2016
DOI: 10.1534/genetics.116.188797
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Abstract: Regulatory variation in gene expression can be described by cis-and trans-genetic components. Here we used RNA-seq data from a population panel of Drosophila melanogaster test crosses to compare allelic imbalance (AI) in female head tissue between mated and virgin flies, an environmental change known to affect transcription. Indeed, 3048 exons (1610 genes) are differentially expressed in this study. A Bayesian model for AI, with an intersection test, controls type I error. There are 200 genes with AI exclusive… Show more

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Cited by 43 publications
(65 citation statements)
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References 126 publications
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“…Table 3). This is consistent with the idea that gene expression is under stabilizing selection in general and gene regulatory networks evolve negative feedback to buffer effects of regulatory changes (Denby et al 2012; Coolon et al 2014; Bader et al 2015; Fear et al 2016). With regard to our P ST outliers, it is possible that cis-acting changes might have evolved to compensate for unfavorable pleiotropic impacts of adaptive trans-regulatory evolution.…”
Section: Discussionsupporting
confidence: 90%
“…Table 3). This is consistent with the idea that gene expression is under stabilizing selection in general and gene regulatory networks evolve negative feedback to buffer effects of regulatory changes (Denby et al 2012; Coolon et al 2014; Bader et al 2015; Fear et al 2016). With regard to our P ST outliers, it is possible that cis-acting changes might have evolved to compensate for unfavorable pleiotropic impacts of adaptive trans-regulatory evolution.…”
Section: Discussionsupporting
confidence: 90%
“…Similarly, pairwise comparisons between species of Drosophila found that, although the number of genes with cis -regulatory divergence increased linearly with divergence time, the number of genes with total expression divergence does not [44]. This suggests that cis changes are often compensated for by changes in trans variants, or by other trans -regulatory feedback mechanisms [4850]. …”
Section: Regulatory Divergence Between Species Is Widespreadmentioning
confidence: 99%
“…The ortholog was considered to have homeologous expression bias if the credible interval did not overlap 0.5 for all priors. This approach has been shown to conservatively control type I error (Fear et al 2016). For diploid read alignment, orthologous regions where reads were predominantly mapping to the "wrong" parent reference were filtered out, and a set of nonbiased contigs was identified for each diploid.…”
Section: Poisson-gamma Modelmentioning
confidence: 99%