Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326–NKX3.2-Regulated Porcine Chondrocyte Differentiation
The porcine body length trait is an essential factor affecting meat production and reproductive performance. It is evident that the development/lengthening of individual vertebrae is one of the main reasons for increases in body length; however, the underlying molecular mechanism remains unclear. In...
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MDPI AG
2023-04-01
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| author | Qiao Xu Yabiao Luo Zhe Chao Jibin Zhang Ximing Liu Qiguo Tang Kejun Wang Shuyi Tan Meiying Fang |
| author_facet | Qiao Xu Yabiao Luo Zhe Chao Jibin Zhang Ximing Liu Qiguo Tang Kejun Wang Shuyi Tan Meiying Fang |
| author_sort | Qiao Xu |
| collection | DOAJ |
| description | The porcine body length trait is an essential factor affecting meat production and reproductive performance. It is evident that the development/lengthening of individual vertebrae is one of the main reasons for increases in body length; however, the underlying molecular mechanism remains unclear. In this study, RNA-seq analysis was used to profile the transcriptome (lncRNA, mRNA, and miRNA) of the thoracic intervertebral cartilage (TIC) at two time points (1 and 4 months) during vertebral column development in Yorkshire (Y) and Wuzhishan pigs (W). There were four groups: 1- (Y1) and 4-month-old (Y4) Yorkshire pigs and 1- (W1) and 4-month-old (W4) Wuzhishan pigs. In total, 161, 275, 86, and 126 differentially expressed (DE) lncRNAs, 1478, 2643, 404, and 750 DE genes (DEGs), and 74,51, 34, and 23 DE miRNAs (DE miRNAs) were identified in the Y4 vs. Y1, W4 vs. W1, Y4 vs. W4, and Y1 vs. W1 comparisons, respectively. Functional analysis of these DE transcripts (DETs) demonstrated that they had participated in various biological processes, such as cellular component organization or biogenesis, the developmental process, the metabolic process, bone development, and cartilage development. The crucial bone development-related candidate genes NK3 Homeobox 2 (<i>NKX3.2</i>), Wnt ligand secretion mediator (<i>WLS</i>), gremlin 1 (<i>GREM1</i>), fibroblast growth factor receptor 3 (<i>FGFR3</i>), hematopoietically expressed homeobox (<i>HHEX</i>), (collagen type XI alpha 1 chain (<i>COL11A1</i>), and Wnt Family Member 16 (<i>WNT16</i>)) were further identified by functional analysis. Moreover, lncRNA, miRNA, and gene interaction networks were constructed; a total of 55 lncRNAs, 6 miRNAs, and 7 genes formed lncRNA–gene, miRNA–gene, and lncRNA–miRNA–gene pairs, respectively. The aim was to demonstrate that coding and non-coding genes may co-regulate porcine spine development through interaction networks. <i>NKX3.2</i> was identified as being specifically expressed in cartilage tissues, and it delayed chondrocyte differentiation. miRNA-326 regulated chondrocyte differentiation by targeting <i>NKX3.2</i>. The present study provides the first non-coding RNA and gene expression profiles in the porcine TIC, constructs the lncRNA–miRNA–gene interaction networks, and confirms the function of <i>NKX3.2</i> in vertebral column development. These findings contribute to the understanding of the potential molecular mechanisms regulating pig vertebral column development. They expand our knowledge about the differences in body length between different pig species and provide a foundation for future studies. |
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| spelling | doaj.art-51a923ab5ad44eb087c4d5a720c5b17f2023-11-17T19:37:40ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-04-01248725710.3390/ijms24087257Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326–NKX3.2-Regulated Porcine Chondrocyte DifferentiationQiao Xu0Yabiao Luo1Zhe Chao2Jibin Zhang3Ximing Liu4Qiguo Tang5Kejun Wang6Shuyi Tan7Meiying Fang8Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaInstitute of Animal Sciences and Veterinary, Hainan Academy of Agricultural Sciences, Haikou 571100, ChinaDepartment of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91006, USADepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaInstitute of Animal Sciences and Veterinary, Hainan Academy of Agricultural Sciences, Haikou 571100, ChinaDepartment of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaThe porcine body length trait is an essential factor affecting meat production and reproductive performance. It is evident that the development/lengthening of individual vertebrae is one of the main reasons for increases in body length; however, the underlying molecular mechanism remains unclear. In this study, RNA-seq analysis was used to profile the transcriptome (lncRNA, mRNA, and miRNA) of the thoracic intervertebral cartilage (TIC) at two time points (1 and 4 months) during vertebral column development in Yorkshire (Y) and Wuzhishan pigs (W). There were four groups: 1- (Y1) and 4-month-old (Y4) Yorkshire pigs and 1- (W1) and 4-month-old (W4) Wuzhishan pigs. In total, 161, 275, 86, and 126 differentially expressed (DE) lncRNAs, 1478, 2643, 404, and 750 DE genes (DEGs), and 74,51, 34, and 23 DE miRNAs (DE miRNAs) were identified in the Y4 vs. Y1, W4 vs. W1, Y4 vs. W4, and Y1 vs. W1 comparisons, respectively. Functional analysis of these DE transcripts (DETs) demonstrated that they had participated in various biological processes, such as cellular component organization or biogenesis, the developmental process, the metabolic process, bone development, and cartilage development. The crucial bone development-related candidate genes NK3 Homeobox 2 (<i>NKX3.2</i>), Wnt ligand secretion mediator (<i>WLS</i>), gremlin 1 (<i>GREM1</i>), fibroblast growth factor receptor 3 (<i>FGFR3</i>), hematopoietically expressed homeobox (<i>HHEX</i>), (collagen type XI alpha 1 chain (<i>COL11A1</i>), and Wnt Family Member 16 (<i>WNT16</i>)) were further identified by functional analysis. Moreover, lncRNA, miRNA, and gene interaction networks were constructed; a total of 55 lncRNAs, 6 miRNAs, and 7 genes formed lncRNA–gene, miRNA–gene, and lncRNA–miRNA–gene pairs, respectively. The aim was to demonstrate that coding and non-coding genes may co-regulate porcine spine development through interaction networks. <i>NKX3.2</i> was identified as being specifically expressed in cartilage tissues, and it delayed chondrocyte differentiation. miRNA-326 regulated chondrocyte differentiation by targeting <i>NKX3.2</i>. The present study provides the first non-coding RNA and gene expression profiles in the porcine TIC, constructs the lncRNA–miRNA–gene interaction networks, and confirms the function of <i>NKX3.2</i> in vertebral column development. These findings contribute to the understanding of the potential molecular mechanisms regulating pig vertebral column development. They expand our knowledge about the differences in body length between different pig species and provide a foundation for future studies.https://www.mdpi.com/1422-0067/24/8/7257pigvertebral columnRNA-seqnon-coding RNAsNKX3.2 |
| spellingShingle | Qiao Xu Yabiao Luo Zhe Chao Jibin Zhang Ximing Liu Qiguo Tang Kejun Wang Shuyi Tan Meiying Fang Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326–NKX3.2-Regulated Porcine Chondrocyte Differentiation International Journal of Molecular Sciences pig vertebral column RNA-seq non-coding RNAs NKX3.2 |
| title | Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326–NKX3.2-Regulated Porcine Chondrocyte Differentiation |
| title_full | Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326–NKX3.2-Regulated Porcine Chondrocyte Differentiation |
| title_fullStr | Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326–NKX3.2-Regulated Porcine Chondrocyte Differentiation |
| title_full_unstemmed | Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326–NKX3.2-Regulated Porcine Chondrocyte Differentiation |
| title_short | Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326–NKX3.2-Regulated Porcine Chondrocyte Differentiation |
| title_sort | integrated analysis of transcriptome expression profiles reveals mirna 326 nkx3 2 regulated porcine chondrocyte differentiation |
| topic | pig vertebral column RNA-seq non-coding RNAs NKX3.2 |
| url | https://www.mdpi.com/1422-0067/24/8/7257 |
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