Zhang, Gaotian et al. (2021) International Worm Meeting "The genetic architectures of gene expression variation in wild C. elegans"

Hahnel, Steffen, Andersen, Erik, Roberto, Nicole, Zhang, Gaotian, Lee, Daehan

[International Worm Meeting, 2021]

Natural variation in gene expression is a major source of phenotypic diversity among individuals. Genetic variants underlying gene expression differences are known as expression quantitative trait loci (eQTL). In Caenorhabditis elegans, both local eQTL (located close to the genes they influence) and distant eQTL (located farther away from the genes they influence) have been identified using linkage analysis from a panel of recombinant inbred advanced intercross lines (RIAILs) between the laboratory reference strain, N2, and a wild strain, CB4856. However, the eQTL detected using RIAILs were limited to genetic variants between N2 and CB4856. Here, we investigated the natural variation in gene expression of 205 genetically distinct C. elegans wild strains by performing RNA-sequencing on synchronized young adult hermaphrodites. We obtained reliable expression of 25,896 protein-coding transcripts (16,106 genes). We used genome-wide association (GWA) analysis to identify 3,342 local eQTL for 3,342 transcripts (2,777 genes), and 2,835 distant eQTL for 2,206 transcripts (2,082 genes). We found that most of the narrow-sense heritability for transcript expression variation is explained by detected eQTL. Of the 2,835 distant eQTL, 1,670 eQTL significantly clustered in 54 hotspots across the C. elegans genome. We will further explore causal genes underlying these distant eQTL hotspots and their functions. Additionally, we applied mediation analysis to the eQTL data and other organism-level quantitative traits to elucidate the genetic effects on phenotypic variation mediated by gene expression. For instance, instead of relying on time-consuming investigations of rare genetic variants missed in GWA studies and prior knowledge of the trait as published in our study of C. elegans responses to benzimidazoles (Hahnel et al. 2018), the significant mediating effect of the expression of ben-1, the causal gene, was quickly and successfully identified by mediation analysis. Our results suggest that mediation analysis using expression data facilitates identification of causal genes in GWA studies in C. elegans.

Wit, Janneke et al. (2021) International Worm Meeting "Natural variation in differential C. elegans responses to the broad-range anthelmintic emodepside"

Andersen, Erik, Wit, Janneke, Rodriguez, Briana, Hahnel, Steffen

[International Worm Meeting, 2021]

Emodepside is an anthelmintic drug effective against parasitic nematodes, including gastrointestinal and filarial nematodes. Resistance to emodepside has not yet been reported, and nematodes that are resistant to other anthelmintic drug classes are susceptible to emodepside. The study of emodepside mode of action and potential mechanisms of resistance in parasitic nematodes is challenging because of their high levels of genetic variation, the inability to culture animals in the laboratory, and a limited genetic toolbox. Caenorhabditis elegans is an ideal model organism to study phenotypic responses to emodepside because of its tractable life cycle, small and well characterized genome, and the availability of genome-editing tools. The C. elegans laboratory strain N2 is sensitive to emodepside. In the presence of the drug, N2 animals have reduced movement, pharyngeal pumping, and egg-laying, and are developmentally delayed. Mutagenesis studies have implicated a calcium-activated potassium channel, SLO-1, in emodepside mode of action. Responses to emodepside differ across wild isolates of C. elegans. If these differences are heritable, we can use C. elegans to discover natural emodepside resistance mechanisms that could be shared with parasitic nematodes. Here, we determined if natural genetic variation across the natural population can explain differences in emodepside responses. In a genome-wide association study, we measured the phenotypic response to emodepside for 154 wild isolates. We found that several genomic regions on chromosome V are associated with differences in emodepside responses. Candidate genes in these regions include UGT enzymes and slo-1. Variation in the genomic region that includes slo-1 is associated with increased susceptibility to emodepside. Currently, we are testing the roles of the candidate genes in emodepside responses. Our results show that other genes in addition to slo-1 affect the response to emodepside and that wild strains vary in the function of slo-1.

Weeks, Janis et al. (2021) International Worm Meeting "Comparison of electrophysiological and motility assays to study drug effects in C. elegans"

Heisler, Iring, Roberts, William, Kulke, Daniel, Hahnel, Steffen, Weeks, Janis

[International Worm Meeting, 2021]

Gibson, Sophia B et al. (2021) MicroPubl Biol

Harper, Clare S, Gibson, Sophia B, Lackner, Laura L, Andersen, Erik C

[MicroPubl Biol, 2021]

Parasitic nematode infections continue to have an enormous impact on human and livestock health worldwide (Hotez et al., 2014; Kaplan & Vidyashankar, 2012). A limited arsenal of anthelmintic drugs are available to combat these infections. One of the most widely used classes is benzimidazoles (BZ), and resistance against this class is widespread (Kaplan & Vidyashankar, 2012). Previous studies to understand parasitic nematode resistance using the free-living model organism Caenorhabditis elegans showed that variation in the C. elegans beta-tubulin gene ben-1, an ortholog of beta-tubulins in parasitic nematodes, confers resistance to BZ drugs (Dilks et al., 2020; Driscoll et al., 1989; Hahnel et al., 2018). The most common missense mutation resistance alleles are F167Y, E198A, and F200Y (Avramenko et al., 2019; Mohammedsalih et al., 2020). Although computational models have predicted that these amino acids are involved in the binding of BZ compounds to beta-tubulins, the binding remains to be investigated empirically at the structural level because nematode-specific beta-tubulin structures have not been created (Aguayo-Ortiz et al., 2013; Hahnel et al., 2018). To better understand the mechanisms of resistance, we sought to obtain those crystallographic structures.

Kruger J et al. (2006) Nucleic Acids Res "RNAhybrid: microRNA target prediction easy, fast and flexible."

Rehmsmeier M, Kruger J

[Nucleic Acids Res, 2006]

In the elucidation of the microRNA regulatory network, knowledge of potential targets is of highest importance. Among existing target prediction methods, RNAhybrid [M. Rehmsmeier, P. Steffen, M. Hochsmann and R. Giegerich (2004) RNA, 10, 1507-1517] is unique in offering a flexible online prediction. Recently, some useful features have been added, among these the possibility to disallow G:U base pairs in the seed region, and a seed-match speed-up, which accelerates the program by a factor of 8. In addition, the program can now be used as a webservice for remote calls from user-implemented programs. We demonstrate RNAhybrid''s flexibility with the prediction of a non-canonical target site for Caenorhabditis elegans miR-241 in the 3''-untranslated region of lin-39. RNAhybrid is available at http://bibiserv.techfak.uni-bielefeld.de/rnahybrid.