3D C. elegans Embryogenesis and Gene Expression

Melissa Chiasson, Timothy Durham, Andrew Hill, and Ning Li, UW Genome Sciences and Statistics

Caenorhabditis elegans (C. elegans) is a small roundworm used widely as a model organism in genetics and genomics. Its development has been well studied; each worm takes around 14 hours to grow from a single fertilized cell to a hatched larvae with 558 cells. Embryonic development proceeds due to the tightly choreographed expression of several genes. These patterns of gene expression contribute to cell identity. Location of cells during embryogenesis is also important, as cell-cell interactions can influence gene regulation.

The Expression Patterns In C. elegans (EPIC – http://epic2.gs.washington.edu/Epic2) project has generated a dataset that describes the spatial orientation of every cell during C. elegans embryogenesis, its developmental lineage and cell fate, and expression measurements for a set of about 227 genes. These data provide an expansive view of gene expression in the C. elegans embryo; however, to derive insights into gene expression patterns in different cells across time we need a tool to integrate and allow interactive exploration of the data.

We seek to address this lack of resource by developing an interactive visualization that includes a 3D plot of the C. elegans developing embryo, a lineage tree that is synched to the 3D plot, and plots of gene expression patterns. Users will be able to explore data using filters for lineage, cell type, and time point. In this way we hope to build a tool that C. elegans researchers can use to easily investigate patterns of gene expression during worm embryogenesis.

Confused about where to start? We have two compelling examples of how this visualization can be used to better understand the development and gene expression patterns of specific lineages and cell types.

For the first example, select "intestine," from the dropdown menu. Hit play on the time slider, and those cells that will form the intestine will then be highlighted in the color of your choice (the default is red). At the gastrulation stage of development these cells migrate dorsally from ventral locations on the outside of the embryo to locations inside the embryo, with other cells migrating ventrally to fill in the space left by their migration. When the intestinal cell type is highlighted in our 3D plot, this migration can be observed clearly from any orientation, and other interacting lineages and cell types can be identified by using the multiple lineage highlighting feature. These cells also exhibit unique gene expression patterns, as evidenced by their grouping in the gene expression PCA plot.

For the second example, select "C" from the dropdown menu. By the end of our time series, cells from the C lineage migrate to the posterior-dorsal edge of the embryo, forming a complex curvature around the back of the embryo from left to right. Patterns like this are hard to understand in two-dimensions (as seen in our 2D small multiple plots), but our 3D plot provides a more natural way to gain this insight. In addition, you will see in the gene expression PCA that these cells have a distinct gene expression pattern.

Gene expression specificity for all genes within the selected population. Gene specificity p-values were calculated using a hypergeometric test for the number of cells expressing each gene in the highlighted selection vs the total population. The p-values are Bonferroni corrected based on the number of genes.