Next Article in Journal
Establishment and Expression of Cytokines in a Theileria annulata-Infected Bovine B Cell Line
Previous Article in Journal
Distribution and Evolution of Nonribosomal Peptide Synthetase Gene Clusters in the Ceratocystidaceae
Erratum published on 10 July 2019, see Genes 2019, 10(7), 520.
Open AccessArticle

Genome-Wide Investigation and Functional Analysis of Sus scrofa RNA Editing Sites across Eleven Tissues

by Zishuai Wang 1,†, Xikang Feng 1,†, Zhonglin Tang 2,* and Shuai Cheng Li 1,*
1
Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
2
Department of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2019, 10(5), 327; https://doi.org/10.3390/genes10050327
Received: 6 March 2019 / Revised: 8 April 2019 / Accepted: 17 April 2019 / Published: 30 April 2019
(This article belongs to the Section Animal Genetics and Genomics)
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). Sus scrofa 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 Sus scrofa RNA editing study. View Full-Text
Keywords: RNA editing; pig; comprehensive analysis; database; tissues RNA editing; pig; comprehensive analysis; database; tissues
Show Figures

Figure 1

MDPI and ACS Style

Wang, Z.; Feng, X.; Tang, Z.; Li, S.C. Genome-Wide Investigation and Functional Analysis of Sus scrofa RNA Editing Sites across Eleven Tissues. Genes 2019, 10, 327.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop