Dataset Information

Detection and integrated analysis of lncRNA and mRNA relevant to plateau adaptation of Yak.

ABSTRACT: Known as the 'ship of the plateau', through thousands of years evolution and cruelty environments selection containing low oxygen and strong ultraviolet radiation, yaks have adapted plateau environments and supplied important goods and materials for the people in the Qinghai-Tibet Plateau. This study aimed to identify differentially expressed (DE) genes and novel long non-coding RNAs (lncRNAs) of yaks for the Plateau adaptation and their underlying co-expression and regulatory network. We carried out RNA-seq analysis for cerebral and cerebellar tissue specimens of Bos taurus, Bos grunniens × Bos Taurus and B. grunniens. Furthermore, 12,072 pseudo lncRNAs were predicted using three software. In total, 4,257 significant DE transcripts were identified using the Ballgown R package (p < .01), of which 1,021 were protein-coding genes, 14 were known lncRNAs, and 661 were novel lncRNAs. Using WGCNA, a co-expression network of DE mRNAs and lncRNAs comprising 5 modules was generated to determine functional associations clusters. This study reveals a valuable sub-network comprising 8 hub genes, one known lncRNA and 5 novel lncRNAs in the major module. These hub genes are associated with blood pressure regulation, generation of reactive oxygen species and metabolism. The analysis of co-expressed genes thus provides a basis for the regulatory mechanisms in PA in Yaks and for the detection of additional genes between cross-breed and parent populations.

SUBMITTER: Wang J

PROVIDER: S-EPMC7756654 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Detection and integrated analysis of lncRNA and mRNA relevant to plateau adaptation of Yak.

Wang Jiabo J Chai Zhixin Z Deng Lei L Wang Jikun J Wang Hui H Tang You Y Zhong Jincheng J Ji Qiumei Q

Reproduction in domestic animals = Zuchthygiene 20201005 11

Known as the 'ship of the plateau', through thousands of years evolution and cruelty environments selection containing low oxygen and strong ultraviolet radiation, yaks have adapted plateau environments and supplied important goods and materials for the people in the Qinghai-Tibet Plateau. This study aimed to identify differentially expressed (DE) genes and novel long non-coding RNAs (lncRNAs) of yaks for the Plateau adaptation and their underlying co-expression and regulatory network. We carrie ...[more]

PMID: 32633845

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Project description:BackgroundMarek's disease virus (MDV) is an oncogenic herpesvirus that can cause T-cell lymphomas in chicken. Long noncoding RNA (lncRNA) is strongly associated with various cancers and many other diseases. In chickens, lncRNAs have not been comprehensively identified. Here, we profiled mRNA and lncRNA repertoires in three groups of spleens from MDV-infected and non-infected chickens, including seven tumorous spleens (TS) from MDV-infected chickens, five spleens from the survivors (SS) without lesions after MDV infection, and five spleens from noninfected chickens (NS), to explore the underlying mechanism of host resistance in Marek's disease (MD).ResultsBy using a precise lncRNA identification pipeline, we identified 1315 putative lncRNAs and 1166 known lncRNAs in spleen tissue. Genomic features of putative lncRNAs were characterized. Differentially expressed (DE) mRNAs, putative lncRNAs, and known lncRNAs were profiled among three groups. We found that several specific intergroup differentially expressed genes were involved in important biological processes and pathways, including B cell activation and the Wnt signaling pathway; some of these genes were also found to be the hub genes in the co-expression network analyzed by WGCNA. Network analysis depicted both intergenic correlation and correlation between genes and MD traits. Five DE lncRNAs including MSTRG.360.1, MSTRG.6725.1, MSTRG.6754.1, MSTRG.15539.1, and MSTRG.7747.5 strongly correlated with MD-resistant candidate genes, such as IGF-I, CTLA4, HDAC9, SWAP70, CD72, JCHAIN, CXCL12, and CD8B, suggesting that lncRNAs may affect MD resistance and tumorigenesis in chicken spleens through their target genes.ConclusionsOur results provide both transcriptomic and epigenetic insights on MD resistance and its pathological mechanism. The comprehensive lncRNA and mRNA transcriptomes in MDV-infected chicken spleens were profiled. Co-expression analysis identified integrated lncRNA-mRNA and gene-gene interaction networks, implying that hub genes or lncRNAs exert critical influence on MD resistance and tumorigenesis.

Dataset Information

Detection and integrated analysis of lncRNA and mRNA relevant to plateau adaptation of Yak.

Publications

Detection and integrated analysis of lncRNA and mRNA relevant to plateau adaptation of Yak.

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