Name
Title | ||
|---|---|---|
Self-Organization of Genome Expression from Embryo to Terminal Cell Fate: Single-Cell Statistical Mechanics of Biological Regulation. |
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 patternscompetition 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. |
Year | DOI | Venue |
|---|---|---|
2018 | 10.3390/e20010013 | ENTROPY |
Keywords | Field | DocType |
early embryo development,reprogramming,single-cell differentiation,single-cell genome dynamics,self-organization,autonomous self-organized criticality,genome avalanche,statistical thermodynamics,critical transition state | Genome,Mathematical optimization,Reprogramming,Self-organization,Cellular differentiation,Cell fate determination,Computational biology,Chromatin,Mathematics,Biological regulation,Epigenetics | Journal |
Volume | Issue | ISSN |
20 | 1 | 1099-4300 |
Citations | PageRank | References |
0 | 0.34 | 1 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Alessandro Giuliani | 1 | 170 | 25.21 |
| Masa Tsuchiya | 2 | 0 | 1.01 |
| Kenichi Yoshikawa | 3 | 16 | 7.78 |