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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Main Authors: Ying Zhang, Woyu Su, Bo Zhang, Yao Ling, Woo Kyun Kim, Hao Zhang
Format: Article
Language:English
Published: BMC 2021-05-01
Series:Journal of Animal Science and Biotechnology
Subjects:
Online Access:https://doi.org/10.1186/s40104-021-00582-2
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spelling 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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