Document Type

Article

Publication Date

5-11-2020

Keywords

JMG

JAX Source

iScience 2020 May 11; 23(6):101150

PMID

32450514

DOI

https://doi.org/10.1016/j.isci.2020.101150

Grant

CA034196,GM128717

Abstract

Many biological processes involve precise cellular state transitions controlled by complex gene regulation. Here, we use budding yeast cell cycle as a model system and explore how a gene regulatory circuit encodes essential information of state transitions. We present a generalized random circuit perturbation method for circuits containing heterogeneous regulation types and its usage to analyze both steady and oscillatory states from an ensemble of circuit models with random kinetic parameters. The stable steady states form robust clusters with a circular structure that are associated with cell cycle phases. This circular structure in the clusters is consistent with single-cell RNA sequencing data. The oscillatory states specify the irreversible state transitions along cell cycle progression. Furthermore, we identify possible mechanisms to understand the irreversible state transitions from the steady states. We expect this approach to be robust and generally applicable to unbiasedly predict dynamical transitions of a gene regulatory circuit.

Comments

This article is available under the Creative Commons CC-BY-NC license

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