Modeling transcriptional regulation of the cell cycle using a novel cybernetic-inspired approach

Biophys J. 2023 Dec 15:S0006-3495(23)04148-6. doi: 10.1016/j.bpj.2023.12.010. Online ahead of print.ABSTRACTQuantitative understanding of cellular processes, such as cell cycle and differentiation, is impeded by various forms of complexity ranging from myriad molecular players and their multilevel regulatory interactions, cellular evolution with multiple intermediate stages, lack of elucidation of cause-effect relationships among the many system players, and the computational complexity associated with the profusion of variables and parameters. In this paper, we present a modeling framework based on the cybernetic concept that biological regulation is inspired by objectives embedding rational strategies for dimension reduction, process stage specification through the system dynamics, and innovative causal association of regulatory events with the ability to predict the evolution of the dynamical system. The elementary step of the modeling strategy involves stage-specific objective functions that are computationally-determined from experiments, augmented with dynamical network computations involving end point objective functions, mutual information, change point detection, and maximal clique centrality. We demonstrate the power of the method through application to the mammalian cell cycle, which involves thousands of biomolecules engaged in signaling, transcription, and regulation. Starting with a fine-grained transcriptional description obtained from RNA sequencing measuremen...
Source: Biophysical Journal - Category: Physics Authors: Source Type: research