Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing

作     者：Yuebo Zhang Longchao Zhang Jingwei Yue Xia Wei Ligang Wang Xin Liu Hongmei Gao Xinhua Hou Fuping Zhao Hua Yan Lixian Wang 

作者机构：Key Laboratory of Animal(Poultry)Genetics Breeding and ReproductionMinistry of Agriculture Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China 

出 版 物：《Journal of Animal Science and Biotechnology》 (畜牧与生物技术杂志（英文版）)

年 卷 期：2019年第10卷第2期

页      面：339-352页

核心收录：

学科分类：0905[农学-畜牧学] 09[农学] 

基　　金：supported by the National Key Technology R&D Program of China(2015BAD03B02–2) Beijing Natural Science Foundation(6174047) earmarked fund for Modern Agro-industry Technology Research System(CARS-35) Agricultural Science and Technology Innovation Program(ASTIP-IAS02) 

主　　题：ADAR A-to-G High-throughput sequencing RNA editing Swine 

摘      要：Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has enabled the identification of RNA edits at unprecedented throughput and resolution. However, our knowledge of RNA editing in swine is still ***: Here, we utilized RES-Scanner to identify RNA editing sites in the brain, subcutaneous fat, heart, liver,muscle, lung and ovary in three 180-day-old Large White gilts based on matched strand-specific RNA sequencing and whole-genome resequencing datasets. In total, we identified 74863 editing sites, and 92.1% of these sites caused adenosine-to-guanosine(A-to-G) conversion. Most A-to-G sites were located in noncoding regions and generally had low editing levels. In total, 151 A-to-G sites were detected in coding regions(CDS), including 94 sites that could lead to nonsynonymous amino acid changes. We provide further evidence supporting a previous observation that pig transcriptomes are highly editable at PRE-1 elements. The number of A-to-G editing sites ranged from 4155(muscle) to 25001(brain) across the seven tissues. The expression levels of the ADAR enzymes could explain some but not all of this variation across tissues. The functional analysis of the genes with tissuespecific editing sites in each tissue revealed that RNA editing might play important roles in tissue ***, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the ***: This study identified a total of 74863 nonredundant RNA editing sites in seven tissues and revealed the potential importance of RNA editing in tissue function. Our findings largely extend the porcine editome and enhance our understanding of RNA editing in swine.