Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish Gonads
Alternative splicing is an important way of regulating gene functions in eukaryotes. Several key genes involved in sex determination and gonadal differentiation, such as <i>nr5a1</i> and <i>ddx4</i>, have sex-biased transcripts between males and females, suggesting a potentia...
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MDPI AG
2022-09-01
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| author | Xing Lin Fei Liu Kaifeng Meng Hairong Liu Yuanli Zhao Yuanyuan Chen Wei Hu Daji Luo |
| author_facet | Xing Lin Fei Liu Kaifeng Meng Hairong Liu Yuanli Zhao Yuanyuan Chen Wei Hu Daji Luo |
| author_sort | Xing Lin |
| collection | DOAJ |
| description | Alternative splicing is an important way of regulating gene functions in eukaryotes. Several key genes involved in sex determination and gonadal differentiation, such as <i>nr5a1</i> and <i>ddx4</i>, have sex-biased transcripts between males and females, suggesting a potential regulatory role of alternative splicing in gonads. Currently, the sex-specific alternative splicing events and genes have not been comprehensively studied at the genome-wide level in zebrafish. In this study, through global splicing analysis on three independent sets of RNA-seq data from matched zebrafish testes and ovaries, we identified 120 differentially spliced genes shared by the three datasets, most of which haven’t been reported before. Functional enrichment analysis showed that the GO terms of mRNA processing, mRNA metabolism and microtubule-based process were strongly enriched. The testis- and ovary-biased alternative splicing genes were identified, and part of them (<i>tp53bp1</i>, <i>tpx2</i>, <i>mapre1a</i>, <i>kif2c</i>, and <i>ncoa5</i>) were further validated by RT-PCR. Sequence characteristics analysis suggested that the lengths, GC contents, and splice site strengths of the alternative exons or introns may have different influences in different types of alternative splicing events. Interestingly, we identified an unexpected high proportion (over 70%) of non-frameshift exon-skipping events, suggesting that in these cases the two protein isoforms derived from alternative splicing may both have functions. Furthermore, as a representative example, we found that the alternative splicing of <i>ncoa5</i> causes the loss of a conserved RRM domain in the short transcript predominantly produced in testes. Our study discovers novel sex-specific alternative splicing events and genes with high reliabilities in zebrafish testes and ovaries, which would provide attractive targets for follow-up studies to reveal the biological significances of alternative splicing events and genes in sex determination and gonadal differentiation. |
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| series | Life |
| spelling | doaj.art-b3bace19bfa749959730f846e1206fed2023-11-23T17:24:12ZengMDPI AGLife2075-17292022-09-01129144110.3390/life12091441Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish GonadsXing Lin0Fei Liu1Kaifeng Meng2Hairong Liu3Yuanli Zhao4Yuanyuan Chen5Wei Hu6Daji Luo7State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, ChinaState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, ChinaState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, ChinaState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, ChinaState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, ChinaState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, ChinaState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, ChinaState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, University of Chinese Academy of Sciences, Wuhan 430072, ChinaAlternative splicing is an important way of regulating gene functions in eukaryotes. Several key genes involved in sex determination and gonadal differentiation, such as <i>nr5a1</i> and <i>ddx4</i>, have sex-biased transcripts between males and females, suggesting a potential regulatory role of alternative splicing in gonads. Currently, the sex-specific alternative splicing events and genes have not been comprehensively studied at the genome-wide level in zebrafish. In this study, through global splicing analysis on three independent sets of RNA-seq data from matched zebrafish testes and ovaries, we identified 120 differentially spliced genes shared by the three datasets, most of which haven’t been reported before. Functional enrichment analysis showed that the GO terms of mRNA processing, mRNA metabolism and microtubule-based process were strongly enriched. The testis- and ovary-biased alternative splicing genes were identified, and part of them (<i>tp53bp1</i>, <i>tpx2</i>, <i>mapre1a</i>, <i>kif2c</i>, and <i>ncoa5</i>) were further validated by RT-PCR. Sequence characteristics analysis suggested that the lengths, GC contents, and splice site strengths of the alternative exons or introns may have different influences in different types of alternative splicing events. Interestingly, we identified an unexpected high proportion (over 70%) of non-frameshift exon-skipping events, suggesting that in these cases the two protein isoforms derived from alternative splicing may both have functions. Furthermore, as a representative example, we found that the alternative splicing of <i>ncoa5</i> causes the loss of a conserved RRM domain in the short transcript predominantly produced in testes. Our study discovers novel sex-specific alternative splicing events and genes with high reliabilities in zebrafish testes and ovaries, which would provide attractive targets for follow-up studies to reveal the biological significances of alternative splicing events and genes in sex determination and gonadal differentiation.https://www.mdpi.com/2075-1729/12/9/1441sex determinationgonadal differentiationalternative splicingRNA-seqzebrafish |
| spellingShingle | Xing Lin Fei Liu Kaifeng Meng Hairong Liu Yuanli Zhao Yuanyuan Chen Wei Hu Daji Luo Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish Gonads Life sex determination gonadal differentiation alternative splicing RNA-seq zebrafish |
| title | Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish Gonads |
| title_full | Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish Gonads |
| title_fullStr | Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish Gonads |
| title_full_unstemmed | Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish Gonads |
| title_short | Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish Gonads |
| title_sort | comprehensive transcriptome analysis reveals sex specific alternative splicing events in zebrafish gonads |
| topic | sex determination gonadal differentiation alternative splicing RNA-seq zebrafish |
| url | https://www.mdpi.com/2075-1729/12/9/1441 |
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