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2016 ; 203
(3
): 1177-90
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Buffering of Genetic Regulatory Networks in Drosophila melanogaster
#MMPMID27194752
Fear JM
; León-Novelo LG
; Morse AM
; Gerken AR
; Van Lehmann K
; Tower J
; Nuzhdin SV
; McIntyre LM
Genetics
2016[Jul]; 203
(3
): 1177-90
PMID27194752
show ga
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 exclusively in mated or
virgin flies, indicating an environmental component of expression regulation. On
average 34% of genes within a cross and 54% of all genes show evidence for
genetic regulation of transcription. Nearly all differentially regulated genes
are affected in cis, with an average of 63% of expression variation explained by
the cis-effects. Trans-effects explain 8% of the variance in AI on average and
the interaction between cis and trans explains an average of 11% of the total
variance in AI. In both environments cis- and trans-effects are compensatory in
their overall effect, with a negative association between cis- and trans-effects
in 85% of the exons examined. We hypothesize that the gene expression level
perturbed by cis-regulatory mutations is compensated through trans-regulatory
mechanisms, e.g., trans and cis by trans-factors buffering cis-mutations. In
addition, when AI is detected in both environments, cis-mated, cis-virgin, and
trans-mated-trans-virgin estimates are highly concordant with 99% of all exons
positively correlated with a median correlation of 0.83 for cis and 0.95 for
trans We conclude that the gene regulatory networks (GRNs) are robust and that
trans-buffering explains robustness.
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