A molecular atlas of C. elegans development at single-cell and single-lineage resolution

Abstract

It takes many cell divisions to produce a complex, multicellular organism such as a human being. Every one of the trillions of cells in a human body was produced by the division of a parent cell, which in turn was produced by the division of its parent; and if one follows this lineage far back enough, one will reach the single zygote cell that is the common progenitor of all of the cells in the body. Collectively, the pattern of cell divisions that produce an organism is called its cell lineage. As cells divide in a developing organism, they also differentiate into specialized cell types. What cell type a cell will adopt—its “cell fate”—is restricted by its lineage. A cell that descends from an endoderm progenitor, for example, may differentiate into a liver cell or an intestine cell, but will not become a bone cell. This general principle, that different parts of an organism’s cell lineage have different developmental potentials, has been known since the early 1800s. But our understanding of the molecular mechanisms that connect the cell lineage to the process of cell differentiation remains incomplete. In this dissertation, I present a near-comprehensive atlas of gene expression in the embryonic cell lineage of the nematode Caenorhabditis elegans, the only animal for which the cell lineage is fully known. I describe the methods used to assemble this atlas from single cell RNA-seq data, which required finding the precise lineage identity of each assayed cell. Using the atlas, I investigate the molecular mechanisms of cell fate commitment, finding that: 1. Multilineage priming is strikingly prevalent, contributing to the differentiation of over half of the cells in the lineage. 2. Distinct lineages that produce the same anatomical cell type tend to converge to a homogenous transcriptional state. This convergence is gradual for lineages that commit to their cell fate early in development, but can be abrupt for lineages that commit late. 3. A cell’s lineage and its transcriptome are correlated, but this correlation is transient, peaking in late gastrulation and falling dramatically during terminal differentiation. 4. Developmental trajectories reconstructed from single cell RNA-seq data often do not accurately reflect the cell lineage, in large part due to the transcriptional convergence of similarly fated lineages. Supplementary datasets, e.g. from fluorescent reporter imaging, are necessary to accurately place single cell RNA-seq data in the context of the cell lineage. This work provides an extensive resource to the C. elegans research community and an outline of the challenges that will need to be overcome in future studies of vertebrate cell lineages by single cell RNA-seq.