Genetical toxicogenomics in Drosophila identifies master-modulatory loci that are regulated by developmental exposure to lead

Abstract

The genetics of gene expression in recombinant inbred lines (RILs) can be mapped as expression quantitative trait loci (eQTLs). So-called "genetical genomics" studies have identified locally-acting eQTLs (cis-eQTLs) for genes that show differences in steady state RNA levels. These studies have also identified distantly-acting master-modulatory trans-eQTLs that regulate tens or hundreds of transcripts (hotspots or transbands). We expand on these studies by performing genetical genomics experiments in two environments in order to identify trans-eQTL that might be regulated by developmental exposure to the neurotoxin lead. Flies from each of 75 RIL were raised from eggs to adults on either control food (made with 250 µM sodium acetate), or lead-treated food (made with 250 µM lead acetate, PbAc). RNA expression analyses of whole adult male flies (5-10 days old) were performed with Affymetrix DrosII whole genome arrays (18,952 probesets). Among the 1,389 genes with cis-eQTL, there were 405 genes unique to control flies and 544 genes unique to leadtreated ones (440 genes had the same cis-eQTLs in both samples). There are 2,396 genes with trans-eQTL which mapped to 12 major transbands with greater than 95 genes. Permutation analyses of the strain labels but not the expression data suggests that the total number of eQTL and the number of transbands are more important criteria for validation than the size of the transband. Two transbands, one located on the 2 nd chromosome and one on the 3 rd chromosome, co-regulate 33 lead-induced genes, many of which are involved in neurodevelopmental processes. For these 33 genes, rather than allelic variation at one locus exerting differential effects in two environments, we found that variation at two different loci are required for optimal effects on lead-induced expression.

Accumulation, elimination, sequestration, and genetic variation of lead (Pb2+) loads within and between generations of Drosophila melanogaster

“…The heritability accounted for 813 pg 2 of the 2,393 pg 2 total phenotypic variance, with 309 pg 2 of the genetic variance explained by the single QTL on Chromosome II. We searched for potential candidate genes in the 50C region by correlating differences in transcription levels between control- and Pb-treated adults for each line with the mean Pb load (methods described in Ruden et al [2009] for 88 transcripts assayed in region 50C). We identified two candidate genes (CG6191-RA and CG8118) where strain differences for changes in transcription in response to Pb are significantly correlated with strain differences in Pb load (p < 0.05).…”

“…Together these mechanisms may serve to minimize Pb exposure in the brain and to offspring, especially during the first d of adult life when experience plays an important role in the development of complex behaviors (Hirsch et al, 2003). The Drosophila model facilitates extending behavioral observations to include genetic (Hirsch et al, 2009; Ruden et al, 2009) and neural mechanisms (He et al, 2009; Morley et al, 2003) mediating these effects, as well as transgenerational effects of anthropogenic Pb.…”

“…Several measurable endpoints have been suggested by others for the use of Drosophila as a toxicology model (Rand, 2010; Rand et al, 2014); these include, but are not limited to, lethality, morphology, behavioral traits, embryonic development, and targeted mechanistic studies. We have established D. melanogaster as a model system to investigate the behavioral, physiological, and genetic effects of chronic, developmental Pb exposure (He et al, 2009; Hirsch et al, 2003; Hirsch et al, 2009; Morley et al, 2003; Ruden et al, 2009). …”

“…Previous studies have found that D. melanogaster readily accumulates Pb (Cohn et al, 1992; Hirsch et al, 2003), and that Pb is toxic for both larvae (Akins et al, 1992) and adults (Hirsch et al, 2003). In previous research, we identified a region of the Drosophila genome that is involved in Pb-dependent changes in locomotor activity (Hirsch et al, 2009) and in extensive changes in patterns of transcription induced by developmental Pb exposure (Ruden et al, 2009). …”

Systems genetics: challenges and developing strategies

“…By using high-throughput microarrays analysis technologies, eQTL can be measured for many genes in the genome, rendering eQTL data information rich and potentially very powerful. Recent studies on a variety of organisms, such as yeast, Drosophila, mouse, rat, human, and plants (Brem et al 2005;Petretto et al 2006;Druka et al 2008;Veyrieras et al 2008;Ruden et al 2009;Lu et al 2011), have shown that levels of gene expression are often highly heritable Göring et al 2007;Emilsson et al 2008). Generally, it is possible for many genes to map cis-and trans-acting factors using linkage (Göring et al 2007;Emilsson et al 2008) or association mapping Stranger et al 2007a).…”