Sex-Biased Expression Is Associated With Chromatin State in DrosophilamelanogasterandDrosophila simulans

Abstract

In D. melanogaster and D. simulans head tissue, 60% of orthologous genes show evidence of sex-biased expression in at least one species. Of these, ∼39% (2,192) are conserved in direction. We hypothesize enrichment of open chromatin in the sex where we see expression bias and closed chromatin in the opposite sex. Male-biased orthologs are significantly enriched for H3K4me3 marks in males of both species (∼89% of male-biased orthologs vs ∼76% of unbiased orthologs). Similarly, female-biased orthologs are significantly enriched for H3K4me3 marks in females of both species (∼90% of female-biased orthologs vs ∼73% of unbiased orthologs). The sex-bias ratio in female-biased orthologs was similar in magnitude between the two species, regardless of the closed chromatin (H3K27me2me3) marks in males. However, in male-biased orthologs, the presence of H3K27me2me3 in both species significantly reduced the correlation between D. melanogaster sex-bias ratio and the D. simulans sex-bias ratio. Male-biased orthologs are enriched for evidence of positive selection in the D. melanogaster group. There are more male-biased genes than female-biased genes in both species. For orthologs with gains/losses of sex-bias between the two species, there is an excess of male-bias compared to female-bias, but there is no consistent pattern in the relationship between H3K4me3 or H3K27me2me3 chromatin marks and expression. These data suggest chromatin state is a component of the maintenance of sex-biased expression and divergence of sex-bias between species is reflected in the complexity of the chromatin status.

A Sex specific homologue of snake Waprin is essential for Embryonic Development in the Red Flour Beetle,Tribolium castaneum

“…Alternatively, we also presume the involvement of chromatin remodelling genes in the female-specific expression of Tc_Wap F . Our hypothesis is in line with a recent report byNanni et al, 2023 which suggests the association of sex-biased expression of genes with differential state (open or closed state) of chromatin in the two sexes of Drosophila melanogaster and D. simulans(Nanni et al 2023).…”

“…Alternatively, the sex-specific expression of Tc_Wap F gene could result from differences in chromatin confirmation between the sexes. This is supported by a recent study highlighting the differential chromatin confirmation as the regulator of sex-biased gene expression in two Drosophila species, D. melanogaster and D. simulans (Nanni et al, 2023).…”

Antioxidant and Anti-Inflammatory Properties of Quail Yolk Oil via Upregulation of Superoxide Dismutase 1 and Catalase Genes and Downregulation of EIGER and Unpaired 2 Genes in a D. melanogaster Model

“…In addition to dimorphism, in the total expression of a gene, the sexes may differ in other aspects of the transcriptome. It has also been stated that SBGE is associated with the chromatin state in Drosophila melanogaster and Drosophila simulans [77]. Furthermore, it has been suggested that sex-related characters evolve rapidly relative to non-sex-related characters in gene expression [78].…”

Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD

“…( 48–50 ), Drosophila sex-determination pathway (e.g. ( 51 ), and reviewed in ( 52 )), and may contribute to the resolution of conflicts between sexes during speciation ( 28 , 53 ). Although challenges remain in studying alternative splicing, long-read sequencing offers promising opportunities for further research in understanding how alternative splicing facilitates evolution.…”