Lineage Tracing and Single-Cell RNA-seq in C. elegans to Analyze Transgenerational Epigenetic Phenotypes Inherited from Germ Cells

The last several years have seen an increasing number of examples of transgenerational epigenetic inheritance, in which phenotypes are inherited for three or more generations without changes to the underlying DNA sequence. One model system that has been particularly useful for studying transgenerational epigenetic inheritance is C. elegans. Their short generation time and hermaphroditic reproduction have allowed multiple transgenerational phenotypes to be identified, including aging, fertility, and behavior. However, it is still not clear how transgenerational epigenetic inheritance from the germline affects embryogenesis. Fortunately, the C. elegans embryo has a unique property that makes it ideal for addressing this question: they develop via an invariant lineage, with each cell undergoing stereotypical cell divisions to adopt the same cell fate in every individual embryo. Because of this invariant cell lineage, automated lineage tracing and single-cell RNA-seq can be employed to determine how transgenerational epigenetic inheritance from the germline affects developmental timing and cell fate. Unfortunately, difficulties with these techniques have severely limited their adoption in the community. Here, we provide a practical guide to automated lineage tracing coupled with single-cell RNA-seq to facilitate their use in studying transgenerational epigenetic inheritance in C. elegans embryos.