ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2020
Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and Reprogramming.
Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Epigenetic remodeling during early embryonic development.Frontiers in cell and developmental biology · 2026Review
- Article
- Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes.Journal of molecular cell biology · 2023Review
- Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle.Open biology · 2023Article
- Three-dimensional genome structure and function.MedComm · 2023Review
- Insights into the cell fate decision-making processes from chromosome structural reorganizations.Biophysics reviews · 2022Article
- Uncovering the Quantitative Relationships Among Chromosome Fluctuations, Epigenetics, and Gene Expressions of Transdifferentiation on Waddington Landscape.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems.Journal of biological physics · 2022Review
- Dynamics and Pathways of Chromosome Structural Organizations during Cell Transdifferentiation.JACS Au · 2022Article
- Extracting multi-way chromatin contacts from Hi-C data.PLoS computational biology · 2021Article
- Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics.PLoS computational biology · 2021Article
- Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and Reprogramming.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2020Article
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2 authors.
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Abstract
As an essential and fundamental process of life, cell development involves large-scale reorganization of the 3D genome architecture, which forms the basis of gene regulation. Here, a landscape-switching model is developed to explore the microscopic chromosomal structural origin of embryonic stem cell (ESC) differentiation and somatic cell reprogramming. It is shown that chromosome structure exhibits significant compartment-switching in the unit of topologically associating domain. It is found that the chromosome during differentiation undergoes monotonic compaction with spatial repositioning of active and inactive chromosomal loci toward the chromosome surface and interior, respectively. In contrast, an overexpanded chromosome, which exhibits universal localization of loci at the chromosomal surface with erasing the structural characteristics formed in the somatic cells, is observed during reprogramming. An early distinct differentiation pathway from the ESC to the terminally differentiated cell, giving rise to early bifurcation on the Waddington landscape for the ESC differentiation is suggested. The theoretical model herein including the non-equilibrium effects, draws a picture of the highly irreversible cell differentiation and reprogramming processes, in line with the experiments. The predictions provide a physical understanding of cell differentiation and reprogramming from the chromosomal structural and dynamical perspective and can be tested by future experiments.
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