基于大规模RNA-seq数据绘制猪RNA编辑图谱的研究  

Study on Constructing an RNA Editing Map of Pig Based on Largescale RNA-seq Data

作　　者：龙佳佳 刘玮玮 范新浩 黎旺长 杨小淦[1] 唐中林 LONG Jia-jia;LIU Wei-wei;FAN Xin-hao;LI Wang-chang;YANG Xiao-gan;TANG Zhong-lin(Guangxi Key Laboratory of Animal Breeding,Disease Control and Prevention,College of Animal Science&Technology,Guangxi University,Nanning 530004;Kunpeng Institute of Modern Agriculture at Foshan,Foshan 528226;Shenzhen Branch,Guangdong Laboratory for Lingnan Modern Agriculture,Key Laboratory of Livestock and Poultry Multi-Omics of MARA,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen 518124;Key Laboratory of Agricultural Animal Genetics,Breeding and Reproduction of Ministry of Education&Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs,Huazhong Agricultural University,Wuhan 430070)

机构地区：[1]广西大学动物科学技术学院广西畜禽繁育与疾病防控重点实验室,南宁530004 [2]佛山鲲鹏现代农业研究院,佛山528226 [3]中国农业科学院深圳农业基因组研究所(岭南现代农业科学与技术广东省实验室深圳分中心)中国农业科学院深圳农业基因组研究所畜禽多组学重点实验室,深圳518124 [4]华中农业大学农用动物遗传育种与繁殖教育部重点实验室农业农村部猪遗传育种重点实验室,武汉430070

出　　处：《生物技术通报》2024年第10期288-295,共8页Biotechnology Bulletin

基　　金：国家自然科学基金项目(U23A20229);巴马县科技人才计划项目(20220018)。

摘　　要：【目的】A-to-I RNA编辑是一种由ADAR酶家族介导的共转录/转录后修饰,系统绘制猪的RNA编辑图谱,为猪的分子育种提供候选靶标。【方法】收集16种猪组织的3461个RNA-seq数据,采用生物信息学方法检测猪RNA编辑位点。【结果】共检测到130989个RNA编辑位点,其中,A-to-I RNA编辑位点有124208个。A-to-I RNA编辑位点特征分析表明,98.2%的位点位于重复区域,且主要位于猪特异性的SINE反转录转座子区域的PRE-1/Pre0_SS元件内。只有12.3%的A-to-I RNA编辑位点具有编码意功能。最后,本研究分析了7种组织(脂肪、大脑、大肠、小肠、骨骼肌、肝和肺)的特异性A-to-I RNA编辑位点,脂肪组织特异性位点宿主基因的功能富集分析表明,这些基因在与细胞脂质代谢过程、脂质代谢过程、硫酯代谢过程等相关的信号通路中富集。在这些通路中,与脂肪沉积相关的基因有PDK1、ACSL1和PDE3B等。【结论】绘制了猪的RNA编辑位点图谱,为猪的分子育种提供了候选靶点。【Objective】A-to-I RNA editing is a co-transcriptional/post-transcriptional modification mediated by the ADAR enzyme family.The systematic mapping of the RNA editome in pigs provided candidate targets for molecular breeding in pigs.【Method】We collected 3461 RNA-seq datasets from 16 types of pig tissues and detected RNA editing sites in pigs using bioinformatics methods.【Result】A total of 130989 RNA editing sites were detected,of which 124208 were A-to-I RNA editing sites.Analysis of the characteristics of the A-to-I RNA editing sites revealed that 98.2%were located in repetitive regions,primarily within the PRE-1/Pre0_SS elements of pig-specific SINE retrotransposons.Only 12.3%of A-to-I RNA editing sites had coding potential.Finally,the study analyzed tissue-specific A-to-I RNA editing sites in seven tissues(adipose,brain,large intestine,small intestine,skeletal muscle,liver,and lung).Functional enrichment analysis of the host genes in adipose tissue-specific sites showed that these genes were enriched in pathways related to cellular lipid metabolic processes,lipid metabolic processes,and thioester metabolic processes.Genes related to fat deposition within these pathways included PDK1,ACSL1 and PDE3B.【Conclusion】This study comprehensively mapped the RNA editing sites in pigs,providing candidate targets for molecular breeding.

关 键 词：A-to-I RNA编辑 脂肪沉积 猪 组织 组织特异性RNA编辑位点 

分 类 号：S828[农业科学—畜牧学] Q78[农业科学—畜牧兽医]