Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue
Abstract Background The rabbit is widely used as an important experimental model for biomedical research, and shows low adipose tissue deposition during growth. Long non-coding RNAs (lncRNAs) are associated with adipose growth, but little is known about the function of lncRNAs in the rabbit adipose...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-11-01
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| Series: | Lipids in Health and Disease |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12944-018-0915-1 |
| _version_ | 1818922705093656576 |
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| author | Guo-Ze Wang Kun Du Shen-Qiang Hu Shi-Yi Chen Xian-Bo Jia Ming-Cheng Cai Yu Shi Jie Wang Song-Jia Lai |
| author_facet | Guo-Ze Wang Kun Du Shen-Qiang Hu Shi-Yi Chen Xian-Bo Jia Ming-Cheng Cai Yu Shi Jie Wang Song-Jia Lai |
| author_sort | Guo-Ze Wang |
| collection | DOAJ |
| description | Abstract Background The rabbit is widely used as an important experimental model for biomedical research, and shows low adipose tissue deposition during growth. Long non-coding RNAs (lncRNAs) are associated with adipose growth, but little is known about the function of lncRNAs in the rabbit adipose tissue. Methods Deep RNA-sequencing and comprehensive bioinformatics analyses were used to characterize the lncRNAs of rabbit visceral adipose tissue (VAT) at 35, 85 and 120 days after birth. Differentially expressed (DE) lncRNAs were identified at the three growth stages by DESeq. The cis and trans prediction ways predicted the target genes of the DE lncRNAs. To explore the function of lncRNAs, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the candidate genes. Results A total of 991,157,544 clean reads were generated after RNA-Seq of the three growth stages, of which, 30,353 and 107 differentially expressed (DE) lncRNAs were identified. Compared to the protein-coding transcripts, the rabbit lncRNAs shared some characteristics such as shorter length and fewer exons. Cis and trans target gene prediction revealed, 43 and 64 DE lncRNAs respectively, corresponding to 72 and 20 protein-coding genes. GO enrichment and KEGG pathway analyses revealed that the candidate DE lncRNA target genes were involved in oxidative phosphorylation, glyoxylate and dicarboxylate metabolism, and other adipose growth-related pathways. Six DE lncRNAs were randomly selected and validated by q-PCR. Conclusions This study is the first to profile the potentially functional lncRNAs in the adipose tissue growth in rabbits, and contributes to our understanding of mammalian adipogenesis. |
| first_indexed | 2024-12-20T01:57:47Z |
| format | Article |
| id | doaj.art-8f9b5e92d4514d95b32575639c33d892 |
| institution | Directory Open Access Journal |
| issn | 1476-511X |
| language | English |
| last_indexed | 2024-12-20T01:57:47Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Lipids in Health and Disease |
| spelling | doaj.art-8f9b5e92d4514d95b32575639c33d8922022-12-21T19:57:26ZengBMCLipids in Health and Disease1476-511X2018-11-0117111010.1186/s12944-018-0915-1Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissueGuo-Ze Wang0Kun Du1Shen-Qiang Hu2Shi-Yi Chen3Xian-Bo Jia4Ming-Cheng Cai5Yu Shi6Jie Wang7Song-Jia Lai8Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityFarm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural UniversityAbstract Background The rabbit is widely used as an important experimental model for biomedical research, and shows low adipose tissue deposition during growth. Long non-coding RNAs (lncRNAs) are associated with adipose growth, but little is known about the function of lncRNAs in the rabbit adipose tissue. Methods Deep RNA-sequencing and comprehensive bioinformatics analyses were used to characterize the lncRNAs of rabbit visceral adipose tissue (VAT) at 35, 85 and 120 days after birth. Differentially expressed (DE) lncRNAs were identified at the three growth stages by DESeq. The cis and trans prediction ways predicted the target genes of the DE lncRNAs. To explore the function of lncRNAs, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the candidate genes. Results A total of 991,157,544 clean reads were generated after RNA-Seq of the three growth stages, of which, 30,353 and 107 differentially expressed (DE) lncRNAs were identified. Compared to the protein-coding transcripts, the rabbit lncRNAs shared some characteristics such as shorter length and fewer exons. Cis and trans target gene prediction revealed, 43 and 64 DE lncRNAs respectively, corresponding to 72 and 20 protein-coding genes. GO enrichment and KEGG pathway analyses revealed that the candidate DE lncRNA target genes were involved in oxidative phosphorylation, glyoxylate and dicarboxylate metabolism, and other adipose growth-related pathways. Six DE lncRNAs were randomly selected and validated by q-PCR. Conclusions This study is the first to profile the potentially functional lncRNAs in the adipose tissue growth in rabbits, and contributes to our understanding of mammalian adipogenesis.http://link.springer.com/article/10.1186/s12944-018-0915-1RabbitAdipose tissueLong non-coding RNARNA-Seq |
| spellingShingle | Guo-Ze Wang Kun Du Shen-Qiang Hu Shi-Yi Chen Xian-Bo Jia Ming-Cheng Cai Yu Shi Jie Wang Song-Jia Lai Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue Lipids in Health and Disease Rabbit Adipose tissue Long non-coding RNA RNA-Seq |
| title | Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue |
| title_full | Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue |
| title_fullStr | Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue |
| title_full_unstemmed | Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue |
| title_short | Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue |
| title_sort | genome wide identification and characterization of long non coding rnas during postnatal development of rabbit adipose tissue |
| topic | Rabbit Adipose tissue Long non-coding RNA RNA-Seq |
| url | http://link.springer.com/article/10.1186/s12944-018-0915-1 |
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