Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing
Abstract 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 re...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-03-01
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| Series: | Journal of Animal Science and Biotechnology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s40104-019-0326-9 |
| _version_ | 1818936335571877888 |
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| author | Yuebo Zhang Longchao Zhang Jingwei Yue Xia Wei Ligang Wang Xin Liu Hongmei Gao Xinhua Hou Fuping Zhao Hua Yan Lixian Wang |
| author_facet | Yuebo Zhang Longchao Zhang Jingwei Yue Xia Wei Ligang Wang Xin Liu Hongmei Gao Xinhua Hou Fuping Zhao Hua Yan Lixian Wang |
| author_sort | Yuebo Zhang |
| collection | DOAJ |
| description | Abstract 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 limited. Results 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 tissue-specific editing sites in each tissue revealed that RNA editing might play important roles in tissue function. Specifically, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the muscle. Conclusions 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. |
| first_indexed | 2024-12-20T05:34:26Z |
| format | Article |
| id | doaj.art-330686585ee641a68bce12faaa96279f |
| institution | Directory Open Access Journal |
| issn | 2049-1891 |
| language | English |
| last_indexed | 2024-12-20T05:34:26Z |
| publishDate | 2019-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Animal Science and Biotechnology |
| spelling | doaj.art-330686585ee641a68bce12faaa96279f2022-12-21T19:51:40ZengBMCJournal of Animal Science and Biotechnology2049-18912019-03-0110111410.1186/s40104-019-0326-9Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencingYuebo Zhang0Longchao Zhang1Jingwei Yue2Xia Wei3Ligang Wang4Xin Liu5Hongmei Gao6Xinhua Hou7Fuping Zhao8Hua Yan9Lixian Wang10Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesKey Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural SciencesAbstract 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 limited. Results 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 tissue-specific editing sites in each tissue revealed that RNA editing might play important roles in tissue function. Specifically, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the muscle. Conclusions 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.http://link.springer.com/article/10.1186/s40104-019-0326-9ADARA-to-GHigh-throughput sequencingRNA editingSwine |
| spellingShingle | Yuebo Zhang Longchao Zhang Jingwei Yue Xia Wei Ligang Wang Xin Liu Hongmei Gao Xinhua Hou Fuping Zhao Hua Yan Lixian Wang Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing Journal of Animal Science and Biotechnology ADAR A-to-G High-throughput sequencing RNA editing Swine |
| title | Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing |
| title_full | Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing |
| title_fullStr | Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing |
| title_full_unstemmed | Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing |
| title_short | Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing |
| title_sort | genome wide identification of rna editing in seven porcine tissues by matched dna and rna high throughput sequencing |
| topic | ADAR A-to-G High-throughput sequencing RNA editing Swine |
| url | http://link.springer.com/article/10.1186/s40104-019-0326-9 |
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