Early signatures of regime shifts in gene expression dynamics

TL;DR

This paper investigates early warning signals of regime shifts in gene expression, focusing on bistability and hysteresis in bacterial competence development, using deterministic and stochastic models to identify signatures like critical slowing down and variance.

Contribution

It introduces a systematic analysis of early signatures of gene expression regime shifts, distinguishing between bistability and excitability mechanisms.

Findings

Critical slowing down observed near transition points

Rising variance and autocorrelation serve as early warning signals

Signatures can differentiate bistability from excitability mechanisms

Abstract

Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene expression dynamics are less systematically investigated. In this paper, we consider sudden regime shifts in the gene expression dynamics described by a fold-bifurcation model involving bistability and hysteresis. We consider two alternative models, Models 1 and 2, of competence development in the bacterial population B. subtilis and determine some early signatures of the regime shifts between competence and noncompetence. We use both deterministic and stochastic formalisms for the purpose of our study. The early signatures studied include the critical slowing down as a transition point is approached, rising variance and the lag-1 autocorrelation function, skewness and a ratio of two mean first passage times. Some of the signatures could provide the experimental basis for distinguishing between bistability and excitability as the correct mechanism for the development of competence.