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

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

Abstract

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

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.

Figures/Tables 5

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

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

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

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

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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