High-throughput capturing and characterization of mutations in essential genes of Caenorhabditis elegans

Abstract

BackgroundEssential genes are critical for the development of all organisms and are associated with many human diseases. These genes have been a difficult category to study prior to the availability of balanced lethal strains. Despite the power of targeted mutagenesis, there are limitations in identifying mutations in essential genes. In this paper, we describe the identification of coding regions for essential genes mutated using forward genetic screens in Caenorhabditis elegans. The lethal mutations described here were isolated and maintained by a wild-type allele on a rescuing duplication.ResultsWe applied whole genome sequencing to identify the causative molecular lesion resulting in lethality in existing C. elegans mutant strains. These strains are balanced and can be easily maintained for subsequent characterization. Our method can be effectively used to analyze mutations in a large number of essential genes. We describe here the identification of 64 essential genes in a region of chromosome I covered by the duplication sDp2. Of these, 42 are nonsense mutations, six are splice signal mutations, one deletion, and 15 are non-synonymous mutations. Many of the essential genes in this region function in cell cycle, transcriptional regulation, and RNA processing.ConclusionsThe essential genes identified here are represented by mutant strains, many of which have more than one mutant allele. The genetic resource can be utilized to further our understanding of essential gene function and will be applicable to the study of C. elegans development, conserved cellular function, and ultimately lead to improved human health.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-361) contains supplementary material, which is available to authorized users.

Combined flow cytometry and high throughput image analysis for the study of essential genes in Caenorhabditis elegans

“…Interestingly, we encounter 303 PHB interactors whose depletion causes a developmental defect. The fact that Chromosome I (left) is particularly enriched in essential genes partially explains this high number of interactions [69]. We uncover 31% of the genes previously described to affect development [57,63].…”

Rapid and Efficient Identification ofCaenorhabditis elegansLegacy Mutations Using Hawaiian SNP-Based Mapping and Whole-Genome Sequencing

“…A recent paper used a non-SNP−based method of WGS to identify the molecular lesion of 64 mutants of essential genes on chromosome I ( Chu et al 2014 ). Although five of the mutants we identified had mutations in genes on chromosome I, none of these were identified in the work by Chu et al (2014) .…”

KH domain containing RNA-binding proteins coordinate with microRNAs to regulateCaenorhabditis elegansdevelopment

“…In C. elegans, both sfa-1 and asd-2 are predicted to play a role in splicing, with asd-2 modulating the alternative splicing of unc-60 and other transcripts (Kuroyanagi 2013) and sfa-1 regulating the pre-mRNA splicing of multiple genes (Heintz et al 2017). Depletion of either sfa-1 or asd-2 was sufficient to induce embryonic lethality and reduce brood sizes (Table 2) (Ma and Horvitz 2009;Chu et al 2014), consistent with their essential roles as potential global regulators of splicing. Unbiased reverse genetic screens have previously identified splicing machinery members as important for miRNAmediated gene regulations (Parry et al 2007).…”