{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T04:17:15Z","timestamp":1760242635680,"version":"build-2065373602"},"reference-count":29,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2017,12,28]],"date-time":"2017-12-28T00:00:00Z","timestamp":1514419200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Entropy"],"abstract":"<jats:p>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\u2014competition 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.<\/jats:p>","DOI":"10.3390\/e20010013","type":"journal-article","created":{"date-parts":[[2017,12,28]],"date-time":"2017-12-28T11:24:33Z","timestamp":1514460273000},"page":"13","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Self-Organization of Genome Expression from Embryo to Terminal Cell Fate: Single-Cell Statistical Mechanics of Biological Regulation"],"prefix":"10.3390","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4640-804X","authenticated-orcid":false,"given":"Alessandro","family":"Giuliani","sequence":"first","affiliation":[{"name":"Environment and Health Department, Istituto Superiore di Sanit\u00e1, 00161 Rome, Italy"}]},{"given":"Masa","family":"Tsuchiya","sequence":"additional","affiliation":[{"name":"SEIKO Life Science Laboratory, SRI, Osaka 540-659, Japan"},{"name":"Systems Biology Program, School of Media and Governance, Keio University, Fujisawa 252-0882, Japan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2751-7136","authenticated-orcid":false,"given":"Kenichi","family":"Yoshikawa","sequence":"additional","affiliation":[{"name":"Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan"}]}],"member":"1968","published-online":{"date-parts":[[2017,12,28]]},"reference":[{"doi-asserted-by":"crossref","unstructured":"Tsuchiya, M., Hashimoto, M., Takenaka, Y., Motoike, I.N., and Yoshikawa, K. 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