Transcriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV
Abstract Infectious spleen and kidney necrosis virus (ISKNV) is a highly virulent and rapidly transmissible fish virus that poses threats to the aquaculture of a wide variety of freshwater and marine fish. N6-methyladenosine (m6A), recognized as a common epigenetic modification of RNA, plays an impo...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-025-11211-x |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841544945008115712 |
|---|---|
| author | Qijin Miao Jing Jiang Siyou Huang Jie Gao Qingqing Liu Rui Zheng Yiling Kang Changjun Guo Jianguo He Junfeng Xie |
| author_facet | Qijin Miao Jing Jiang Siyou Huang Jie Gao Qingqing Liu Rui Zheng Yiling Kang Changjun Guo Jianguo He Junfeng Xie |
| author_sort | Qijin Miao |
| collection | DOAJ |
| description | Abstract Infectious spleen and kidney necrosis virus (ISKNV) is a highly virulent and rapidly transmissible fish virus that poses threats to the aquaculture of a wide variety of freshwater and marine fish. N6-methyladenosine (m6A), recognized as a common epigenetic modification of RNA, plays an important regulatory role during viral infection. However, the impact of m6A RNA methylation on the pathogenicity of ISKNV remains unexplored. Here, methylated RNA immunoprecipitation sequencing (MeRIP-seq) coupled with RNA sequencing (RNA-seq) was used to systematically detect variations in m6A methylation and gene expression between ISKNV-infected and noninfected MFF-1 cells, followed by functional enrichment and co-expression joint analysis. The findings revealed that the m6A methylation peaks were located mainly in coding sequences (CDSs), with more than 90% of the transcripts containing 1–5 m6A peaks. Through MeRIP-seq, 4361 differentially m6A-methylated mRNAs were identified. Gene enrichment analysis revealed that m6A-related genes were enriched in biological processes and pathways such as gene expression, cellular structure, immune responses, and cell death. Co-expression analysis revealed that the genes differentially expressed at both the mRNA and m6A modification levels were enriched in pathways such as the hippo, ErbB, and JAK-STAT pathways. The m6A modification at the genome-wide transcription level of ISKNV was subsequently shown to be pronounced in several pivotal genes, such as putative vascular endothelial growth factor, ribonucleotide reductase small subunit, and E3 ubiquitin ligase. This study comprehensively describes the m6A expression profile in ISKNV- and ISKNV-infected MFF-1 cells, providing a basis for investigating the role of m6A modification during ISKNV infection. |
| format | Article |
| id | doaj-art-077769293860461085a9b5667d8e9cf9 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-077769293860461085a9b5667d8e9cf92025-01-12T12:09:25ZengBMCBMC Genomics1471-21642025-01-0126111310.1186/s12864-025-11211-xTranscriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNVQijin Miao0Jing Jiang1Siyou Huang2Jie Gao3Qingqing Liu4Rui Zheng5Yiling Kang6Changjun Guo7Jianguo He8Junfeng Xie9State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen UniversitySchool of Marine Sciences, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen UniversityState Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-sen UniversityAbstract Infectious spleen and kidney necrosis virus (ISKNV) is a highly virulent and rapidly transmissible fish virus that poses threats to the aquaculture of a wide variety of freshwater and marine fish. N6-methyladenosine (m6A), recognized as a common epigenetic modification of RNA, plays an important regulatory role during viral infection. However, the impact of m6A RNA methylation on the pathogenicity of ISKNV remains unexplored. Here, methylated RNA immunoprecipitation sequencing (MeRIP-seq) coupled with RNA sequencing (RNA-seq) was used to systematically detect variations in m6A methylation and gene expression between ISKNV-infected and noninfected MFF-1 cells, followed by functional enrichment and co-expression joint analysis. The findings revealed that the m6A methylation peaks were located mainly in coding sequences (CDSs), with more than 90% of the transcripts containing 1–5 m6A peaks. Through MeRIP-seq, 4361 differentially m6A-methylated mRNAs were identified. Gene enrichment analysis revealed that m6A-related genes were enriched in biological processes and pathways such as gene expression, cellular structure, immune responses, and cell death. Co-expression analysis revealed that the genes differentially expressed at both the mRNA and m6A modification levels were enriched in pathways such as the hippo, ErbB, and JAK-STAT pathways. The m6A modification at the genome-wide transcription level of ISKNV was subsequently shown to be pronounced in several pivotal genes, such as putative vascular endothelial growth factor, ribonucleotide reductase small subunit, and E3 ubiquitin ligase. This study comprehensively describes the m6A expression profile in ISKNV- and ISKNV-infected MFF-1 cells, providing a basis for investigating the role of m6A modification during ISKNV infection.https://doi.org/10.1186/s12864-025-11211-xSiniperca chuatsiN6-methyladenosineISKNVMeRIP-seqMFF-1 cells |
| spellingShingle | Qijin Miao Jing Jiang Siyou Huang Jie Gao Qingqing Liu Rui Zheng Yiling Kang Changjun Guo Jianguo He Junfeng Xie Transcriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV BMC Genomics Siniperca chuatsi N6-methyladenosine ISKNV MeRIP-seq MFF-1 cells |
| title | Transcriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV |
| title_full | Transcriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV |
| title_fullStr | Transcriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV |
| title_full_unstemmed | Transcriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV |
| title_short | Transcriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV |
| title_sort | transcriptome wide dynamics of m6a methylation in isknv and siniperca chuatsi cells infected with isknv |
| topic | Siniperca chuatsi N6-methyladenosine ISKNV MeRIP-seq MFF-1 cells |
| url | https://doi.org/10.1186/s12864-025-11211-x |
| work_keys_str_mv | AT qijinmiao transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv AT jingjiang transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv AT siyouhuang transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv AT jiegao transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv AT qingqingliu transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv AT ruizheng transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv AT yilingkang transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv AT changjunguo transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv AT jianguohe transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv AT junfengxie transcriptomewidedynamicsofm6amethylationinisknvandsinipercachuatsicellsinfectedwithisknv |