Abstract
Simple SummaryIn order to investigate RNA editing sites affecting IMF (which is associated with pork quality and human insulin resistance.), we analyzed the transcriptome and genome sequencing data of a high- and low- groups composed of full-sib pairs pig with opposite IMF phenotypes. Finally, a total of 36 nonredundant RNA editing sites in the longissimus dorsi muscle, which may reveal the potential importance of RNA editing in IMF were identified. Four were selected as candidate sites associated with IMF. Our findings provide some new insights of RNA editing function in pig longissimus dorsi muscle.Intramuscular fat (IMF) is essential for improving the palatability and flavor of meat, and it is strongly associated with human insulin resistance. RNA editing is a widespread regulating event in different tissues. Here, we investigated the global RNA editing difference of two groups of pig with different IMF contents to find the potential editing sites affecting IMF. In this research, RES-Scanner and REDItools were used to identify RNA editing sites based on the whole genome and transcriptome sequencing data of the high and low groups composed of three full-sib pairs with opposite IMF phenotypes. A total of 295 RNA editing sites were investigated in the longissimus dorsi muscle, and 90.17% of these sites caused A to G conversion. After annotation, most editing sites were located in noncoding regions (including five sites located on the 3′ UTR regions). Five editing sites (including two sites that could lead to nonsynonymous amino acid changes) were located in the exons of genes. A total of 36 intergroup (high and low IMF) differential RNA editing sites were found in 33 genes. Some candidate editing sites, such as sites in acyl-coenzymeA: cholesterol acyltransferase 1 (ACAT1), coatomer protein, subunit alpha (COPA), and nuclear receptor coactivator 3 (NCOA3), were selected as candidate RNA editing sites associated with IMF. One site located on the 3′ UTR region of growth hormone secretagogue receptor (GHSR) may regulate GHSR expression by affecting the interaction of miRNA and mRNA. In conclusion, we identified a total of 36 nonredundant RNA editing sites in the longissimus dorsi muscle, which may reveal the potential importance of RNA editing in IMF. Four were selected as candidate sites associated with IMF. Our findings provide some new insights of RNA editing function in pig longissimus dorsi muscle which useful for pig IMF breeding or human insulin resistances research.
Highlights
RNA editing is the post-transcriptional or co-transcriptional process which could make transcripts more complicated and results in potential functional consequences [1,2]
RNA editing is associated with disease [3,4,5]; in animals, RNA editing was found to be associated with embryo and tissue development [1], production traits [17], and Newcastle disease virus [18]
To investigate the RNA editing sites at the transcriptome-wide level in longissimus dorsi muscle, DNA sequencing and matched strand-specific RNA sequencing were performed for the six pigs
Summary
RNA editing is the post-transcriptional or co-transcriptional process which could make transcripts more complicated and results in potential functional consequences [1,2]. Animals 2020, 10, 1616 been found in different vertebrates, including humans [3,4,5,6], mice [4], pigs [1,7,8], bovines [9], and chickens [10]. RNA editing sites in intergenic region may associated with nuclear retention [15], and in introns may disrupt alternative splicing [16]. RNA editing is associated with disease [3,4,5]; in animals, RNA editing was found to be associated with embryo and tissue development [1], production traits [17], and Newcastle disease virus [18]
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