Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens
Abstract Background Tibetan chickens, a unique native breed in the Qinghai-Tibet Plateau of China, possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) play rol...
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doaj-8147dd01a1184f16ae8ece01b06105c82021-05-09T11:05:29ZengBMCJournal of Animal Science and Biotechnology2049-18912021-05-0112111410.1186/s40104-021-00582-2Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickensYing Zhang0Woyu Su1Bo Zhang2Yao Ling3Woo Kyun Kim4Hao Zhang5National Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural UniversityNational Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural UniversityNational Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural UniversityNational Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural UniversityDepartment of Poultry Science, University of Georgia, 303 Poultry Science BuildingNational Engineering Laboratory for Animal Breeding, Plateau Animal Genetic Resources Center, China Agricultural UniversityAbstract Background Tibetan chickens, a unique native breed in the Qinghai-Tibet Plateau of China, possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) play roles in the hypoxic adaptation of high-altitude animals, although their exact involvement remains unclear. Results This study aimed to elucidate the global landscape of mRNAs, lncRNAs, and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs (ceRNAs) and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos. In total, 354 differentially expressed genes (DE genes), 389 differentially expressed lncRNAs (DE lncRNAs), and 73 differentially expressed miRNAs (DE miRNAs) were identified between Tibetan chickens (TC) and control Chahua chickens (CH). GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis (including blood vessel development and blood circulation) and energy metabolism (including glucose, carbohydrate, and lipid metabolism). The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions, which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens. Conclusions Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism. These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.https://doi.org/10.1186/s40104-021-00582-2ceRNAHypoxic adaptationNon-coding RNATibetan chickenTranscriptome |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ying Zhang Woyu Su Bo Zhang Yao Ling Woo Kyun Kim Hao Zhang |
spellingShingle |
Ying Zhang Woyu Su Bo Zhang Yao Ling Woo Kyun Kim Hao Zhang Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens Journal of Animal Science and Biotechnology ceRNA Hypoxic adaptation Non-coding RNA Tibetan chicken Transcriptome |
author_facet |
Ying Zhang Woyu Su Bo Zhang Yao Ling Woo Kyun Kim Hao Zhang |
author_sort |
Ying Zhang |
title |
Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens |
title_short |
Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens |
title_full |
Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens |
title_fullStr |
Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens |
title_full_unstemmed |
Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens |
title_sort |
comprehensive analysis of coding and non-coding rna transcriptomes related to hypoxic adaptation in tibetan chickens |
publisher |
BMC |
series |
Journal of Animal Science and Biotechnology |
issn |
2049-1891 |
publishDate |
2021-05-01 |
description |
Abstract Background Tibetan chickens, a unique native breed in the Qinghai-Tibet Plateau of China, possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) play roles in the hypoxic adaptation of high-altitude animals, although their exact involvement remains unclear. Results This study aimed to elucidate the global landscape of mRNAs, lncRNAs, and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs (ceRNAs) and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos. In total, 354 differentially expressed genes (DE genes), 389 differentially expressed lncRNAs (DE lncRNAs), and 73 differentially expressed miRNAs (DE miRNAs) were identified between Tibetan chickens (TC) and control Chahua chickens (CH). GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis (including blood vessel development and blood circulation) and energy metabolism (including glucose, carbohydrate, and lipid metabolism). The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions, which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens. Conclusions Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism. These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs. |
topic |
ceRNA Hypoxic adaptation Non-coding RNA Tibetan chicken Transcriptome |
url |
https://doi.org/10.1186/s40104-021-00582-2 |
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