Beyond the reference: gene expression variation and transcriptional response to RNA interference in Caenorhabditis elegans

Abstract

Though natural systems harbor genetic and phenotypic variation, research in model organisms is often restricted to a reference strain. Focusing on a reference strain yields a great depth of knowledge but potentially at the cost of breadth of understanding. Furthermore, tools developed in the reference context may introduce bias when applied to other strains, posing challenges to defining the scope of variation within model systems. Here, we evaluate how genetic differences among 5 wild Caenorhabditis elegans strains affect gene expression and its quantification, in general and after induction of the RNA interference (RNAi) response. Across strains, 34% of genes were differentially expressed in the control condition, including 411 genes that were not expressed at all in at least 1 strain; 49 of these were unexpressed in reference strain N2. Reference genome mapping bias caused limited concern: despite hyperdiverse hotspots throughout the genome, 92% of variably expressed genes were robust to mapping issues. The transcriptional response to RNAi was highly strain- and target-gene-specific and did not correlate with RNAi efficiency, as the 2 RNAi-insensitive strains showed more differentially expressed genes following RNAi treatment than the RNAi-sensitive reference strain. We conclude that gene expression, generally and in response to RNAi, differs across C. elegans strains such that the choice of strain may meaningfully influence scientific inferences. Finally, we introduce a resource for querying gene expression variation in this dataset at https://wildworm.biosci.gatech.edu/rnai/.

Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains

“…DNA sequencing data are available from the NCBI Sequence Read Archive via projects PRJNA1025857 (assembled PacBio data for 2 strains) and PRJNA1025861 (raw Illumina short reads for 9 strains). RNA-seq data and analysis scripts are available via a companion manuscript ( Bell et al 2023 ) reporting genome-wide gene expression patterns in the 5 strains for which we describe gene expression at RNAi genes. RNA-seq data are also available for gene-specific queries via https://wildworm.biosci.gatech.edu/rnai/ .…”