Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis
Abstract Background 5-methylcytosine (m5C) modification is widely associated with many biological and pathological processes. However, knowledge of m5C modification in osteoarthritis (OA) remains lacking. Thus, our study aimed to identify common m5C features in OA. Results In the present study, we i...
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09651-4 |
| _version_ | 1827724442106593280 |
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| author | Yang Yu Shitao Lu Xiaoming Liu Yu Li Jianzhong Xu |
| author_facet | Yang Yu Shitao Lu Xiaoming Liu Yu Li Jianzhong Xu |
| author_sort | Yang Yu |
| collection | DOAJ |
| description | Abstract Background 5-methylcytosine (m5C) modification is widely associated with many biological and pathological processes. However, knowledge of m5C modification in osteoarthritis (OA) remains lacking. Thus, our study aimed to identify common m5C features in OA. Results In the present study, we identified 1395 differentially methylated genes (DMGs) and 1673 differentially expressed genes (DEGs) using methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq) and RNA-sequencing. A co-expression analysis of DMGs and DEGs showed that the expression of 133 genes was significantly affected by m5C methylation. A protein–protein interaction network of the 133 genes was constructed using the STRING database, and the cytoHubba plug-in of Cytoscape was used to hub genes were screen out 11 hub genes, including MMP14, VTN, COL15A1, COL6A2, SPARC, COL5A1, COL6A3, COL6A1, COL8A2, ADAMTS2 and COL7A1. The Pathway enrichment analysis by the ClueGO and CluePedia plugins in Cytoscape showed that the hub genes were significantly enriched in collagen degradation and extracellular matrix degradation. Conclusions Our study indicated that m5C modification might play an important role in OA pathogenesis, and the present study provides worthwhile insight into identifying m5C-related therapeutic targets in OA. |
| first_indexed | 2024-03-10T22:15:51Z |
| format | Article |
| id | doaj.art-e064c6ce0a064aebab26a36958e49a6c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:51Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e064c6ce0a064aebab26a36958e49a6c2023-11-19T12:28:02ZengBMCBMC Genomics1471-21642023-09-0124111310.1186/s12864-023-09651-4Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritisYang Yu0Shitao Lu1Xiaoming Liu2Yu Li3Jianzhong Xu4Department of Orthopedics, the First Affiliated Hospital of Zhengzhou UniversityDepartment of Orthopedics, the First Affiliated Hospital of Zhengzhou UniversityDepartment of Gastroenterology, the Third Xiangya Hospital, Central South UniversityDepartment of Orthopedics, the First Affiliated Hospital of Zhengzhou UniversityDepartment of Orthopedics, the First Affiliated Hospital of Zhengzhou UniversityAbstract Background 5-methylcytosine (m5C) modification is widely associated with many biological and pathological processes. However, knowledge of m5C modification in osteoarthritis (OA) remains lacking. Thus, our study aimed to identify common m5C features in OA. Results In the present study, we identified 1395 differentially methylated genes (DMGs) and 1673 differentially expressed genes (DEGs) using methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq) and RNA-sequencing. A co-expression analysis of DMGs and DEGs showed that the expression of 133 genes was significantly affected by m5C methylation. A protein–protein interaction network of the 133 genes was constructed using the STRING database, and the cytoHubba plug-in of Cytoscape was used to hub genes were screen out 11 hub genes, including MMP14, VTN, COL15A1, COL6A2, SPARC, COL5A1, COL6A3, COL6A1, COL8A2, ADAMTS2 and COL7A1. The Pathway enrichment analysis by the ClueGO and CluePedia plugins in Cytoscape showed that the hub genes were significantly enriched in collagen degradation and extracellular matrix degradation. Conclusions Our study indicated that m5C modification might play an important role in OA pathogenesis, and the present study provides worthwhile insight into identifying m5C-related therapeutic targets in OA.https://doi.org/10.1186/s12864-023-09651-4Osteoarthritism5C methylationCollagen degradationMethylome profileMeRIP-seq |
| spellingShingle | Yang Yu Shitao Lu Xiaoming Liu Yu Li Jianzhong Xu Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis BMC Genomics Osteoarthritis m5C methylation Collagen degradation Methylome profile MeRIP-seq |
| title | Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis |
| title_full | Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis |
| title_fullStr | Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis |
| title_full_unstemmed | Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis |
| title_short | Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis |
| title_sort | identification and analysis of rna 5 methylcytosine related key genes in osteoarthritis |
| topic | Osteoarthritis m5C methylation Collagen degradation Methylome profile MeRIP-seq |
| url | https://doi.org/10.1186/s12864-023-09651-4 |
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