Mutagenesis of mouse embryonic stem cells with ethylmethanesulfonate

Detection of functional protein domains by unbiased genome-wide forward genetic screening

Establishing genetic and chemo-genetic interactions has played key roles in elucidating mechanisms by which certain chemicals perturb cellular functions. In contrast to gene disruption/depletion strategies to identify mechanisms of drug resistance, searching for point-mutational genetic suppressors that can identify separation- or gain-of-function mutations has been limited. Here, by demonstrating its utility in identifying chemical-genetic suppressors of sensitivity to the DNA topoisomerase I poison camptothecin or the poly(ADP-ribose) polymerase inhibitor olaparib, we detail an approach allowing systematic, large-scale detection of spontaneous or chemically-induced suppressor mutations in yeast or haploid mammalian cells in a short timeframe, and with potential applications in other haploid systems. In addition to applications in molecular biology research, this protocol can be used to identify drug targets and predict drug-resistance mechanisms. Mapping suppressor mutations on the primary or tertiary structures of protein suppressor hits provides insights into functionally relevant protein domains. Importantly, we show that olaparib resistance is linked to missense mutations in the DNA binding regions of PARP1, but not in its catalytic domain. This provides experimental support to the concept of PARP1 trapping on DNA as the prime source of toxicity to PARP inhibitors, and points to a novel olaparib resistance mechanism with potential therapeutic implications.

Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells

In model organisms, classical genetic screening via random mutagenesis provides key insights into the molecular bases of genetic interactions, helping to define synthetic lethality, synthetic viability and drug-resistance mechanisms. The limited genetic tractability of diploid mammalian cells, however, precludes this approach. Here, we demonstrate the feasibility of classical genetic screening in mammalian systems by using haploid cells, chemical mutagenesis and next-generation sequencing, providing a new tool to explore mammalian genetic interactions.

Assessment of the in vitro γH2AX assay by High Content Screening as a novel genotoxicity test

The γH2AX assay is widely used as a marker of DNA damage in multiple scientific fields such as cancer biomarker, clinical studies and radiation biology. In particular, the in vitro γH2AX assay has been suggested as a novel in vitro genotoxicity test with potential as a pre-screening tool. However, to date, limited assessments have been carried out to evaluate the sensitivity, specificity and accuracy of the in vitro γH2AX assay. In this study, the microscopy-based system combining automated cellular image acquisition with software quantification for High Content Screening (HCS) has been used for the first time to evaluate the in vitro γH2AX assay. A panel of well-characterised genotoxic and non-genotoxic compounds was selected to assess the performance of the in vitro γH2AX assay in the human bronchial epithelial cell line BEAS-2B. The results obtained during this preliminary assessment indicate that the in vitro γH2AX assay has a high accuracy (86%) as a result of high sensitivity and specificity (86-92% and 80-88% respectively). Our data highlight the potential for γH2AX detection in HCS as a complement to the current regulatory genotoxicity battery of in vitro assays. We therefore recommend more comprehensive assessments to confirm the performance of the in vitro γH2AX assay by HCS with a more extensive set of compounds.

Mutation of a U2 snRNA gene causes global disruption of alternative splicing and neurodegeneration

Although uridine-rich small nuclear RNAs (U-snRNAs) are essential for pre-mRNA splicing, little is known regarding their function in the regulation of alternative splicing or of the biological consequences of their dysfunction in mammals. Here, we demonstrate that mutation of Rnu2-8, one of the mouse multicopy U2 snRNA genes, causes ataxia and neurodegeneration. Coincident with the observed pathology, the level of mutant U2 RNAs was highest in the cerebellum and increased after granule neuron maturation. Furthermore, neuron loss was strongly dependent on the dosage of mutant and wild-type snRNA genes. Comprehensive transcriptome analysis identified a group of alternative splicing events, including the splicing of small introns, which were disrupted in the mutant cerebellum. Our results suggest that the expression of mammalian U2 snRNA genes, previously presumed to be ubiquitous, is spatially and temporally regulated, and dysfunction of a single U2 snRNA causes neuron degeneration through distortion of pre-mRNA splicing.