基于大规模RNA-seq数据绘制猪RNA编辑图谱的研究

doi:10.13560/j.cnki.biotech.bull.1985.2024-0455

生物技术通报 ›› 2024, Vol. 40 ›› Issue (10): 288-295.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0455

基于大规模RNA-seq数据绘制猪RNA编辑图谱的研究

龙佳佳¹^,²^,³(), 刘玮玮¹^,²^,³, 范新浩²^,³^,⁴, 黎旺长¹, 杨小淦¹, 唐中林¹^,²^,³^,⁴()

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

收稿日期:2024-05-15 出版日期:2024-10-26 发布日期:2024-11-20
通讯作者: 唐中林，男，博士，研究员，研究方向：猪遗传育种；E-mail: tangzhonglin@caas.cn
作者简介:龙佳佳，男，硕士研究生，研究方向：动物遗传育种；E-mail: 2118301022@st.gxu.edu.cn
基金资助:
国家自然科学基金项目(U23A20229);巴马县科技人才计划项目(20220018)

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

LONG Jia-jia¹^,²^,³(), LIU Wei-wei¹^,²^,³, FAN Xin-hao²^,³^,⁴, LI Wang-chang¹, YANG Xiao-gan¹, TANG Zhong-lin¹^,²^,³^,⁴()

1. Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004
2. Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226
3. 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
4. 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

Received:2024-05-15 Published:2024-10-26 Online:2024-11-20

摘要/Abstract

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3 461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130 989个RNA编辑位点，其中，A-to-I RNA编辑位点有124 208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。

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

Abstract:

【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 3 461 RNA-seq datasets from 16 types of pig tissues and detected RNA editing sites in pigs using bioinformatics methods.【Result】 A total of 130 989 RNA editing sites were detected, of which 124 208 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.

Key words: A-to-I RNA editing, fat deposition, pig, tissue, tissue-specific RNA editing sites

龙佳佳, 刘玮玮, 范新浩, 黎旺长, 杨小淦, 唐中林. 基于大规模RNA-seq数据绘制猪RNA编辑图谱的研究[J]. 生物技术通报, 2024, 40(10): 288-295.

LONG Jia-jia, LIU Wei-wei, FAN Xin-hao, LI Wang-chang, YANG Xiao-gan, TANG Zhong-lin. Study on Constructing an RNA Editing Map of Pig Based on Large-scale RNA-seq Data[J]. Biotechnology Bulletin, 2024, 40(10): 288-295.

图/表 5

表1 所有组织的RNA编辑位点过滤标准

Table 1 Filtering criteria for RNA editing sites of all tissues

组织 Tissue	RNA-seq数据量 Number of RNA-seq data	过滤阈值 Filtering threshold
骨骼肌Skeletal muscle	1427	16
肝Liver	367	6
大肠Large intestine	74	6
大脑Brain	215	9
肺Lung	118	11
小肠Small intestine	239	11
卵巢Ovary	99	5
输卵管Oviduct	22	5
脂肪Adipose	332	16
心Heart	89	5
睾丸Testis	133	7
子宫Uterus	150	7
淋巴Lymph	32	5
垂体Pituitary	52	8
脾Spleen	78	5
肾Kindy	34	5

图1 RNA编辑位点的鉴定结果及验证 A：所有组织的RNA编辑位点主成分析图；B：所有RNA编辑位点类型及重复区域分布图；C：本研究与其他研究位点的韦恩图；D：Sanger测序验证RNA编辑位点，蓝色箭头表示RNA编辑位点位置

Fig. 1 Identification result and validation of RNA editing sites A：PCA analysis plot of RNA editing sites across all tissues. B：Distribution of all RNA editing site types and repeat regions. C：Venn diagram of sites from this study and other studies. D：Validation of RNA editing sites by sanger, the blue arrows indicates the locations of RNA editing sites

图2 所有组织的A-to-I RNA编辑位点特征 A：A-to-I RNA编辑位点的总体编辑水平分布直方图；B：不同组织样本平均位点数量；C：A-to-I RNA编辑位点在基因组区域分布的直方图；D：A-to-I RNA编辑位点在重复区域分布；E：A-to-I RNA编辑位点上下游5 bp碱基偏好性分析；F：不同组织位点的编辑水平

Fig. 2 Characteristics of A-to-I RNA editing sites across all tissues A: Histogram of overall editing levels of A-to-I RNA editing sites. B：Average number of sites per sample in different tissues. C：Histogram of the genomic distribution of A-to-I RNA editing sites. D：Distribution of A-to-I RNA editing sites in repeat regions. E：Upstream and downstream 5 bp base preference analysis of A-to-I RNA editing sites. F：Editing levels of sites in different tissues

图3 ADAR酶家族基因在每个组织中的表达水平

Fig. 3 Expression levels of ADAR enzyme family genes in each tissue

图4 脂肪和其他组织的特异性位点 A：7种组织的特异性位点热图；B：脂肪组织特异性位点在基因组分布直方图；C：脂肪组织特异性位点宿主基因的GO富集柱状图

Fig. 4 Specific sites of adipose and other tissue A：Heatmap of tissue-specific sites in seven tissues. B：Histogram of the genomic distribution of adipose tissue-specific sites. C：Bar chart of GO enrichment of host genes for adipose tissue-specific sites

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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 Large-scale RNA-seq Data

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