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A comprehensive microRNA expression profile related to hypoxic adaptation in Tibetan pig

ABSTRACT: In this study, miRNA-seq technique was used to identify differentially expressed miRNAs (DE miRNAs) in cardiac muscle of the Tibetan pig (TP) and Yorkshire pig (YP), which were both raised in highland environments. We obtained 108 M clean reads and 372 unique miRNAs that included 210 known pre-miRNAs and 162 novel pre-miRNAs. In addition, 20 DE miRNAs, including 10 upregulated and 10 downregulated miRNAs, were identified by comparing TP and YP. Based on the expression abundance and differentiation between the two populations, we predicted their targets, and KEGG pathway analyses suggested that DE miRNAs between the Tibetan pigs and Yorkshire pigs are involved in hypoxia-related pathways, such as the MAPK, mTOR, and VEGF signaling pathways, cancer-related signaling pathways, etc. Five DE miRNAs were randomly selected to validate the veracity of miRNA-seq using real-time PCR. The results showed that the expression corresponds to the trend in miRNA-seq, hence the deep-sequencing methods were feasible and efficient. This study expanded the number of hypoxic-adaptation-related miRNAs in pig and indicated that the expression patterns of hypoxia-related miRNAs are significantly altered in the Tibetan pig. DE miRNAs may play important roles in hypoxic adaptation after migration to hypoxic environments.

ORGANISM(S): Sus scrofa

PROVIDER: GSE71550 | GEO | 2015/07/31

SECONDARY ACCESSION(S): PRJNA291498

REPOSITORIES: GEO

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A comprehensive microRNA expression profile related to hypoxic adaptation in Tibetan pig

Project description:In this study, miRNA-seq technique was used to identify differentially expressed miRNAs (DE miRNAs) in cardiac muscle of the Tibetan pig (TP) and Yorkshire pig (YP), which were both raised in highland environments. We obtained 108 M clean reads and 372 unique miRNAs that included 210 known pre-miRNAs and 162 novel pre-miRNAs. In addition, 20 DE miRNAs, including 10 upregulated and 10 downregulated miRNAs, were identified by comparing TP and YP. Based on the expression abundance and differentiation between the two populations, we predicted their targets, and KEGG pathway analyses suggested that DE miRNAs between the Tibetan pigs and Yorkshire pigs are involved in hypoxia-related pathways, such as the MAPK, mTOR, and VEGF signaling pathways, cancer-related signaling pathways, etc. Five DE miRNAs were randomly selected to validate the veracity of miRNA-seq using real-time PCR. The results showed that the expression corresponds to the trend in miRNA-seq, hence the deep-sequencing methods were feasible and efficient. This study expanded the number of hypoxic-adaptation-related miRNAs in pig and indicated that the expression patterns of hypoxia-related miRNAs are significantly altered in the Tibetan pig. DE miRNAs may play important roles in hypoxic adaptation after migration to hypoxic environments. mRNA profiles of 6-month old Tibetan pig (TP) and Yorkshire pig (YP) were generated by deep sequencing, in duplicate, using Hiseq 2000.

2015-07-31 | E-GEOD-71550 | biostudies-arrayexpress

Comparative transcriptomic and proteomic analysis provides insight into the key genes involved in high-altitude adaptation in Tibetan pig (RNA-seq)

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2016-12-29 | GSE92981 | GEO

A comparison of genome-wide DNA methylation profiles between Tibetan and Yorkshire pigs

Project description:We investigated the heart tissue whole-genome DNA methylation data of Tibetan and Yorkshire pigs raised at high and low altitudes using MeDIP-seq (methylated DNA immunoprecipitation sequencing) technologies, in order to comparatively analyze epigenetic regulation in the two breeds under normoxic and hypoxic conditions. In addition, we aimed to identify the key genes and molecular mechanisms that are involved in adaptation to high altitude in the Tibetan pig. The results of bisulphite sequencing and RT-qPCR indicated that the differentially methylated genes identified in MeDIP-seq were credible. Our results provide new insights into the molecular mechanisms and the epigenetic mechanism involved in hypoxic adaptation in pigs, and a greater understanding of human hypoxic diseases.

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2015-06-29 | E-GEOD-49299 | biostudies-arrayexpress

Integrating transcriptome and proteome profiles of prenatal muscle tissue to reveal the postnatal growth differences in pigsof Pig Muscle Tissue

Project description:We using RNA sequences (from RNA-seq) from the prenatal muscle tissues of three pig breeds (Tibetan pig [TP], Wujin pig [WJ], and Large White pig [LW]) were analyzed to compare the differentially expressed genes related to embryonic myogenesis and to identify the genes related to postnatal growth rate and growth potential in pigs. We obtained 38.7-50.1 million clean data through the RNA-seq and detected that 19,626 genes were positively expressed and 13,660 of them were co-expressed in the muscle tissues of the four samples. The 3,626 unique DEGs in TP were mainly enriched in 76 GO terms and 35 KEGG pathways.The GO terms mainly included ATP binding, calcium ion binding, negative regulation of transcription from RNA polymerase II promoter, and cell components of cytoplasm, nucleus, and extracellular exosome . The top 20 KEGG pathways mainly included metabolic, insulin signaling, FoxO signaling, and AMPK signaling pathways that are mostly involved in muscle development and growth.

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Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue [mRNA]

Project description:RNA sequences (from RNA-seq) from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small Ear pig [DSP] and Tibetan pig [TP]) and two introduced pig breeds (Landrace [LL] and Yorkshire [YY]) were examined using HiSeq 2000 to identify and compare the differential expression of functional genes related to muscle growth and lipid deposition. We obtained 27.18 G clean data through the RNA-seq and detected that 18,208 genes were positively expressed and 14,633 of them were co-expressed in the muscle tissues of the four samples. In all, 315 DEGs were found between the Chinese pig group and the introduced pig group, 240 of which were enriched with functional annotations from the David database and significantly enriched in 27 Gene Ontology (GO) terms that were mainly associated with muscle fiber contraction, cadmium ion binding, response to organic substance and contractile fiber part. Based on functional annotation, we identified 85 DEGs related to growth traits that were mainly involved in muscle tissue development, muscle system process, regulation of cell development, and growth factor binding, and 27 DEGs related to lipid deposition that were mainly involved in lipid metabolic process and fatty acid biosynthetic process.

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