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Chen C, Tang X, Yan S, Yang A, Xiang J, Deng Y, Yin Y, Chen B, Gu J. Comprehensive Analysis of the Transcriptome-Wide m 6A Methylome in Shaziling Pig Testicular Development. Int J Mol Sci 2023; 24:14475. [PMID: 37833923 PMCID: PMC10572705 DOI: 10.3390/ijms241914475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
RNA N6-methyladenosine (m6A) modification is one of the principal post-transcriptional modifications and plays a dynamic role in testicular development and spermatogenesis. However, the role of m6A in porcine testis is understudied. Here, we performed a comprehensive analysis of the m6A transcriptome-wide profile in Shaziling pig testes at birth, puberty, and maturity. We analyzed the total transcriptome m6A profile and found that the m6A patterns were highly distinct in terms of the modification of the transcriptomes during porcine testis development. We found that key m6A methylated genes (AURKC, OVOL, SOX8, ACVR2A, and SPATA46) were highly enriched during spermatogenesis and identified in spermatogenesis-related KEGG pathways, including Wnt, cAMP, mTOR, AMPK, PI3K-Akt, and spliceosome. Our findings indicated that m6A methylations are involved in the complex yet well-organized post-transcriptional regulation of porcine testicular development and spermatogenesis. We found that the m6A eraser ALKBH5 negatively regulated the proliferation of immature porcine Sertoli cells. Furthermore, we proposed a novel mechanism of m6A modification during testicular development: ALKBH5 regulated the RNA methylation level and gene expression of SOX9 mRNA. In addition to serving as a potential target for improving boar reproduction, our findings contributed to the further understanding of the regulation of m6A modifications in male reproduction.
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Affiliation(s)
- Chujie Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (C.C.); (X.T.); (S.Y.); (A.Y.); (J.X.); (Y.D.); (Y.Y.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Xiangwei Tang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (C.C.); (X.T.); (S.Y.); (A.Y.); (J.X.); (Y.D.); (Y.Y.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Saina Yan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (C.C.); (X.T.); (S.Y.); (A.Y.); (J.X.); (Y.D.); (Y.Y.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Anqi Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (C.C.); (X.T.); (S.Y.); (A.Y.); (J.X.); (Y.D.); (Y.Y.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Jiaojiao Xiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (C.C.); (X.T.); (S.Y.); (A.Y.); (J.X.); (Y.D.); (Y.Y.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Yanhong Deng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (C.C.); (X.T.); (S.Y.); (A.Y.); (J.X.); (Y.D.); (Y.Y.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (C.C.); (X.T.); (S.Y.); (A.Y.); (J.X.); (Y.D.); (Y.Y.)
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Bin Chen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (C.C.); (X.T.); (S.Y.); (A.Y.); (J.X.); (Y.D.); (Y.Y.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
| | - Jingjing Gu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (C.C.); (X.T.); (S.Y.); (A.Y.); (J.X.); (Y.D.); (Y.Y.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Changsha 410128, China
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Zhou L, Tian S, Qin G. RNA methylomes reveal the m 6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening. Genome Biol 2019; 20:156. [PMID: 31387610 PMCID: PMC6683476 DOI: 10.1186/s13059-019-1771-7] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay between 5mC and m6A remain uncharacterized. RESULTS Here, we show that mRNA m6A methylation exhibits dynamic changes similar to DNA methylation during tomato fruit ripening. RNA methylome analysis reveals that m6A methylation is a prevalent modification in the mRNA of tomato fruit, and the m6A sites are enriched around the stop codons and within the 3' untranslated regions. In the fruit of the ripening-deficient epimutant Colorless non-ripening (Cnr) which harbors DNA hypermethylation, over 1100 transcripts display increased m6A levels, while only 134 transcripts show decreased m6A enrichment, suggesting a global increase in m6A. The m6A deposition is generally negatively correlated with transcript abundance. Further analysis demonstrates that the overall increase in m6A methylation in Cnr mutant fruit is associated with the decreased expression of RNA demethylase gene SlALKBH2, which is regulated by DNA methylation. Interestingly, SlALKBH2 has the ability to bind the transcript of SlDML2, a DNA demethylase gene required for tomato fruit ripening, and modulates its stability via m6A demethylation. Mutation of SlALKBH2 decreases the abundance of SlDML2 mRNA and delays fruit ripening. CONCLUSIONS Our study identifies a novel layer of gene regulation for key ripening genes and establishes an essential molecular link between DNA methylation and mRNA m6A methylation during fruit ripening.
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Affiliation(s)
- Leilei Zhou
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093, China.
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