Negative feedback buffers effects of regulatory variants

Abstract

Mechanisms conferring robustness against regulatory variants have been controversial. Previous studies suggested widespread buffering of RNA misexpression on protein levels during translation. We do not find evidence that translational buffering is common. Instead, we find extensive buffering at the level of RNA expression, exerted through negative feedback regulation acting in trans, which reduces the effect of regulatory variants on gene expression. Our approach is based on a novel experimental design in which allelic differential expression in a yeast hybrid strain is compared to allelic differential expression in a pool of its spores. Allelic differential expression in the hybrid is due to cis-regulatory differences only. Instead, in the pool of spores allelic differential expression is not only due to cis-regulatory differences but also due to local trans effects that include negative feedback. We found that buffering through such local trans regulation is widespread, typically compensating for about 15% of cis-regulatory effects on individual genes. Negative feedback is stronger not only for essential genes, indicating its functional relevance, but also for genes with low to middle levels of expression, for which tight regulation matters most. We suggest that negative feedback is one mechanism of Waddington's canalization, facilitating the accumulation of genetic variants that might give selective advantage in different environments.

Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4grass

“…Nonetheless, our experiment had surprisingly strong power to detect cis effects. We found that >47% (7699) of gene expression patterns were affected by cis factors, a finding that exceeded other published studies using linear modeling to test for cis effects, which ranged from 15% to 30% (Cubillos et al 2014;Bader et al 2015). The increased power is likely attributable to significant genomic divergence between the parents and individual, rather than pooled, sequencing of each biological replicate (Liu et al 2014).…”

“…3; Bader et al 2015). We estimated that the expression of 5969 (π 0 = 0.63) of the 16,465 genes with quantifiable ASE were affected by trans factors; however, in many cases the trans effect size was relatively small (Fig.…”

“…S4,S5) that have been traditionally used to assess cis-and trans-acting gene expression regulation (Wittkopp et al 2004;McManus et al 2010;Bader et al 2015); however, linear modeling affords several benefits, including the capability to incorporate biological replicates and to control for experimental design variables (i.e., blocking, treatment, and other covariates). We tested the effect of cis, trans, experimental treatments, and all additive and interactive combinations therein using a linear model specification within the DESeq2 negative binomial framework (Bader et al 2015) (see the Supplemental Material for comparisons between the DESeq2 model specification, mixed models, and traditional cis-trans test methods). We found 17,524 (78.7%) genes that were differentially expressed when contrasting the parents; however, only 8086 (49.8%) of the 16,465 genes that had detectable ASE had significant cis-or trans-regulated allele-specific expression (Fig.…”

Buffering of Genetic Regulatory Networks inDrosophila melanogaster

“…GRN robustness has been explicitly formulated to account for the prevalence of compensatory cis-trans interactions (Denby et al 2012;Bader et al 2015). Denby et al (2012) have proposed that negative feedback controlling the level of RNA expression could be a common mechanism to buffer effects of regulatory variants in yeast.…”

“…This study demonstrated for a single gene that negative feedback could act as a buffering mechanism for regulatory variants. Bader et al (2015) quantified buffering by feedback against naturally occurring regulatory variants genome-wide to be 15%. Note that when buffering arises from feedback, it is not necessary to invoke additional genetic variation across the genome to explain the trans-effects.…”