Self-Organizing Global Gene Expression Regulated through Criticality: Mechanism of the Cell-Fate Change

PloS One
Masa TsuchiyaKenichi Yoshikawa

Abstract

A fundamental issue in bioscience is to understand the mechanism that underlies the dynamic control of genome-wide expression through the complex temporal-spatial self-organization of the genome to regulate the change in cell fate. We address this issue by elucidating a physically motivated mechanism of self-organization. Building upon transcriptome experimental data for seven distinct cell fates, including early embryonic development, we demonstrate that self-organized criticality (SOC) plays an essential role in the dynamic control of global gene expression regulation at both the population and single-cell levels. The novel findings are as follows: i) Mechanism of cell-fate changes: A sandpile-type critical transition self-organizes overall expression into a few transcription response domains (critical states). A cell-fate change occurs by means of a dissipative pulse-like global perturbation in self-organization through the erasure of initial-state critical behaviors (criticality). Most notably, the reprogramming of early embryo cells destroys the zygote SOC control to initiate self-organization in the new embryonal genome, which passes through a stochastic overall expression pattern. ii) Mechanism of perturbation of SOC con...Continue Reading

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Citations

Jan 8, 2020·International Journal of Molecular Sciences·Jekaterina Erenpreisa, Alessandro Giuliani
Jul 27, 2020·Environmental Epigenetics·Corrado Spadafora
Jul 2, 2020·International Journal of Molecular Sciences·Masa TsuchiyaKenichi Yoshikawa
Sep 2, 2020·Annual Review of Genetics·Jonathan FiorentinoAntonio Scialdone
Jan 17, 2021·Biophysical Journal·Jekabs KrigertsJekaterina Erenpreisa
Apr 25, 2021·BMC Bioinformatics·Makros N XenakisHubert J Smeets
Jul 3, 2021·Cells·Jekaterina ErenpreisaAlessandro Giuliani

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Datasets Mentioned

BETA
GSE13009
GSE14500

Methods Mentioned

BETA
RNA-Seq

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