Variability in Gene Expression Underlies Incomplete Penetrance in C. Elegans: Using Single Molecules To Study the Development of Single Cells

Abstract

Phenotypic variation is ubiquitous in biology and is often traceable to underlying genetic and environmental variation. However, even genetically identical organ-isms in homogenous environments vary, suggesting that random processes may play an important role in generating phenotypic diversity. Few studies, have ex-plored the impact of stochastic fluctuations in gene expression on phenotypic variation and cell fate decisions in multicellular organisms. In order to examine the consequences of gene expression variability in development, we explored intestinal specification in C. elegans, in which wild-type cell fate is invariant and controlled by a small transcriptional network. In contrast, cell fates in embryos with mutant skn-1, the first gene expressed in this network, are variable: while most mutant embryos fail to develop intestinal cells, some embryos nevertheless produce intestinal precursors. By counting transcripts in individual embryos, we show that mutations in skn-1 result in large variability in the expression of the downstream gene end-1, arising partly from misregulation of chromatin remodel-ing. end-1 expression is are subsequently thresholded during a critical time win-dow to produce an ON/OFF expression pattern of elt-2, the master regulator of intestinal differentiation. The loss of skn-1 activity eliminates redundancy in the network, making elt-2 activation particularly sensitive to variability in end-1 ex-pression. Although end-3 can also activate elt-2, deleting end-3 in wild-type ani-mals results in variability in levels and timing of elt-2 expression, suggesting that robust expression of the downstream target requires multiple transcriptional acti-vators and also hinting at subtle differences in the roles of putatively redundant elements in the network. Our results show that mutations in developmental net-works can expose otherwise buffered stochastic variability in gene expression, leading to pronounced phenotypic variation.