Single-nucleus resolution of the adult C. elegans and its application to the mapping of inter-generational response to alcohol exposure [scRNA-seq]

Single-cell RNA sequencing technologies have significantly contributed to our understanding of tissue heterogeneity as well as developmental and cell differentiation trajectories. They also provide an opportunity to map an organism's response to environmental cues with high resolution and identify sensitive tissues and cell types. However, the requirement for cellular integrity during extraction has limited the examination of organs that are syncytial or of cell types, such as neurons, that have significant cellular projections. We developed a mechanical method for single nucleus extraction in C. elegans that, combined with snRNA-seq, identifies a remarkable number of cell types in the adult nematode. Clustering analysis recapitulated established morphological and functional categories as well as the differentiation trajectory of the syncytial germline. Our approach also uncovered novel features of C. elegans biology, such as previously uncharacterized intestinal subpopulations and the up-regulation of X-linked transcripts in the somatic compartment of the hermaphrodite spermatheca. We applied this method to identify the impact of intergenerational exposure to a human-relevant dose of alcohol. We show that parental ethanol exposure causes a highly cell type-specific response in the adult F1 with oocytes, motor neurons, mechanosensory neurons, and neuronal support cells displaying the highest number of differentially expressed genes, the majority of which were downregulated. Cluster-level GO analysis revealed pathways previously not known to be altered by ethanol such as sister chromatid dynamics in the oocyte and autophagy in the uterine epithelium. Together, snRNA-seq provides a powerful approach for the detailed examination of an adult organism physiology. Overall design: 31 single nuclei C. elegans datasets were generated, divided into 5 batchs, four treatment group (normal, water, 0.5% ethanol, 0.05% ethanol) and two generations (F1 and F3)