Genetical genomics reveals Ras/MAPK modifier loci

Abstract

The oncogenic Ras/MAPK pathway is evolutionary conserved across metazoans and is essential for many cellular functions. Mutant screens in the model nematode Caenorhabditis elegans have been invaluable for elucidating Ras/MAPK pathway characteristics and identification of the genes involved. Almost all of these screens have been conducted in a single genetic background. However, phenotypic traits of induced mutations can vary widely depending on the genetic background. At the moment, we lack insight into how different genetic backgrounds modulate Ras/MAPK-signaling and which genetic modifiers are involved.\n\nWe previously introduced a gain-of-function mutation in the Ras/MAPK pathway gene let-60 in over 200 recombinant inbred lines (mutant introgressed RILs: miRILs) and detected genetic modifiers affecting this pathway by studying variation in vulval development. In the present study, we investigate how gene expression regulation is affected by the let-60 gain-of-function mutation and the genetic background by mapping eQTL using 33 miRILs. We found that the majority ([~]73%) of the 1516 detected cis-eQTL are not specific for the let-60 mutation, whereas most ([~]76%) of the 898 detected trans-eQTL are associated with the let-60 mutation. We detected 6 eQTL trans-bands that were specific for the interaction between the genetic background and the mutation. One of these eQTL hotspots co-localizes with the previously identified polymorphic Ras/MAPK modifier amx-2. Comparing gene expression profiles between transgenic lines expressing either the N2 or the CB4856 alleles of amx-2 showed the involvement of amx-2 in 79% of the trans-eQTLs for genes mapping to this trans-band.\n\nTogether, our results have revealed hidden loci affecting Ras/MAPK signaling using sensitized backgrounds in C. elegans. These loci harbor putative polymorphic modifier genes that would not have been detected using mutant screens in single genetic backgrounds.