Cell-Intrinsic Adaptation Arising from Chronic Ablation of a Key Rho GTPase Regulator

Genome-editing technologies allow systematic inactivation of human genes. Whether knockout phenotypes always reflect gene functions as determined by acute RNAi is an important question. Here we show how the acute knockdown of the Adams-Oliver syndrome (AOS) gene DOCK6, coding for a RAC1/CDC42 guanine nucleotide exchange factor, results in strikingly different phenotypes to those generated by genomic DOCK6 disruption. Cell-intrinsic adaptation compensates for loss of DOCK6 function. Prolonged DOCK6 loss impacts upon the MRTF-A/SRF transcription factor, reducing levels of the ubiquitin-like modifier ISG15. Reduced ISGylation of the IQGAP1 protein increases levels of active CDC42 and RAC1 to compensate for DOCK6 disruption. Similar downregulation of ISG15 in cells from DOCK6 AOS patients indicates that such adaptation can compensate for genetic defects during development. Thus, phenotypes of gene inactivation are critically dependent on the timescale, as acute knockdown reflects a transient state of adjustment to a new equilibrium that is attained following compensation. •DOCK6 GEF function is required for cell spreading and normal mitotic progression•Adaptation to DOCK6 disruption leads to milder phenotypes compared with knockdown•Actin polymerization state regulates transcription of ISG15 through MRTF-A/SRF•Reduced ISGylation of IQGAP1 increases the level of active CDC42 and RAC1 GTPases Cerikan et al. describe the mechanism behind a cell-intrinsic adaptation to DOCK6 gene function loss. They show that DOCK6-GEF loss induces increased monomeric actin levels, negatively regulating the levels of ISG15 through MRTF-A/SRF transcription machinery. Decreased ISG15 levels reduce the ISGylation of IQGAP1, resulting in restoration of the active CDC42/RAC1 levels.