Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China.
Department of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
Genes (Basel). 2019 Apr 30;10(5):327. doi: 10.3390/genes10050327.
Recently, the prevalence and importance of RNA editing have been illuminated in mammals. However, studies on RNA editing of pigs, a widely used biomedical model animal, are rare. Here we collected RNA sequencing data across 11 tissues and identified more than 490,000 RNA editing sites. We annotated their biological features, detected flank sequence characteristics of A-to-I editing sites and the impact of A-to-I editing on miRNA-mRNA interactions, and identified RNA editing quantitative trait loci (edQTL). RNA editing sites showed high enrichment in repetitive regions with a median editing level as 15.38%. Expectedly, 96.3% of the editing sites located in non-coding regions including intron, 3' UTRs, intergenic, and gene proximal regions. There were 2233 editing sites located in the coding regions and 980 of them caused missense mutation. Our results indicated that to an A-to-I editing site, the adjacent four nucleotides, two before it and two after it, have a high impact on the editing occurrences. A commonly observed editing motif is CCAGG. We found that 4552 A-to-I RNA editing sites could disturb the original binding efficiencies of miRNAs and 4176 A-to-I RNA editing sites created new potential miRNA target sites. In addition, we performed edQTL analysis and found that 1134 edQTLs that significantly affected the editing levels of 137 RNA editing sites. Finally, we constructed PRESDB, the first pig RNA editing sites database. The site provides necessary functions associated with RNA editing study.
最近，RNA 编辑在哺乳动物中的普遍性和重要性已经得到了阐明。然而，作为广泛使用的生物医学模型动物的猪的 RNA 编辑研究却很少。在这里，我们收集了 11 种组织的 RNA 测序数据，鉴定了超过 490,000 个 RNA 编辑位点。我们注释了它们的生物学特征，检测了 A-to-I 编辑位点侧翼序列特征以及 A-to-I 编辑对 miRNA-mRNA 相互作用的影响，并鉴定了 RNA 编辑数量性状基因座（edQTL）。RNA 编辑位点在重复区域高度富集，中位编辑水平为 15.38%。不出所料，96.3%的编辑位点位于非编码区，包括内含子、3'UTR、基因间区和基因近端区。有 2233 个编辑位点位于编码区，其中 980 个导致错义突变。我们的结果表明，对于一个 A-to-I 编辑位点，其相邻的四个核苷酸、前两个和后两个，对编辑发生有很大的影响。一个常见的编辑基序是 CCAGG。我们发现，4552 个 A-to-I RNA 编辑位点可以干扰 miRNA 的原始结合效率，4176 个 A-to-I RNA 编辑位点创造了新的潜在 miRNA 靶位点。此外，我们进行了 edQTL 分析，发现 1134 个 edQTL 显著影响 137 个 RNA 编辑位点的编辑水平。最后，我们构建了 PRESDB，这是第一个猪 RNA 编辑位点数据库。该网站提供了与 RNA 编辑研究相关的必要功能。
