

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RNA editing is a post-transcription maturation process that diversifies genomically encoded information and can lead to diversity and complexity of transcriptome, especially in the brain.Thanks to next-generation sequencing technologies, a large number of editing sites have been identified in different species, especially in human, mouse and rat. While this mechanism is well described in mammals, only a few studies have been performed in the chicken. Here, we developed a rigorous computational strategy to identify RNA editing sites in eight different tissues of the chicken (brain, spleen, colon, lung, kidney, heart, testes and liver), based on RNA sequencing data alone. We identified 68 A-to-G editing sites in 46 genes. Only two of these were previously reported in chicken. We found no C-to-U sites, attesting the lack of this type of editing mechanism in the chicken. Similar to mammals, the editing sites were enriched in non-coding regions, rarely resulted in change of amino acids, showed a critical role in nervous system and had a low guanosine level upstream of the editing site and some enrichment downstream from the site.Moreover, in contrast to mammals, editing sites were weakly enriched in interspersed repeats and the frequency and editing ratio of non-synonymous sites were higher than those of synonymous sites.Interestingly, we found several tissue-specific edited genes including GABRA3, SORL1 and HTR1D in brain and RYR2 and FHOD3 in heart that were associated with functional processes relevant to the corresponding tissue. This finding highlighted the importance of the RNA editing in several chicken tissues, especially the brain. This study extends our understanding of RNA editing in chicken tissues and establish a foundation for further exploration of this process.

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Section: Discussionsupporting

confidence: 79%

Section: )mentioning

confidence: 99%

Large-scale RNA editing profiling in different adult chicken tissues

Shafiei

Salehi

2018

Preprint

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“…; Franzén et al . ) and bovine (Bakhtiarizadeh et al . ), for which strand‐specific RNA‐seq data was used for RNA editing detection.…”

Section: Discussionmentioning

confidence: 99%

Large‐scale potential RNA editing profiling in different adult chicken tissues

2019

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RNA editing is a post-transcription maturation process that diversifies genomically encoded information and can lead to transcriptome diversity. Thanks to next-generation sequencing technologies, a large number of editing sites have been identified in different species. Although this mechanism is well described in mammals, only a few studies have been performed in chicken. Here, candidate or potential RNA editing sites were identified in eight different tissues of chicken (brain, spleen, colon, lung, kidney, heart, testes and liver). We identified 68 A-to-G editing sites in 46 genes. Only two of these were previously reported in chicken. We found no C-to-T sites, attesting to the lack of this type of editing mechanism in chicken. Similar to mammals, the editing sites were enriched in non-coding regions, rarely resulted in a change in amino acids, showed a critical role in the nervous system and had a low guanosine level upstream of the editing site and some enrichment downstream from the site. Moreover, in contrast to mammals, editing sites were weakly enriched in interspersed repeats and the number and editing ratio of non-synonymous sites were higher than for those of synonymous sites. Interestingly, we found several tissue-specific edited genes, including GABRA3, SORL1 and HTR1D in brain and RYR2 and FHOD3 in heart, that were associated with functional processes relevant to the corresponding tissue. This finding highlights the importance of RNA editing in several chicken tissues, especially the brain, and establishes a foundation for further exploration of this process.

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“…Recently, global editing level has been investigated across tissues and in different species [21,22] and has also been correlated with the genetic background of human population [30,50] and with common disease variants [29]. However, the published studies lack a detailed characterization of samples that allows assessing the role of biological and environmental factors.…”

Section: Discussionmentioning

confidence: 99%

“…In parallel, the development of computational pipelines to search for RNA editing sites on RNA-Seq data, allowed a global analysis of the editing reaction, shedding light on its evolutionary conservation [20], tissues specificity [21,22], cellular specificity [23] and its role in diseases such cancer [24] or neurological disorders [9,25].About 2.5 million editing sites have been identified so far and are listed in RNA editing databases [26,27], but only recently the dynamic and regulation of RNA editing has been systematically investigated in human tissues [22]. However, little is known about how editing process could be influenced by genetic variations [28,29], biological and environmental variables [30]. Here, we want to go further in characterizing and understanding the complexity of RNA editing.…”

mentioning

confidence: 99%