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Zhang Y, Liu X, Zhang L, Wang L, He J, Ma H, Wang L. Preliminary identification and analysis of differential RNA editing between higher and lower backfat thickness pigs using DNA-seq and RNA-seq data. Anim Genet 2022; 53:327-339. [PMID: 35342974 DOI: 10.1111/age.13193] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/24/2021] [Accepted: 03/03/2022] [Indexed: 12/31/2022]
Abstract
RNA editing is an essential post-transcriptional regulatory mechanism. However, few studies have investigated the functional RNA edits in the economic traits of livestock on a genome-wide scale. Pigs are one of the most important livestock species and their fat is the principal organ involved in the regulation of adipose deposition. Here, we used three full-sibling pairs, with each pair comprising a pig with higher backfat (BF) thickness and lower backfat thickness, to identify RNA editing events based on whole-genome and transcriptome sequencing data. A total of 60,903 non-redundant RNA editing sites with 59,472 (97.7%) A-to-G edits were detected using a revised bioinformatics pipeline. A specific sequence context with G preference was found one base downstream of the edited site, and the editing level was associated with the distribution of nucleotides across nearly sites. Moreover, the A-to-G editing sites mostly occurred in the pig-special short interspersed nuclear elements, Pre0_SS. Comparing the difference between pigs with higher BF and lower BF, we found 211 differentially edited sites (DESites). Functional enrichment analyses revealed a significant enrichment of genes containing DESites in terms of adipose deposition. The DESites located in the six adipose-related genes (SKP1, GSK3B, COL5A3, MDM4, NT5C2, and DENND2A) were selected as candidate RNA editing sites associated with adipose deposition, and thus require further evaluation. This study mined the potentially functional RNA editing sites in pig adipose tissue and indicated that RNA editing may play an important role in adipose deposition, which provides a new insight into the post-transcriptionally mediated regulation mechanism of fat development.
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Affiliation(s)
- Yuebo Zhang
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha, China
| | - Xin Liu
- Institute of Animal Science, State Key Laboratory of Animal Nutrition, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Institute of Animal Science, State Key Laboratory of Animal Nutrition, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ligang Wang
- Institute of Animal Science, State Key Laboratory of Animal Nutrition, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun He
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha, China
| | - Lixian Wang
- Institute of Animal Science, State Key Laboratory of Animal Nutrition, Chinese Academy of Agricultural Sciences, Beijing, China
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Conservation of A-to-I RNA editing in bowhead whale and pig. PLoS One 2021; 16:e0260081. [PMID: 34882682 PMCID: PMC8659423 DOI: 10.1371/journal.pone.0260081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 11/02/2021] [Indexed: 01/18/2023] Open
Abstract
RNA editing is a post-transcriptional process in which nucleotide changes are introduced into an RNA sequence, many of which can contribute to proteomic sequence variation. The most common type of RNA editing, contributing to nearly 99% of all editing events in RNA, is A-to-I (adenosine-to-inosine) editing mediated by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. A-to-I editing at 'recoding' sites results in non-synonymous substitutions in protein-coding sequences. Here, we present studies of the conservation of A-to-I editing in selected mRNAs between pigs, bowhead whales, humans and two shark species. All examined mRNAs-NEIL1, COG3, GRIA2, FLNA, FLNB, IGFBP7, AZIN1, BLCAP, GLI1, SON, HTR2C and ADAR2 -showed conservation of A-to-I editing of recoding sites. In addition, novel editing sites were identified in NEIL1 and GLI1 in bowhead whales. The A-to-I editing site of human NEIL1 in position 242 was conserved in the bowhead and porcine homologues. A novel editing site was discovered in Tyr244. Differential editing was detected at the two adenosines in the NEIL1 242 codon in both pig and bowhead NEIL1 mRNAs in various tissues and organs. No conservation of editing of KCNB1 and EEF1A mRNAs was seen in bowhead whales. In silico analyses revealed conservation of five adenosines in ADAR2, some of which are subject to A-to-I editing in bowheads and pigs, and conservation of a regulatory sequence in GRIA2 mRNA that is responsible for recognition of the ADAR editing enzyme.
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3
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Adetula AA, Fan X, Zhang Y, Yao Y, Yan J, Chen M, Tang Y, Liu Y, Yi G, Li K, Tang Z. Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs ( Sus-scrofa). RNA Biol 2021; 18:439-450. [PMID: 34314293 PMCID: PMC8677025 DOI: 10.1080/15476286.2021.1954380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/08/2022] Open
Abstract
RNA editing generates genetic diversity in mammals by altering amino acid sequences, miRNA targeting site sequences, influencing the stability of targeted RNAs, and causing changes in gene expression. However, the extent to which RNA editing affect gene expression via modifying miRNA binding site remains unexplored. Here, we first profiled the dynamic A-to-I RNA editome across tissues of Duroc and Luchuan pigs. The RNA editing events at the miRNA binding sites were generated. The biological function of the differentially edited gene in skeletal muscle was further characterized in pig muscle-derived satellite cells. RNA editome analysis revealed a total of 171,909 A-to-I RNA editing sites (RESs), and examination of its features showed that these A-to-I editing sites were mainly located in SINE retrotransposons PRE-1/Pre0_SS element. Analysis of differentially edited sites (DESs) revealed a total of 4,552 DESs across tissues between Duroc and Luchuan pigs, and functional category enrichment analysis of differentially edited gene (DEG) sets highlighted a significant association and enrichment of tissue-developmental pathways including TGF-beta, PI3K-Akt, AMPK, and Wnt signaling pathways. Moreover, we found that RNA editing events at the miRNA binding sites in the 3'-UTR of HSPA12B mRNA could prevent the miRNA-mediated mRNA downregulation of HSPA12B in the muscle-derived satellite (MDS) cell, consistent with the results obtained from the Luchuan skeletal muscle. This study represents the most systematic attempt to characterize the significance of RNA editing in regulating gene expression, particularly in skeletal muscle, constituting a new layer of regulation to understand the genetic mechanisms behind phenotype variance in animals.Abbreviations: A-to-I: Adenosine-to-inosine; ADAR: Adenosine deaminase acting on RNA; RES: RNA editing site; DEG: Differentially edited gene; DES: Differentially edited site; FDR: False discovery rate; GO: Gene Ontology; KEGG: Kyoto Encyclopaedia of Genes and Genomes; MDS cell: musclederived satellite cell; RPKM: Reads per kilobase of exon model in a gene per million mapped reads; UTR: Untranslated coding regions.
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Affiliation(s)
- Adeyinka A. Adetula
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinhao Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongsheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yilong Yao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junyu Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Muya Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yijie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Group of Pig Genome and Design Breeding, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
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Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is an essential post-transcriptional modification. Although hundreds of thousands of RNA editing sites have been reported in mammals, brain-wide analysis of the RNA editing in the mammalian brain remains rare. Here, a genome-wide RNA-editing investigation is performed in 119 samples, representing 30 anatomically defined subregions in the pig brain. We identify a total of 682,037 A-to-I RNA editing sites of which 97% are not identified before. Within the pig brain, cerebellum and olfactory bulb are regions with most edited transcripts. The editing level of sites residing in protein-coding regions are similar across brain regions, whereas region-distinct editing is observed in repetitive sequences. Highly edited conserved recoding events in pig and human brain are found in neurotransmitter receptors, demonstrating the evolutionary importance of RNA editing in neurotransmission functions. Although potential data biases caused by age, sex or health status are not considered, this study provides a rich resource to better understand the evolutionary importance of post-transcriptional RNA editing. Huang et al performed a genome-wide RNA editing investigation in the porcine brain in which they found over 680,000 A-to-I RNA editing sites. They identified conserved recoding events between pig and human brains thus providing an extensive resource to aid our understanding of the evolutionary importance of post-transcriptional RNA editing.
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Wang Y, Song X, Xu T. Identification and Analysis of RNA Editing Events in Ovarian Serous Cystadenoma Using RNA-seq Data. Curr Gene Ther 2021; 21:258-269. [PMID: 33573552 DOI: 10.2174/1566523221666210211111324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent studies have revealed thousands of A-to-I RNA editing events in primates. These events are closely related to the occurrence and development of multiple cancers, but the origination and general functions of these events in ovarian cancer remain incompletely understood. OBJECTIVE To further the determination of molecular mechanisms of ovarian cancer from the perspective of RNA editing. METHODS Here, we used the SNP-free RNA editing Identification Toolkit (SPRINT) to detect RNA editing sites. These editing sites were then annotated, and related functional analysis was performed. RESULTS In this study, about 1.7 million RES were detected in each sample, and 98% of these sites were due to A-to-G editing and were mainly distributed in non-coding regions. More than 1,000 A-- to-G RES were detected in CDS regions, and nearly 700 could lead to amino acid changes. Our results also showed that editing in the 3'UTR regions could influence miRNA-target binding. We predicted the network of changed miRNA-mRNA interaction caused by the A-to-I RNA editing sites. We also screened the differential RNA editing sites between ovarian cancer and adjacent normal tissues. We then performed GO and KEGG pathway enrichment analysis on the genes that contained these differential RNA editing sites. Finally, we identified the potential dysregulated RNA editing events in ovarian cancer samples. CONCLUSION This study systematically identified and analyzed RNA editing events in ovarian cancer and laid a foundation to explore the regulatory mechanism of RNA editing and its function in ovarian cancer.
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Affiliation(s)
- Yulan Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
| | - Tianyi Xu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 211106, China
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Duan Y, Tang X, Lu J. Evolutionary driving forces of A-to-I editing in metazoans. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1666. [PMID: 33998151 DOI: 10.1002/wrna.1666] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 04/24/2021] [Indexed: 11/05/2022]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is an evolutionarily conserved mechanism that converts adenosines to inosines in metazoans' transcriptomes. However, the landscapes of editomes have considerably changed during evolution. Here, we review some of our current knowledge of A-to-I editing in the metazoan transcriptomes, focusing on the possible evolutionary driving forces underlying the editing events. First, we review the evolution of ADAR gene family in animals. Then, we summarize the recent advances in characterizing the editomes of various metazoan species. Next, we highlight several factors contributing to the interspecies differences in editomes, including variations in copy number and expression patterns of ADAR genes, the differences in genomic architectures and contents, and the differences in the efficacy of natural selection. After that, we review the possible diversifying and restorative effects of the editing (recoding) events that change the protein sequences. Finally, we discuss the possible convergent evolution of RNA editing in distantly related clades. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, China
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Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs. Animals (Basel) 2020; 10:ani10091616. [PMID: 32927662 PMCID: PMC7552122 DOI: 10.3390/ani10091616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/19/2022] Open
Abstract
Simple Summary In order to investigate RNA editing sites affecting IMF (which is associated with pork quality and human insulin resistance.), we analyzed the transcriptome and genome sequencing data of a high- and low- groups composed of full-sib pairs pig with opposite IMF phenotypes. Finally, a total of 36 nonredundant RNA editing sites in the longissimus dorsi muscle, which may reveal the potential importance of RNA editing in IMF were identified. Four were selected as candidate sites associated with IMF. Our findings provide some new insights of RNA editing function in pig longissimus dorsi muscle. Abstract Intramuscular fat (IMF) is essential for improving the palatability and flavor of meat, and it is strongly associated with human insulin resistance. RNA editing is a widespread regulating event in different tissues. Here, we investigated the global RNA editing difference of two groups of pig with different IMF contents to find the potential editing sites affecting IMF. In this research, RES-Scanner and REDItools were used to identify RNA editing sites based on the whole genome and transcriptome sequencing data of the high and low groups composed of three full-sib pairs with opposite IMF phenotypes. A total of 295 RNA editing sites were investigated in the longissimus dorsi muscle, and 90.17% of these sites caused A to G conversion. After annotation, most editing sites were located in noncoding regions (including five sites located on the 3′ UTR regions). Five editing sites (including two sites that could lead to nonsynonymous amino acid changes) were located in the exons of genes. A total of 36 intergroup (high and low IMF) differential RNA editing sites were found in 33 genes. Some candidate editing sites, such as sites in acyl-coenzymeA: cholesterol acyltransferase 1 (ACAT1), coatomer protein, subunit alpha (COPA), and nuclear receptor coactivator 3 (NCOA3), were selected as candidate RNA editing sites associated with IMF. One site located on the 3′ UTR region of growth hormone secretagogue receptor (GHSR) may regulate GHSR expression by affecting the interaction of miRNA and mRNA. In conclusion, we identified a total of 36 nonredundant RNA editing sites in the longissimus dorsi muscle, which may reveal the potential importance of RNA editing in IMF. Four were selected as candidate sites associated with IMF. Our findings provide some new insights of RNA editing function in pig longissimus dorsi muscle which useful for pig IMF breeding or human insulin resistances research.
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Zhou R, Yao W, Xie C, Zhang L, Pei Y, Li H, Feng Z, Yang Y, Li K. Developmental stage-specific A-to-I editing pattern in the postnatal pineal gland of pigs ( Sus scrofa). J Anim Sci Biotechnol 2020; 11:90. [PMID: 32944232 PMCID: PMC7487922 DOI: 10.1186/s40104-020-00495-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/07/2020] [Indexed: 11/10/2022] Open
Abstract
Background RNA editing is a widespread post-transcriptional modification mechanism in mammalian genomes. Although many editing sites have been identified in domestic pigs (Sus scrofa), little is known about the characteristics and dynamic regulation of RNA editing in the pineal gland (PG), a small neuroendocrine gland that synthesizes and secretes melatonin, which is primarily responsible to modulate sleep patterns. Results This study analyzed the expression of adenosine-to-inosine (A-to-I) editing regulators and profiled the first dynamic A-to-I RNA editome during postnatal PG development. The results identified ADAR1 as the most abundantly expressed ADAR enzyme, which was down-regulated during postnatal PG development. Furthermore, 47,284 high-confidence RNA editing sites were identified, the majority of which (93.6%) were of the canonical A-to-I editing type, followed by C-to-T editing. Analysis of its characteristics showed that the A-to-I editing sites mostly localized in SINE retrotransposons PRE-1/Pre0_SS. Moreover, a strong deficiency and preference for guanine nucleotides at positions of one base upstream or downstream were found, respectively. The overall editing level at the puberty stage was higher than at both infancy and adulthood stages. Additionally, genome-wide RNA editing was found to exhibit a dynamic stage-specific fashion (postnatally). Genes that underwent developmental changes in RNA editing were associated with catabolic processes as well as protein localization and transport functions, implying that RNA editing might be responsible for the molecular machineries of the postnatal developing PG. Remarkably, RNA editing in 3'-UTRs might regulate gene expression by influencing miRNA binding during PG development. Conclusions This study profiles the first comprehensive developmental RNA editome in the pig PG, which contributes to the understanding of the importance of post-transcriptionally mediated regulation during mammalian postnatal PG development. Moreover, this study widely extends RNA editome resources in mammals.
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Affiliation(s)
- Rong Zhou
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231 Guangdong China.,State Key Laboratory of Animal Nutrition; Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Wenye Yao
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Chundi Xie
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Leixia Zhang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231 Guangdong China
| | - Yangli Pei
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231 Guangdong China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231 Guangdong China
| | - Zheng Feng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231 Guangdong China
| | - Yalan Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231 Guangdong China
| | - Kui Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan, 528231 Guangdong China.,State Key Laboratory of Animal Nutrition; Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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9
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Yang L, Li L, Kyei B, Guo J, Zhan S, Zhao W, Song Y, Zhong T, Wang L, Xu L, Zhang H. Systematic analyses reveal RNA editing events involved in skeletal muscle development of goat (Capra hircus). Funct Integr Genomics 2020; 20:633-643. [PMID: 32447468 DOI: 10.1007/s10142-020-00741-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 11/24/2022]
Abstract
RNA editing is a posttranscriptional molecular process involved with specific nucleic modification, which can enhance the diversity of gene products. Adenosine-to-inosine (A-to-I, I is read as guanosine by both splicing and translation machinery) is the main type of RNA editing in mammals, which manifested as AG (adenosine-to-guanosine) in sequence data. Here, we aimed to explore patterns of RNA editing using RNA sequencing data from skeletal muscle at four developmental stages (three fetal periods and one postnatal period) in goat. We found the occurrences of RNA editing events raised at fetal periods and declined at the postnatal period. Also, we observed distinct editing levels of AG editing across stages, and significant difference was found between postnatal period and fetal periods. AG editing patterns in newborn goats are similar to those of 45-day embryo compared with embryo at 105 days and embryo at 60 days. In this study, we found a total of 1415 significantly differential edited AG sites among four groups. Moreover, 420 sites were obviously clustered into six time-series profiles, and one profile had significant association between editing level and gene expression. Our findings provided some novel insights into understanding the molecular mechanism of muscle development in mammals.
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Affiliation(s)
- Liu Yang
- Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bismark Kyei
- Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Zhao
- Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yumo Song
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
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10
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Wang Z, Feng X, Tang Z, Li SC. Genome-Wide Investigation and Functional Analysis of Sus scrofa RNA Editing Sites across Eleven Tissues. Genes (Basel) 2019; 10:genes10070520. [PMID: 31295957 PMCID: PMC6678271 DOI: 10.3390/genes10070520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zishuai Wang
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong.
| | - Xikang Feng
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong.
| | - Zhonglin Tang
- Department of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong.
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