Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigs
Abstract Background The Tibetan pig, an indigenous breed adapted to plateau environments in China, exhibits remarkable tolerance to extreme high-altitude conditions. Recent studies have highlighted the pivotal role of non-coding RNAs (ncRNAs) in regulating hypoxic adaptation. However, the complex re...
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BMC
2025-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11783-8 |
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| author | Pan Li Wei Cheng Zhandui Pubu Peng Shang Hao Zhang Bo Zhang |
| author_facet | Pan Li Wei Cheng Zhandui Pubu Peng Shang Hao Zhang Bo Zhang |
| author_sort | Pan Li |
| collection | DOAJ |
| description | Abstract Background The Tibetan pig, an indigenous breed adapted to plateau environments in China, exhibits remarkable tolerance to extreme high-altitude conditions. Recent studies have highlighted the pivotal role of non-coding RNAs (ncRNAs) in regulating hypoxic adaptation. However, the complex regulatory network involving mRNAs and ncRNAs that mediate this adaptation in Tibetan pigs remains poorly understood. Results We performed whole-transcriptome sequencing to analyze expression profiles of mRNAs, lncRNAs, and miRNAs in heart tissues of Tibetan pigs (TH) and Yorkshire pigs (YH) at high altitude. We identified 795 differentially expressed lncRNAs (DE lncRNAs), 149 differentially expressed miRNAs (DE miRNAs), and 2,206 differentially expressed mRNAs (DE mRNAs) between TH and YH. Functional enrichment analysis showed that target genes of DE miRNAs, DE lncRNAs, and DE mRNAs significantly enriched pathways related to hypoxic adaptation, including Dilated Cardiomyopathy (DCM) and Hypertrophic Cardiomyopathy (HCM). We constructed a competing endogenous RNA (ceRNA) regulatory network comprising 8 DE lncRNAs, 37 DE miRNAs, and 7 DE mRNAs. Notably, we validated the MSTRG.19853.1/ssc-miR-361-3p/NPPA axis, a candidate regulator of cardiac adaptation, using quantitative real-time PCR (qRT-PCR) and dual-luciferase reporter assays. Conclusion Our findings elucidate comprehensive RNA expression profiles and ncRNA-mRNA interactions underlying hypoxic adaptation in Tibetan pig hearts compared to Yorkshire pigs at high altitude. The MSTRG.19853.1/ssc-miR-361-3p/NPPA axis represents a promising candidate for regulating cardiac adaptation under hypoxia, pending in vivo validation. These insights enhance our understanding of the genetic mechanisms driving high-altitude adaptation in Tibetan pigs, offering a foundation for comparative studies of hypoxic resilience in plateau mammals. Graphical Abstract The model of MSTRG.19853.1/ssc-miR-361-3p/NPPA axis for regulating hypoxia adaptation in Tibetan and Yorkshire pigs. |
| format | Article |
| id | doaj-art-9b2b1ca338704793b3e096a349937da0 |
| institution | DOAJ |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-9b2b1ca338704793b3e096a349937da02025-08-20T03:03:41ZengBMCBMC Genomics1471-21642025-07-0126111810.1186/s12864-025-11783-8Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigsPan Li0Wei Cheng1Zhandui Pubu2Peng Shang3Hao Zhang4Bo Zhang5Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding (MOE), China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding (MOE), China Agricultural UniversityDepartment of Animal Husbandry, Xizang Agricultural and Animal Husbandry UniversityFrontiers Science Center for Molecular Design Breeding (MOE), China Agricultural UniversityFrontiers Science Center for Molecular Design Breeding (MOE), China Agricultural UniversityAbstract Background The Tibetan pig, an indigenous breed adapted to plateau environments in China, exhibits remarkable tolerance to extreme high-altitude conditions. Recent studies have highlighted the pivotal role of non-coding RNAs (ncRNAs) in regulating hypoxic adaptation. However, the complex regulatory network involving mRNAs and ncRNAs that mediate this adaptation in Tibetan pigs remains poorly understood. Results We performed whole-transcriptome sequencing to analyze expression profiles of mRNAs, lncRNAs, and miRNAs in heart tissues of Tibetan pigs (TH) and Yorkshire pigs (YH) at high altitude. We identified 795 differentially expressed lncRNAs (DE lncRNAs), 149 differentially expressed miRNAs (DE miRNAs), and 2,206 differentially expressed mRNAs (DE mRNAs) between TH and YH. Functional enrichment analysis showed that target genes of DE miRNAs, DE lncRNAs, and DE mRNAs significantly enriched pathways related to hypoxic adaptation, including Dilated Cardiomyopathy (DCM) and Hypertrophic Cardiomyopathy (HCM). We constructed a competing endogenous RNA (ceRNA) regulatory network comprising 8 DE lncRNAs, 37 DE miRNAs, and 7 DE mRNAs. Notably, we validated the MSTRG.19853.1/ssc-miR-361-3p/NPPA axis, a candidate regulator of cardiac adaptation, using quantitative real-time PCR (qRT-PCR) and dual-luciferase reporter assays. Conclusion Our findings elucidate comprehensive RNA expression profiles and ncRNA-mRNA interactions underlying hypoxic adaptation in Tibetan pig hearts compared to Yorkshire pigs at high altitude. The MSTRG.19853.1/ssc-miR-361-3p/NPPA axis represents a promising candidate for regulating cardiac adaptation under hypoxia, pending in vivo validation. These insights enhance our understanding of the genetic mechanisms driving high-altitude adaptation in Tibetan pigs, offering a foundation for comparative studies of hypoxic resilience in plateau mammals. Graphical Abstract The model of MSTRG.19853.1/ssc-miR-361-3p/NPPA axis for regulating hypoxia adaptation in Tibetan and Yorkshire pigs.https://doi.org/10.1186/s12864-025-11783-8Tibetan pigHypoxic adaptationceRNA networkNon-coding RNAs |
| spellingShingle | Pan Li Wei Cheng Zhandui Pubu Peng Shang Hao Zhang Bo Zhang Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigs BMC Genomics Tibetan pig Hypoxic adaptation ceRNA network Non-coding RNAs |
| title | Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigs |
| title_full | Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigs |
| title_fullStr | Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigs |
| title_full_unstemmed | Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigs |
| title_short | Comprehensive transcriptome analysis reveals MSTRG.19853.1/ssc-miR-361-3p/NPPA axis is related to hypoxic adaptation in Tibetan pigs |
| title_sort | comprehensive transcriptome analysis reveals mstrg 19853 1 ssc mir 361 3p nppa axis is related to hypoxic adaptation in tibetan pigs |
| topic | Tibetan pig Hypoxic adaptation ceRNA network Non-coding RNAs |
| url | https://doi.org/10.1186/s12864-025-11783-8 |
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