Emergent Self-Organized Criticality in Gene Expression Dynamics: Temporal Development of Global Phase Transition Revealed in a Cancer Cell Line

PloS One
Masa TsuchiyaKenichi Yoshikawa

Abstract

The underlying mechanism of dynamic control of the genome-wide expression is a fundamental issue in bioscience. We addressed it in terms of phase transition by a systemic approach based on both density analysis and characteristics of temporal fluctuation for the time-course mRNA expression in differentiating MCF-7 breast cancer cells. In a recent work, we suggested criticality as an essential aspect of dynamic control of genome-wide gene expression. Criticality was evident by a unimodal-bimodal transition through flattened unimodal expression profile. The flatness on the transition suggests the existence of a critical transition at which up- and down-regulated expression is balanced. Mean field (averaging) behavior of mRNAs based on the temporal expression changes reveals a sandpile type of transition in the flattened profile. Furthermore, around the transition, a self-similar unimodal-bimodal transition of the whole expression occurs in the density profile of an ensemble of mRNA expression. These singular and scaling behaviors identify the transition as the expression phase transition driven by self-organized criticality (SOC). Emergent properties of SOC through a mean field approach are revealed: i) SOC, as a form of genomic ...Continue Reading

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Feb 28, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Mariano BizzarriAlessandra Cucina
Jul 16, 2017·Physical Review. E·Eun-Jin Kim, Rainer Hollerbach
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Jul 2, 2020·International Journal of Molecular Sciences·Masa TsuchiyaKenichi Yoshikawa
Jan 17, 2021·Biophysical Journal·Jekabs KrigertsJekaterina Erenpreisa
Dec 9, 2020·Entropy·Takayuki NiizatoToshiki Fukushima
Dec 15, 2020··Oleg Naimark, Oleg Naimark

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Datasets Mentioned

BETA
GSE13009

Methods Mentioned

BETA
Hi-C
protein folding
chip

Software Mentioned

DEAB
Hi
Mathematica
DEAB Dynamic Emergent Averaging Behavior
nrmsf

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