Genetic compensation induced by deleterious mutations but not gene knockdowns

Abstract

Cells sense their environment and adapt to it by fine-tuning their transcriptome. Wired into this network of gene expression control are mechanisms to compensate for gene dosage. The increasing use of reverse genetics in zebrafish, and other model systems, has revealed profound differences between the phenotypes caused by genetic mutations and those caused by gene knockdowns at many loci, an observation previously reported in mouse and Arabidopsis. To identify the reasons underlying the phenotypic differences between mutants and knockdowns, we generated mutations in zebrafish egfl7, an endothelial extracellular matrix gene of therapeutic interest, as well as in vegfaa. Here we show that egfl7 mutants do not show any obvious phenotypes while animals injected with egfl7 morpholino (morphants) exhibit severe vascular defects. We further observe that egfl7 mutants are less sensitive than their wild-type siblings to Egfl7 knockdown, arguing against residual protein function in the mutants or significant off-target effects of the morpholinos when used at a moderate dose. Comparing egfl7 mutant and morphant proteomes and transcriptomes, we identify a set of proteins and genes that are upregulated in mutants but not in morphants. Among them are extracellular matrix genes that can rescue egfl7 morphants, indicating that they could be compensating for the loss of Egfl7 function in the phenotypically wild-type egfl7 mutants. Moreover, egfl7 CRISPR interference, which obstructs transcript elongation and causes severe vascular defects, does not cause the upregulation of these genes. Similarly, vegfaa mutants but not morphants show an upregulation of vegfab. Taken together, these data reveal the activation of a compensatory network to buffer against deleterious mutations, which was not observed after translational or transcriptional knockdown.

The guanine nucleotide exchange factor Net1 facilitates the specification of dorsal cell fates in zebrafish embryos by promoting maternal β-catenin activation

“…Such properties have also been described in zebrafish genetic studies. Embryos injected with egfl7 morpholinos exhibit severe vascular defects, while egfl7 mutants do not show any obvious phenotypes, as a set of genes are upregulated to compensate for the induced genetic alteration [76]. Interestingly, we also observed a clear upregulation of a subset of genes encoding GEFs, GTPases and GTPase effectors in net1 mutants.…”

“…The phenotypic differences between mutants and morphants may be due to the activation of a compensatory network in mutants [76,77]. Actually, net1 MO1 or siRNA1 injection caused dorsal fate defects in wild-type embryos, but did not influence the dorsal development of mutants (Supplementary information, Figure S13F and S13G), indicating the specificity of the MOs and siRNAs used to knock-down zebrafish net1 in our study and the insensitiveness of the net1 mutants to net1 MOs and siRNAs.…”

Fast revascularization of the injured area is essential to support zebrafish heart regeneration

“…S4C). To further explore the role of vegfaa in heart regeneration, we took advantage of a recently generated vegfaa mutant (28). vegfaa −/− embryos display severe angiogenic defects from an early stage (29).…”

When evolution is the solution to pollution: Key principles, and lessons from rapid repeated adaptation of killifish (Fundulus heteroclitus) populations

“…Similarly, compensatory adaptation for the fitness costs of antibiotic resistance can quickly evolve in bacteria (Andersson & Hughes, 2010). In the short term, physiological adjustments could at least partially compensate for the negative pleiotropic consequences of rapid adaptation; for example, the functional impacts of specific gene mutations may be rescued through up‐regulation of paralogs that retain functions that are redundant to the mutated gene (Rossi et al., 2015). Presumably compensatory genetic changes would only be favored by selection if physiological compensation were insufficient.…”