Variability in gene expression underlies incomplete penetrance

Abstract

The phenotypic differences between individual organisms can often be ascribed to underlying genetic and environmental variation. However, even genetically identical organisms in homogeneous environments vary, indicating that randomness in developmental processes such as gene expression may also generate diversity. To examine the consequences of gene expression variability in multicellular organisms, we studied intestinal specification in the nematode Caenorhabditis elegans in which wild-type cell fate is invariant and controlled by a small transcriptional network. Mutations in elements of this network can have indeterminate effects: some mutant embryos fail to develop intestinal cells, whereas others produce intestinal precursors. By counting transcripts of the genes in this network in individual embryos, we show that the expression of an otherwise redundant gene becomes highly variable in the mutants and that this variation is subjected to a threshold, producing an ON/OFF expression pattern of the master regulatory gene of intestinal differentiation. Our results demonstrate that mutations in developmental networks can expose otherwise buffered stochastic variability in gene expression, leading to pronounced phenotypic variation.

Figure 1. Gene expression in the C. elegans intestinal cell fate specification network

a. The early embryonic lineage leading to the formation of the E cell. b. The gene regulatory network governing intestinal cell specification. skn-1 and pop-1 transcripts are maternally deposited. c–f. Visualization of single transcripts in individual wild-type (N2) embryos with DAPI as a nuclear counterstain. For Cy5, we assigned transcripts to med-1,2 in embryos with less than 30 nuclei and to elt-2 in those with more than 30 nuclei (f). Expression of elt-2 in g. wild-type (N2) and h. mutant embryos harboring the skn-1(zu129) allele.

Figure 2. Expression dynamics in wild-type and skn-1 mutant embryos

a. Transcript number vs. number of nuclei for a collection of randomly staged wild-type (N2) (left) and zu135 mutant (right) early embryos. b. Depiction of the operation of the gut differentiation network in skn-1 mutant embryos. c. Number of cells expressing end-1 (top) or elt-2 (bottom) within individual wild-type and zu135 mutant embryos vs. number of nuclei. d. Transcript number vs. number of cells expressing end-1 (top) or elt-2 (bottom) in zu135 mutant embryos.

Figure 3. High levels of end-1 are required for elt-2 expression in skn-1 mutant embryos

a. Model in which end-1 expression must surpass a threshold during a window of developmental time in order to activate elt-2 expression. b. Scatter plots of end-1 and elt-2 transcript numbers in wild-type (N2; blue) and skn-1 mutant embryos (red). c. Transcript number vs. number of cells expressing end-1 in zu67 mutant embryos containing between 65 and 120 nuclei. d. Number of elt-2 vs. end-1 transcripts in zu67 mutant embryos (c) with 1 through 8 (top to bottom) cells expressing end-1.

Figure 4. Chromatin regulators and indirect network connections regulate variability in end-1 expression

a. Expression dynamics in the zu135 strain subjected to RNAi against hda-1. b. Depiction of the role of hda-1 in the gut differentiation network. c. Histograms of the number of end-1 transcripts in wild-type (top; coefficient of variation of 0.20±0.057; error obtained by bootstrapping), skn-1(zu135) (middle; cv of 0.69±0.066) and skn-1(zu135); hda-1(RNAi) (bottom; cv of 0.44±0.056) embryos containing between 45 and 75 nuclei. d. Expression dynamics with an end-3 deletion. e. Depiction of the gut differentiation network with end-3 deleted.