Self-organization of genome expression from embryo to terminal cell fate: Single-cell statistical mechanics of biological regulation

Alessandro Giuliani, Masa Tsuchiya, Kenichi Yoshikawa

Research output: Contribution to journalArticlepeer-review

Abstract

A statistical mechanical mean-field approach to the temporal development of biological regulation provides a phenomenological, but basic description of the dynamical behavior of genome expression in terms of autonomous self-organization with a critical transition (Self-Organized Criticality: SOC). This approach reveals the basis of self-regulation/organization of genome expression, where the extreme complexity of living matter precludes any strict mechanistic approach. The self-organization in SOC involves two critical behaviors: scaling-divergent behavior (genome avalanche) and sandpile-type critical behavior. Genome avalanche patterns-competition between order (scaling) and disorder (divergence) reflect the opposite sequence of events characterizing the self-organization process in embryo development and helper T17 terminal cell differentiation, respectively. On the other hand, the temporal development of sandpile-type criticality (the degree of SOC control) in mouse embryo suggests the existence of an SOC control landscape with a critical transition state (i.e., the erasure of zygote-state criticality). This indicates that a phase transition of the mouse genome before and after reprogramming (immediately after the late 2-cell state) occurs through a dynamical change in a control parameter. This result provides a quantitative open-thermodynamic appreciation of the still largely qualitative notion of the epigenetic landscape. Our results suggest: (i) the existence of coherent waves of condensation/de-condensation in chromatin, which are transmitted across regions of different gene-expression levels along the genome; and (ii) essentially the same critical dynamics we observed for cell-differentiation processes exist in overall RNA expression during embryo development, which is particularly relevant because it gives further proof of SOC control of overall expression as a universal feature.

Original languageEnglish
Article number13
JournalEntropy
Volume20
Issue number1
DOIs
Publication statusPublished - Jan 1 2018

Keywords

  • Autonomous self-organized criticality
  • Critical transition state
  • Early embryo development
  • Genome avalanche
  • Reprogramming
  • Self-organization
  • Single-cell differentiation
  • Single-cell genome dynamics
  • Statistical thermodynamics

ASJC Scopus subject areas

  • Physics and Astronomy(all)

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