Worms with the Guts to Play Games of Chance: Stochastic Effects and Binary Output in Gene Expression

How do you explain the phenomenon of incomplete penetrance, which happens when individuals carrying an allele for a given phenotype don’t always express the phenotype? For instance, individuals carrying the same mutation associated with a genetic disease do not always develop that disease.

Sometimes environment influences gene expression and plays a role, or other genetic differences among the individuals of a population can affect the expression of the gene in question. But, incomplete penetrance is also observed in model organisms that are raised in controlled environmental conditions and that have “identical” genetic makeup.

Biologists have proposed that random variability in gene expression could account for such events, and in clonal populations of microorganisms random variation in gene expression may even be important for generating genetic variability. However, in more complex organisms that have specific cell types organized into tissues and organs, gene expression needs to be highly controlled for the organism to develop properly. So, if there are random fluctuations in gene expression, somehow they need to be “buffered” in normal development.

Until the recent Nature paper published by Raj et al. (1), little experimental data existed to support the theory that essential developmental pathways include mechanisms to buffer the effects of random variations in gene expression.

In their study, Raj et al. use a highly sensitive Fluorescence in situ Hybridization (FISH) technique that can detect single mRNA molecules (2) to look at gene expression during specification of the intestine in single Caenorhabditis elegans (C. elegans) embryos. (Blogger’s digression: Think about this technique for a second. This technique allows researchers to see gene expression events when and where they occur in single cells. Wow. And it works not only in C. elegans but also in Drosophila imaginal discs, yeast, rat neurons and mammalian cells. Way cool.)

In C. elegans, the entire cell lineage has been mapped from fertilized egg to adult. The intestine consists of 20 cells that are all descended from a single cell called “E”, which arises after three asymmetric cell divisions following fertilization. The genetic pathway that controls intestinal cell-fate specification is fairly simple (well as fairly simple as any genetic pathway in a metazoan can be) and well understood.

Maternal transcripts of the gene skn-1 activate the genes med-1, med-2, end-3 and end-1. The protein encoded by end-3 also activates the end-1 gene, and both the end-1 and end-3 gene products can activate elt-2, which also acts on its own expression in a positive-feedback loop. Expression of elt-2 ultimately activates the genes necessary to make an intestine. So even this “simple” transcriptional pathway of six genes includes a great deal of redundancy, and all of this redundancy apparently insures that wild type embryos develop according to an invariant set of cell divisions and specifications.

Raj et al. used the FISH technique to count transcripts in hundreds of wild type and mutant embryos at various stages of development. Embryos with mutations in skn-1 showed considerably more variation in the expression of the genes examined than did wild type embryos, in which gene expression was fairly constant. skn-1 mutants have an incompletely penetrant phenotype for failure to produce an intestine. Mutations in skn-1 greatly reduced or eliminated expression of med-1, med-2, end-3 and elt-1. The end-1 gene was expressed one cell cycle later than wild type in skn-1 mutants, and the variation of expression seen between embryos of the same stages that carried the skn-1 mutations was quite high. The number of cells expressing elt-2 and end-1 varied among the mutant embryos, but interestingly the total level of elt-2 expressed always correlated with the number of cells expressing it, suggesting that each cell was producing the same amount of elt-2 transcript. This indicated that elt-2 was expressed in an ON/OFF (binary) manner, but end-1 was not, and that end-1 expression needed to reach a threshold before elt-2 would be expressed. The authors were able to show that indeed, in skn-1 mutants, elt-2 expression was only found in embryos with high levels of end-1 expression at a critical time point.

So, these results suggest that stochastic variation in gene expression can lead to a bimodal output and incomplete penetrance of a mutant phenotype. More importantly, this stochastic variation can be “buffered” by genetic redundancy in developmental pathways to ensure that essential developmental events occur.



  1. Raj, A., Rifkin, S., Andersen, E., & van Oudenaarden, A. (2010). Variability in gene expression underlies incomplete penetrance Nature, 463 (7283), 913-918 DOI: 10.1038/nature08781
  2. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, & Tyagi S (2008). Imaging individual mRNA molecules using multiple singly labeled probes. Nature methods, 5 (10), 877-9 PMID: 18806792
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Michele Arduengo

Senior Content Developer / Social Media Lead at Promega Corporation
Michele earned her B.A. in biology at Wesleyan College in Macon, GA, and her PhD through the BCDB Program at Emory University in Atlanta, GA. Michele manages the Promega Connections blog. She enjoys leisure reading, writing creative nonfiction and knitting, and the occasional cross-country skiing jaunt.

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