bioRxiv2025
A unique balance of seemingly contradictory properties like robustness and plasticity, or evolvability and functional canalisation, characterises biological systems. To understand the basis of these properties, we investigate gene regulation, which is at the core of biological function. We simulate dynamical models of over 190 million genetic circuits covering all possible three-gene circuit structures. Our computational pipeline classifies these circuits into functional clusters by matching their temporal response shapes. Thus, we generate a dataset linking circuit structure, parameters and a corresponding functional label. Our key finding is a finite list of 20 functions that three-node genetic circuits can perform. Moreover, the structure-parameter space for these circuits tends to be primed for responses that stabilise over time following a perturbation. Every structure exhibits potential for multifunctionality with a range of 2-17 functions contingent upon parameters. We quantify network degeneracy, showing that many structural changes can be made to circuits without altering function. We define three quantities: structural, parametric, and functional diversities. Using these diversities, we construct a UNified FramewOrk for reguLatory Dynamics (UNFOLD) to analyse four key biological properties--robustness, plasticity, evolvability, and functional canalisation. Using UNFOLD, we identify that only 6.5% of network structures are non-plastic, while parameter sets enabling parametric robustness exist for every three-node network. We identify functionally canalised circuits from structure pairs that can be interchanged for a large number of parameter sets without a change in function. Overall, our framework offers insights into the fundamental organisation of biological networks by thorough analysis of three-node networks. Significance StatementBiological systems exhibit remarkable properties like robustness, plasticity, evolvability, and canalisation. This study presents a unified computational framework to understand these properties by exhaustively exploring the design space of three-node genetic circuits, identifying that only 20 functions are achievable, and revealing a natural bias toward stability. We uncover key principles of network degeneracy and multifunctionality, highlighting the versatility of genetic circuits. By analysing structural, parametric, and functional diversities, we identify structural and parametric changes that can transition a genetic circuit from robust behaviour to plasticity or from being canalised to becoming evolvable. Our work advances theoretical insights into biological function. It provides a method to identify alternate designs and parametric conditions for genetic circuits, paving the way for the design of reliable synthetic genetic circuits.