Sex-Specific Splicing in Drosophila: Widespread Occurrence, Tissue Specificity and Evolutionary Conservation

Abstract

Many genes in eukaryotic genomes produce multiple transcripts through a variety of molecular mechanisms including alternative splicing. Alternatively spliced transcripts often encode functionally distinct proteins, indicating that gene regulation at this level makes an important contribution to organismal complexity. The multilevel splicing cascade that regulates sex determination and sex-specific development in Drosophila is a classical example of the role of alternative splicing in cell differentiation. Recent evidence suggests that a large proportion of genes in the Drosophila genome may be spliced in a sex-biased fashion, raising the possibility that alternative splicing may play a more general role in sexually dimorphic development and physiology. However, the prevalence of sex-specific splicing and the extent to which it is shared among genotypes are not fully understood. Genetic variation in the splicing of key components of the sex determination pathway is known to influence the expression of downstream target genes, suggesting that alternative splicing at other loci may also vary in functionally important ways. In this study, we used exon-specific microarrays to examine 417 multitranscript genes for evidence of sex-specific and genotype-specific splicing in 80 different genotypes of Drosophila melanogaster. Most of these loci showed sex-biased splicing, whereas genotype-specific splicing was rare. One hundred thirty-five genes showed different alternative transcript use in males vs. females. Real-time PCR analysis of 6 genes chosen to represent a broad range of biological functions showed that most sex-biased splicing occurs in the gonads. However, somatic tissues, particularly adult heads, also show evidence of sexspecific splicing. Comparison of splicing patterns at orthologous loci in seven Drosophila species shows that sexual biases in alternative exon representation are highly conserved, indicating that sex-specific splicing is an ancient feature of Drosophila biology. To investigate potential mechanisms of sex-biased splicing, we used realtime PCR to examine the expression of six known regulators of alternative splicing in males vs. females. We found that all six loci are themselves spliced sex specifically in gonads and heads, suggesting that regulatory hierarchies based on alternative splicing may be an important feature of sexual differentiation.

The Y Chromosome Modulates Splicing and Sex-Biased Intron Retention Rates in Drosophila

“…Recent studies have identified numerous differentially regulated AS events in a variety of conditions (MCINTYRE et al 2006;WANG et al 2008;TELONIS-SCOTT et al 2009;GAN et al 2010;CHANG et al 2011;HARTMANN et al 2011;STURGILL et al 2013;WANG et al 2014) and highlighted the role of IR as a cellular mechanism to influence mRNA abundance and alter biological outcomes (BRAUNSCHWEIG et al 2014;JUNG et al 2015;EDWARDS et al 2016;MAUGER et al 2016;NI et al 2016;MIDDLETON et al 2017;NARO et al 2017). However, the occurrence and extent of sex-biased IR has not been addressed and the role of sex chromosomes in the modulation of splicing has not been investigated.…”

“…Accordingly, studies focusing on Drosophila and primates have described AS events that are differentially regulated between the sexes in both somatic and gonadal tissues (MCINTYRE et al 2006;TELONIS-SCOTT et al 2009;BLEKHMAN et al 2010;GAN et al 2010;CHANG et al 2011;HARTMANN et al 2011;STURGILL et al 2013;TRABZUNI et al 2013). In Drosophila, the mechanism of sex-determination hinges on the post-transcriptional regulation of the sex-lethal (Sxl) gene (BELL et al 1988;SALZ AND ERICKSON 2010); Sxl encodes 21 protein isoforms, with all male-specific isoforms containing a translation-terminating exon.…”

The Resolution of Sexual Antagonism by Gene Duplication

“…Recent studies using mammals and Drosophila indicate an association between alternative splicing and sex-biased transcription (McIntyre et al 2006;Telonis-Scott et al 2009;Blekhman et al 2010). The evolution of male-and female-specific splice forms may evolve by tandem duplication of an exon under sexual antagonism, followed by substitutions causing alternative splicing of male-and female-beneficial exons (e.g., exon shuffling).…”

Buffering of Genetic Regulatory Networks inDrosophila melanogaster

“…jim is also involved in chromatin silencing (Mugat et al 2015) and PIWIinteracting RNA processes in follicle cells (Saito et al 2009). Finally, ps is spliced sex specifically (Telonis-Scott et al 2009) and is a splicing factor (Seshaiah et al 2001) and Vmat is involved in transmembrane transport as a splice variant that is involved in dopamine, serotonin, and octopamine transport (Greer et al 2005). Both dopamine signaling and octopamine signaling are implicated in mediating the postmating response (Rezaval et al 2014;Landis et al 2015).…”