Montagna Sara, Braccini Michele, Roli Andrea
IEEE/ACM Trans Comput Biol Bioinform. 2021 Nov-Dec;18(6):2702-2713. doi: 10.1109/TCBB.2020.2968310. Epub 2021 Dec 8.
Boolean networks are a notable model of gene regulatory networks and, particularly, prominent theories discuss how they can capture cellular differentiation processes. One frequent motif in gene regulatory networks, especially in those circuits involved in cell differentiation, is autoregulation. In spite of this, the impact of autoregulation on Boolean network attractor landscape has not yet been extensively discussed in literature. In this paper we propose to model autoregulation as self-loops, and analyse how the number of attractors and their robustness may change once they are introduced in a well-known and widely used Boolean networks model, namely random Boolean networks. Results show that self-loops provide an evolutionary advantage in dynamic mechanisms of cells, by increasing both number and maximal robustness of attractors. These results provide evidence to the hypothesis that autoregulation is a straightforward functional component to consolidate cell dynamics, mainly in differentiation processes.
布尔网络是基因调控网络的一个显著模型，特别是有突出理论探讨了它们如何能够捕捉细胞分化过程。基因调控网络中一个常见的基序，尤其是在那些参与细胞分化的回路中，是自动调节。尽管如此，自动调节对布尔网络吸引子格局的影响在文献中尚未得到广泛讨论。在本文中，我们建议将自动调节建模为自环，并分析一旦将其引入一个著名且广泛使用的布尔网络模型，即随机布尔网络，吸引子的数量及其鲁棒性可能会如何变化。结果表明，自环通过增加吸引子的数量和最大鲁棒性，在细胞的动态机制中提供了一种进化优势。这些结果为以下假设提供了证据：自动调节是巩固细胞动态的一个直接功能组件，主要在分化过程中。
