Sex-Specific Effects ofCis-Regulatory Variants inDrosophila melanogaster

Abstract

Sexual dimorphism at the level of gene expression is common and well documented, but much less is known about how different cis-regulatory alleles interact with the different trans-regulatory environments present in males and females. Here we show that sex-specific effects of cis-regulatory variants are common in Drosophila.A hallmark of dioecious organisms is sexual dimorphism, phenotypic differences between males and females of a species such as size, coloration, and behavior. Differences in these organism-level exophenotypes are governed by sexual dimorphism in underlying endophenotypes including the regulation of gene expression (reviewed in Williams and Carroll 2009). Gene regulation is central to sexual dimorphism because males and females carry the same genome, except for their sex chromosomes. Indeed, the extent to which the genome is differently expressed in the two sexes is quite striking-estimates in Drosophila suggest that approximately half of the genes in the genome are expressed differently in males and females (Jin et al. 2001;Gnad and Parsch 2006;Innocenti and Morrow 2010).Mechanistically, the regulation of gene expression is governed by the interaction of cis-regulatory DNA sequences at each gene with trans-regulatory proteins and RNAs present in each cell (reviewed in Wray et al. 2003); the same cisacting sequences have different activities in the different trans-regulatory environments of males and females. But, do sex-specific differences in the trans-regulatory environment generally have similar effects on alternative cis-regulatory alleles of a gene? Or, put another way, how often do cis-regulatory variants have sex-specific effects? A recent QTL study of expression variation in D. melanogaster found that sex-specific trans-regulatory factors appear to often have different effects on alternative cis-regulatory alleles (Massouras et al. 2012).Here, we investigate the magnitude of such cis-by-sex effects and compare them to the frequency and magnitude of cis-by-trans effects from other sources. To do this, we used pyrosequencing (Ahmadian et al. 2000) to measure relative allele-specific expression for 11 randomly selected autosomal genes in male and female F 1 progeny from reciprocal crosses between the highly inbred Drosophila melanogaster lines zhr and z30 (Begun and Aquadro 1993;Sawamura et al. 1993;Wu et al. 1995;Ferree and Barbash 2009;Coolon et al. 2012). Relative allele-specific expression in heterozygous genotypes provides a direct readout of relative cis-regulatory activity (Cowles et al. 2002;Wittkopp et al. 2004). These reciprocal crosses produced four genetically distinct progeny with identical autosomal genotypes (i.e., heterozygous for the zhr and z30 alleles at all autosomal loci) that differ in the identity of their sex chromosomes and/or the parent of origin for all of their chromosomes ( Figure 1A). For each genotype, RNA and genomic DNA were extracted from four biological replicates containing 20 whole flies (7-10 days old) each and analyzed by pyrosequencing usin...

Support for the dominance theory inDrosophilatranscriptomes

“…Our analysis of gene expression divergence on the highly female--biased dot chromosome suggests that weakly deleterious regulatory mutations are major contributors to gene expression divergence of genes with sex--biased expression but only in the sex toward which the expression is biased. Our results also suggest that sexes adopt different expression strategies for their specialized function (GIBILISCO et al 2016), possibly through sexually dimorphic trans--regulatory environments that often interact with cis--regulatory variation differently in females than in males (COOLON et al 2013;MEIKLEJOHN et al 2014).…”

Genetic basis of octanoic acid resistance inDrosophila sechellia: functional analysis of a fine‐mapped region

“…RNA was extracted from each pool of flies or tissues using the promega SV total RNA extraction system with modified protocol ( promega , Coolon et al . ). cDNA was synthesized from total RNA using T(18) primers and Superscript II (Invitrogen) according to manufacturer recommendations.…”

“…Flies were then aged for 3 days in this treatment, anesthetized with CO 2 and snap frozen whole, or dissected into tubes containing 10 heads (abbreviated NS), intestine (abbreviated IN), salivary glands and associated tissue (abbreviated SG), and fat body and associated dorsal abdominal cuticle (Krupp & Levine 2010) (abbreviated FB) and kept at À80°C until use. RNA was extracted from each pool of flies or tissues using the PROMEGA SV total RNA extraction system with modified protocol (PROMEGA, Coolon et al 2013). cDNA was synthesized from total RNA using T (18) primers and Superscript II (Invitrogen) according to manufacturer recommendations.…”

Investigating the role ofOsirisgenes inDrosophila sechellialarval resistance to a host plant toxin

“…After the exposure period, larvae were immediately collected and snap‐frozen in liquid nitrogen, placed on dry ice, and stored at −80°C until use. RNA was extracted using the Promega SV Total RNA Isolation System with modified protocol (Promega, Coolon et al, ). cDNA synthesis was performed using total RNA with T(18) primers and SuperScript II (Invitrogen) according to manufacturer recommendations.…”

“…After the exposure period, larvae were immediately collected and snapfrozen in liquid nitrogen, placed on dry ice, and stored at −80°C until use. RNA was extracted using the Promega SV Total RNA Isolation System with modified protocol (Promega, Coolon et al, 2013 Information Table S2) were added (0.5 µl each forward and reverse) for a total volume of 10 µl per reaction. Cycling conditions for PCR were the same for all genes except for different annealing temperatures: 50°C for 2 min followed by 95°C for 2 min, followed by 50 cycles of 95°C for 15 s, annealing temp (56°C for Osi6, Osi7, and Osi8, 63°C for αTub84B) for 30 s, and 72°C for 30 s.…”