Comprehensive Transcriptome Analysis Reveals Sex-Specific Alternative Splicing Events in Zebrafish Gonads

Abstract

Alternative splicing is an important way of regulating gene functions in eukaryotes. Several key genes involved in sex determination and gonadal differentiation, such as nr5a1 and ddx4, 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 (tp53bp1, tpx2, mapre1a, kif2c, and ncoa5) 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 ncoa5 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.

Consequences of Cancer on ZebrafishDanio rerio: Insights into Sex Determination, Sex Ratio, and Offspring Survival

“…Indeed, regarding Experiment 1, cancer does not appear to be associated with differential sex-specific mortality at the embryonic stage, nor does it play a role in sex determination (since both phenomena would have skewed the sex-ratio). These results contrasts with numerous studies that have identified sex-specific responses in zebrafish regarding various factors (e.g., (Zhou et al 2010, Li et al 2019, Giommi et al 2022, Lin et al 2022, Park et al 2022, van Gelderen et al 2022, Zhai et al 2022, Zheng et al 2022, Zhong et al 2023)), including cancers (e.g., (Lee et al 2018, 2021, Mensah et al 2019, Montal et al 2023)). One possible explanation is that the cancer type used in our study may have too low aggressiveness, as possibly evidenced by the ability of individuals affected at the embryo stage to develop into adulthood.…”

Alternative splicing and its regulation in the malaria vectorAnopheles gambiae

“…AS has been widely studied in model organisms like Drosophila melanogaster , Danio renio or Caenorhabditis elegans (Zahler, 2005, Venables, Tazi and Juge, 2012, Lin et al, 2022). In Drosophila melanogaster AS plays important roles in sex-determination, muscle, neural development among other biological processes (Venables, Tazi and Juge, 2012).…”