Transcriptional and epigenetic responses to mating and aging in Drosophila melanogaster

Abstract

Background: Phenotypic plasticity allows organisms to respond rapidly to changing environmental circumstances, and understanding its genomic basis can yield insights regarding the underlying genes and genetic networks affecting complex phenotypes. Female Drosophila melanogaster undergo dramatic physiological changes mediated by seminal fluid components transferred upon mating, including decreased longevity. Their physiological and behavioral effects have been well characterized, but little is known about resulting changes in regulation of gene expression or the extent to which mating-induced changes in gene expression are the same as those occurring during aging.

Results: We assessed genome-wide mRNA, microRNA, and three common histone modifications implicated in gene activation for young and aged virgin and mated female D. melanogaster in a factorial design. We identified phenotypically plastic transcripts and epigenetic modifications associated with mating and aging. We used these data to derive phenotypically plastic regulatory networks associated with mating of young flies, and aging of virgin and mated flies. Many of the mRNAs, microRNAs and epigenetic modifications associated with mating of young flies also occur with age in virgin flies, which may reflect mating-induced accelerated aging. We functionally tested the plastic regulatory networks by overexpressing environmentally sensitive microRNAs. Overexpression resulted in altered expression of ~70% of candidate target genes, and in all cases affected oviposition.

Conclusions: Our results implicate microRNAs as mediators of phenotypic plasticity associated with mating and provide a comprehensive documentation of the genomic and epigenomic changes that accompany mating- and aging-induced physiological changes in female D. melanogaster.

Figure 1

Gene ontology enrichment of transcripts with altered expression as a result of mating or aging. Gene ontology enrichment was assessed for transcripts that changed expression levels in young flies before and after mating (a) and in young vs aged virgin flies (b) Light blue bars exceed the Benjamini corrected threshold of P <0.05.

Figure 2

Size distributions of small RNAs in young (blue) and aged (red) virgin and mated flies. Black and open arrowheads indicate the regions corresponding to miRNAs and rasiRNAs, respectively. The arrows point at small fragments apparent only in young flies after mating that likely reflect mRNA degradation products generated during the maternal to zygotic transition.

Figure 3

Changes in mir-309 cluster expression after mating in young (blue) and old (red) flies.

Figure 4

A network of miRNAs, their target genes, and potential interacting partners associated with post-mating changes. miRNAs that change expression in young flies after mating are shown in the inner circle in yellow boxes and are connected to their target genes, shown in the middle circle, with red lines. The miRNA target genes are connected with known interaction partners, shown in the outer circle, with grey lines. Genes that are targets for H3K4me1, H3K4me3 and H3K9ac, are shown in orange, green and red boxes, respectively. Targets for two histone 3 marks are indicated with an additional border color. Note that only miRNAs and target genes that undergo altered transcriptional regulation are included in the network, and only genes interacting with more than one miRNA target are represented in the outer circle.

Figure 5

A network of miRNAs, their target genes, and potential interacting partners associated with aging. miRNAs that change expression upon aging of virgin flies are shown in the inner circle in yellow boxes and are connected to their target genes, shown in the middle circle, with red lines. The miRNA target genes are connected with known interaction partners, shown in the outer circle, with grey lines. Genes that are targets for H3K4me1, H3K4me3 and H3K9ac, are shown in orange, green and red boxes, respectively. Myb is a target for both H3K4me3 and H3K9ac, as indicated by the red border around the green box. Note that only miRNAs and target genes that undergo altered transcriptional regulation are included in the network, and only genes interacting with more than one miRNA target are represented in the outer circle.

Figure 6

miRNAs, their target genes, and potential interacting partners associated with aging and mating. miRNAs that change expression after aging are shown in the inner circle in yellow boxes and are connected to their target genes, shown in the middle circle, with red lines. The miRNA target genes are connected with known interaction partners, shown in the outer circle, with grey lines. Genes that are targets for H3K4me1, H3K4me3 and H3K9ac, are shown in orange, green and red boxes, respectively. Targets for two histone 3 marks are indicated with an additional border color. Note that only miRNAs and target genes that undergo altered transcriptional regulation are included in the network, and only genes interacting with more than one miRNA target are represented in the outer circle.

Figure 7

Effects of miRNA overexpression on egg laying by mated females. Number of eggs laid by five young mated females over 18 hours between control and mir-286, mir-34, mir-92b and mir-988 overexpression lines. Two stars indicate P <0.01 and three stars indicate P <0.0001. Error bar shows standard error.