Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat

Abstract

Sexually dimorphic traits are common in sexually reproducing organisms and can be encoded by differential gene regulation between males and females. Although alternative splicing is common mechanism in generating transcriptional diversity, its role in generating sex differences relative to differential gene expression is less clear. Here, we investigate the relative roles of differential gene expression and alternative splicing between male and female the horseshoe bat species, Rhinolophus sinicus. Horseshoe bats are an excellent model to study acoustic differences between sexes. Using RNA-seq analyses of two somatic tissues (brain and liver) from males and females of the same population, we identified 3,471 and 2,208 differentially expressed genes between the sexes (DEGs) in the brain and liver, respectively. DEGs were enriched with functional categories associated with physiological difference of the sexes (e.g.,gamete generation and energy production for reproduction in females). In addition, we also detected many differentially spliced genes between the sexes (DSGs, 2,231 and 1,027 in the brain and liver, respectively) which were mainly involved in regulation of RNA splicing and mRNA metabolic process. Interestingly, we found a significant enrichment of DEGs on the X chromosome, but not for DSGs. As for the extent of overlap between the two sets of genes, more than expected overlap of DEGs and DSGs was observed in the brain but not in the liver. This suggests that more complex tissues, such as the brain, may require the intricate and simultaneous interplay of both differential gene expression and splicing of genes to govern sex-specific functions. Overall, our results support that variation in gene expression and alternative splicing are important and complementary mechanisms governing sex differences.

Sex Differences in Cochlear Transcriptomes in Horseshoe Bats

“…Consistent with the results of a recent study based on the RNA-seq data of liver and brain [40], we found two Y-linked genes (KDM5D and DDX3Y) specifically expressed in males' cochlear tissue in R. sinicus. In addition, DDX3Y was also detected to be a malespecific gene in R. affinis hainanus.…”

“…Compared to a recent study on sex differences in AS in the liver and brain of R. sinicus [40], we identified a smaller number of alternatively spliced genes (ASGs) in the cochlear tissue (over 1000 in [40] and less than 250 in this study, see Figure 3a). This mainly resulted from the different methods used between studies (rMATs in [40]; DEXSeq in this study).…”

“…Compared to a recent study on sex differences in AS in the liver and brain of R. sinicus [40], we identified a smaller number of alternatively spliced genes (ASGs) in the cochlear tissue (over 1000 in [40] and less than 250 in this study, see Figure 3a). This mainly resulted from the different methods used between studies (rMATs in [40]; DEXSeq in this study). Another recent study that used both rMATs and DEXSeq when performing AS analysis in the same tissue revealed that the former method detected much more ASGs than the latter [73] (1932 with rMATs and 1267 with DEXSeq).…”

“…To test whether differential gene expression and alternative splicing act independently in gene regulation, we assessed the extent of overlap between the DEGs and ASGs identified in each taxon. Following previous studies [38,40], we first calculated the expected number of genes that are both DEGs and ASGs as (total no. DEGs × total no.…”

“…In addition, alternative splicing (AS), as an alternative form of gene regulation, has also been proved to be important in generating sexually dimorphic traits [36][37][38]. Several recent studies have been performed to assess the relative roles of DGE and AS in sexual differences and their results suggested that DGE and AS might function independently to mediate sexual differences [39,40]. However, few studies have been performed to explore the molecular mechanisms underlying the sexual differences of vocalizations and acoustic signals (but see [41]) and none have been conducted for the differences in echolocation pulse frequencies between males and females in bats.…”