Worm Embryogenesis: Cell by Cell and Gene by Gene
Worm Embryogenesis: Cell by Cell and Gene by Gene

Worm Embryogenesis: Cell by Cell and Gene by Gene

A single-cell map of C. elegans’s transcriptome during development finds cell lineages that start out genetically different and end up as cells of similar function and genetic profile.

Dec 1, 2019
Kerry Grens

ABOVE: Each cell in the C. elegans embryo arranged by transcriptome similarity and color coded for when in development they are present.
© COLE TRAPNELL, UNIVERSITY OF WASHINGTON

EDITOR’S CHOICE IN DEVELOPMENTAL BIOLOGY

The paper

J.S. Packer et al., “A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution,” Science, 365:eaax1971, 2019.

Since the late Sydney Brenner first slid a C. elegans under the microscope more than a half century ago, scientists have used the species in one of the most exhaustive investigations of any animal—one that continues to this day. They have tracked each of the nematode’s cells as it blinks in and out of existence during development, sequenced the animal’s genome, and cataloged the transcriptome of the whole organism or the occasional tissue or cell. Now, Junhyong Kim, a developmental biologist at the University of Pennsylvania, and his colleagues have traced the gene expression in nearly every cell, one by one, in developing worms, from fertilization to hatching. 

“For every gene, you see where and when it’s expressed,” says Itai Yanai, a computational biologist at New York University’s School of Medicine who was not involved in the study. “That’s a tremendous step forward.”

By the time an individual C. elegans reaches adulthood it has had just 1,341 cells, although they don’t all exist in the animal’s body at the same time. Kim and his team gathered embryos from various stages of development and isolated individual cells by centrifugation or filtration, collecting more than 86,000 cells in total. Using marker genes whose expression Kim’s colleagues had previously traced to certain cells at certain times, along with developmental stage and other identifiers, the team was able to categorize each cell into one of 502 cell types and use RNA-seq analyses to index its transcriptome.

The team found that cells in different lineages can have similar gene expression profiles, a pattern that occurs in mice as well, suggesting this is a common feature of animal development. Kim likens this to a tree—while the branches might be different, the leaves on one side are quite similar to those on the other side. “They converge to the same kind of cell identity,” he says.

Kerry Grens is a senior editor and the news director of The Scientist. Email her at kgrens@the-scientist.com.