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Open AccessArticle

Self-Organization of Genome Expression from Embryo to Terminal Cell Fate: Single-Cell Statistical Mechanics of Biological Regulation

1
Environment and Health Department, Istituto Superiore di Sanitá, 00161 Rome, Italy
2
SEIKO Life Science Laboratory, SRI, Osaka 540-659, Japan
3
Systems Biology Program, School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
4
Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
*
Author to whom correspondence should be addressed.
Entropy 2018, 20(1), 13; https://doi.org/10.3390/e20010013
Received: 4 December 2017 / Revised: 19 December 2017 / Accepted: 20 December 2017 / Published: 28 December 2017
(This article belongs to the Special Issue Entropy and Its Applications across Disciplines)
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. View Full-Text
Keywords: early embryo development; reprogramming; single-cell differentiation; single-cell genome dynamics; self-organization; autonomous self-organized criticality; genome avalanche; statistical thermodynamics; critical transition state early embryo development; reprogramming; single-cell differentiation; single-cell genome dynamics; self-organization; autonomous self-organized criticality; genome avalanche; statistical thermodynamics; critical transition state
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Giuliani, A.; Tsuchiya, M.; Yoshikawa, K. Self-Organization of Genome Expression from Embryo to Terminal Cell Fate: Single-Cell Statistical Mechanics of Biological Regulation. Entropy 2018, 20, 13.

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