Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing

Understanding animal development, physiology and individual variation at a molecular-biological level has been advanced by the ability to determine at high resolution the repertoire of mRNA molecules, by whole transcriptome resequencing. This includes the ability to detect and quantify rare abundance transcripts and isoform-specific mRNA variants produced from a gene. We have used deep RNA sequencing to gain insight into how the Drosophila sex hierarchy generates somatic sex differences, by examining gene and isoform-specific transcript expression differences between the sexes, in adult head tissues. The sex hierarchy consists of a pre-mRNA splicing cascade that directs the production of sex-specific transcription factors that specify nearly all sexual dimorphism. Here we find 1,384 genes that differ in overall expression levels and 1,371 isoform-specific transcripts that differ between males and females. Additionally, we find 504 genes not regulated downstream of transformer that are more highly expressed in males than females. These 504 genes are enriched on the X chromosome and are likely to reside adjacent to dosage compensation complex entry sites, which taken together suggests that their residence on the X chromosome might be sufficient to confer male-biased expression. There is no significant enrichment of a set of transcription unit features in sex differentially expressed isoform-specific transcripts, as compared to all isoform-specific transcripts expressed in head tissues, suggesting that there is no single molecular mechanism that generates isoform-specific transcript differences between the sexes, even though the sex hierarchy is known to include three pre-mRNA splicing factors.