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Genome Structure, Function and Dynamic Regulation of Cell Fate

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 November 2025) | Viewed by 11377

Special Issue Editors


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Guest Editor
Faculty of Engineering, University of Applied Science Aschaffenburg, Wuerzburger Str. 45, 63743 Aschaffenburg, Germany
Interests: bioinformatics; biophysics; medical technology

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Guest Editor
Experimental Biophysics, Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
Interests: genom-architecture on the micro- and nano-scale during tumor genesis and after ionizing radiation exposure; nano-probes for DNA; DNA patterning; protein arrangements on the nano-scale in cell membranes
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Special Issue Information

Dear Colleagues,

The cell nucleus is a complex system in which simultaneous reactions and functions take place to keep the cell as a well-running individualized, specialized system. The cell nucleus contains chromatin packed in various degrees of density and separated into sub-volumes of territories and sub-chromosomal domains. Between the chromatin, there is enough “free” space for floating RNA, proteins, enzymes, ATPs, ions, water molecules, etc., which are trafficked either actively (using ATP energy) or passively by super- and supra-diffusion to the interaction points where they are required. It seems that this trafficking works somehow automatically and drives the system perfectly. So, genome organization and structure seem to be in an “entanglement” with genome function and molecular dynamics. This “landscape” of genome structure, function, and dynamics represents an advancement in biophysical, biological, and biomedical research. Recent advancements in molecular biology have, on the one hand, revolutionized our understanding of how genetic information is encoded and dynamically regulated. On the other hand, biophysical research has shown that epigenetic pathways impact chromatin organization and vice versa. These complex interactions govern cell function and cell fate decisions. This Special Issue aims to gather cutting-edge research that explores the latest developments in this exciting field. Topics of interest for this Special Issue include, but are not limited to, experimental and theoretical investigations of molecular mechanisms underlying chromatin remodeling, epigenetic regulation, DNA damage response, and transcriptional control in relation to their impact on cellular development, differentiation, and (re)programming or, in general, on cell fate. We invite submissions from researchers across the globe to contribute to this vibrant discussion and propel this field forward.

Prof. Dr. Georg Hildenbrand
Prof. Dr. Michael Hausmann
Guest Editors

Manuscript Submission Information

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Keywords

  • genome structure and organization
  • DNA sequence patterning and functional genomics
  • epigenetic regulation and chromatin remodeling
  • DNA damage response and cellular developments
  • cellular differentiation and cell fate
  • transcriptional control
  • chromatin architecture

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Published Papers (2 papers)

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Research

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32 pages, 34411 KB  
Article
A Single-Cell Transcriptomic Atlas of Epithelial Cell Heterogeneity During the Crown-to-Root Transition in the Mouse Molar
by Fei Bi, Tian Chen, Jiusi Guo, Wei Qiao, Zhi Liu and Xianglong Han
Int. J. Mol. Sci. 2026, 27(3), 1162; https://doi.org/10.3390/ijms27031162 - 23 Jan 2026
Cited by 1 | Viewed by 690
Abstract
The mechanisms driving the crown-to-root transition in tooth development remain incompletely understood, particularly the functional heterogeneity of dental epithelium. To address this gap and deconstruct this complexity, we aimed to analyze dental epithelial heterogeneity during this critical transition and to identify subpopulation-specific programs [...] Read more.
The mechanisms driving the crown-to-root transition in tooth development remain incompletely understood, particularly the functional heterogeneity of dental epithelium. To address this gap and deconstruct this complexity, we aimed to analyze dental epithelial heterogeneity during this critical transition and to identify subpopulation-specific programs relevant to root development. We therefore established a single-cell transcriptomic atlas of the mouse molar at postnatal days 3.5 and 7.5, integrating 30,951 cells to profile the pan-tissue landscape and performing an in-depth analysis of 4323 dental epithelial cells. Our results reveal that the dental epithelium is composed of seven distinct subpopulations with a clear lineage hierarchy, originating from multipotent progenitors and bifurcating into self-renewing and differentiating trajectories. The identified particular functions of each subcluster include the following: structural maintaining progenitor that inhibits mineralization (Cluster 4), proliferation driver (Cluster 0), key signaling center (Cluster 1), terminally differentiated executing enamel formation (Cluster 3 and Cluster 6), and extracellular matrix-organizing hub (Cluster 5), communicating extensively via the Bmp, Tgf-β, and Wnt pathways. Our work defines dental epithelium as a dynamic and heterogeneous orchestrator of root morphogenesis, providing a foundational framework for understanding developmental biology and pioneering future regenerative strategies based on precise epithelial cell functions. Full article
(This article belongs to the Special Issue Genome Structure, Function and Dynamic Regulation of Cell Fate)
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Review

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18 pages, 2833 KB  
Review
An Overview of the Current State of Cell Viability Assessment Methods Using OECD Classification
by Eneko Madorran, Miha Ambrož, Jure Knez and Monika Sobočan
Int. J. Mol. Sci. 2025, 26(1), 220; https://doi.org/10.3390/ijms26010220 - 30 Dec 2024
Cited by 19 | Viewed by 9739
Abstract
Over the past century, numerous methods for assessing cell viability have been developed, and there are many different ways to categorize these methods accordingly. We have chosen to use the Organisation for Economic Co-operation and Development (OECD) classification due to its regulatory importance. [...] Read more.
Over the past century, numerous methods for assessing cell viability have been developed, and there are many different ways to categorize these methods accordingly. We have chosen to use the Organisation for Economic Co-operation and Development (OECD) classification due to its regulatory importance. The OECD categorizes these methods into four groups: non-invasive cell structure damage, invasive cell structure damage, cell growth, and cellular metabolism. Despite the variety of cell viability methods available, they can all be categorized within these four groups, except for two novel methods based on the cell membrane potential, which we added to the list. Each method operates on different principles and has its own advantages and disadvantages, making it essential for researchers to choose the method that best fits their experimental design. This review aims to assist researchers in making this decision by describing these methods regarding their potential use and providing direct references to the cell viability assessment methods. Additionally, we use the OECD classification to facilitate potential regulatory use and to highlight the need for adding a new category to their list. Full article
(This article belongs to the Special Issue Genome Structure, Function and Dynamic Regulation of Cell Fate)
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