An Atlas of Network Topologies Reveals Design Principles for Caenorhabditis elegans Vulval Precursor Cell Fate Patterning

Abstract

The vulval precursor cell (VPC) fate patterning in Caenorhabditis elegans is a classic model experimental system for cell fate determination and patterning in development. Despite its apparent simplicity (six neighboring cells arranged in one dimension) and many experimental and computational efforts, the patterning strategy and mechanism remain controversial due to incomplete knowledge of the complex biology. Here, we carry out a comprehensive computational analysis and obtain a reservoir of all possible network topologies that are capable of VPC fate patterning under the simulation of various biological environments and regulatory rules. We identify three patterning strategies: sequential induction, morphogen gradient and lateral antagonism, depending on the features of the signal secreted from the anchor cell. The strategy of lateral antagonism, which has not been reported in previous studies of VPC patterning, employs a mutual inhibition of the 2° cell fate in neighboring cells. Robust topologies are built upon minimal topologies with basic patterning strategies and have more flexible and redundant implementations of modular functions. By simulated mutation, we find that all three strategies can reproduce experimental error patterns of mutants. We show that the topology derived by mapping currently known biochemical pathways to our model matches one of our identified functional topologies. Furthermore, our robustness analysis predicts a possible missing link related to the lateral antagonism strategy. Overall, we provide a theoretical atlas of all possible functional networks in varying environments, which may guide novel discoveries of the biological interactions in vulval development of Caenorhabditis elegans and related species.

Adaptation with transcriptional regulation

“…For example, the adaptation networks has either negative feedback loops or incoherent feedforward loops 6 . Other groups have also shown similar properties of function-topology relationship in other biological systems 7 8 9 10 11 12 13 . One remaining question of this kind of study is whether specific regulation forms or rules could change the function-topology relationship.…”

Adaptation through proportion

“…Behind the rich behaviors of natural and synthetic biological systems, such as bistable switch [1,2], oscillation [3,4], and spatial patterning [5,6], are particular network motifs. Mapping out the relationship between function and architecture of biological networks and identifying the underlying design principles are of broad interest [7][8][9][10][11][12]. Among the biological functions, adaptation has been extensively studied in the context of various sensory and signaling systems [13][14][15][16][17][18][19][20][21][22].…”