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Recent Advances in Chromatin Structure and Dynamics
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Recent Advances in Chromatin Structure and Dynamics

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

Deadline for manuscript submissions: 20 March 2026 | Viewed by 5116

Special Issue Editor

Dr. Stephanie Portillo-Ledesma

E-Mail Website
Guest Editor
Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA
Interests: chromatin structure and function; molecular modeling; enzyme kinetics

Special Issue Information

Dear Colleagues,

The complexity of chromatin folding in the eukaryotic nucleus has captivated researchers worldwide for over fifty years. From the early days of electron microscopy images to revolutionary chromosome conformation caption techniques for measuring genomic interactions, and now to advanced methodologies such as super-resolution microscopy, next-generation sequencing, single-cell techniques, and high-resolution genome modeling, the study of chromatin architecture has yielded invaluable insights into the role of genome multiscale organization in various cellular processes and human diseases.

We now understand that the genome is hierarchically organized into loops, topologically associated domains, compartments, and chromosome territories. Additionally, epigenetic regulation through post-translational modifications of histone tails, DNA methylation, histone variants, and protein binding provides a diverse array of mechanisms for modulating chromatin structure and dynamics, which in turn influences gene expression.

In this Special Issue, we invite researchers to submit original articles and reviews that focus on chromatin structure and dynamics, as well as its regulation by epigenetic modifications in the context of cellular function and human diseases.

Dr. Stephanie Portillo-Ledesma
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • chromatin structure and dynamics
  • genome architecture
  • epigenetic regulation

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Published Papers (5 papers)

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Research

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33 pages, 4694 KB  
Article
The Influence of Cohesin on the Short-Scale Dynamics of Intact and Damaged Chromatin in Different Phases of the Cell Cycle
by Vladimir S. Viushkov, Nikolai A. Lomov, Polina O. Kalitina, Daria M. Potashnikova, Anastasia S. Shtompel, Sergey V. Ulianov, Sergey V. Razin and Mikhail A. Rubtsov
Int. J. Mol. Sci. 2025, 26(18), 8837; https://doi.org/10.3390/ijms26188837 - 11 Sep 2025
Viewed by 496
Abstract
Cohesin organizes the genome into spatially segregated loops and topologically associated domains by loop extrusion. In addition, it ensures cohesion of sister chromatids after replication. Thus, cohesin is expected to limit chromatin dynamics by ensuring cohesion and compacting chromatin in the interphase. Nonetheless, [...] Read more.
Cohesin organizes the genome into spatially segregated loops and topologically associated domains by loop extrusion. In addition, it ensures cohesion of sister chromatids after replication. Thus, cohesin is expected to limit chromatin dynamics by ensuring cohesion and compacting chromatin in the interphase. Nonetheless, loop extrusion is an example of chromatin dynamics; thus, cohesin could promote the dynamics of genomic loci at the scale of individual loops and contact domains. Moreover, given that the extruding activity of cohesin after replication is supplemented by its cohesive activity, the impact of cohesin on chromatin dynamics in different phases of the cell cycle may vary. Of particular interest is the cohesin’s role in the regulation of the dynamics of damaged chromatin, which remains insufficiently studied. Here, we visualized a genomic locus using the CRISPR-Sirius system in human cells with auxin-induced depletion of the cohesin subunit RAD21. Cohesin depletion increased the local spatial dynamics of the visualized locus on a time scale of fractions of a second to one minute. This effect was observed in both replicated and unreplicated chromatin. However, the increase in the mobility of the visualized locus upon cohesin depletion was more pronounced in the former. In addition, we showed that cohesin depletion did not affect the local mobility of double-strand break repair foci visualized using a fluorescent fragment of the repair factor 53BP1. Cohesin depletion did not affect the local mobility of repair foci in either replicated or unreplicated chromatin. The results indicate that cohesin constrains local spatial dynamics of genomic loci. At the same time, cohesive activity of cohesin is not indispensable for restricting chromatin dynamics, although it enhances the confinement effect. On the other hand, repair foci are less mobile structures than point chromatin loci, and cohesin does not affect their dynamics on the studied time scales. Full article
(This article belongs to the Special Issue Recent Advances in Chromatin Structure and Dynamics)
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21 pages, 9235 KB  
Article
NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization
by Ziwei Li and Jia Fei
Int. J. Mol. Sci. 2025, 26(10), 4874; https://doi.org/10.3390/ijms26104874 - 19 May 2025
Viewed by 752
Abstract
The Nucleosome Destabilizing Factor (NDF) facilitates transcription through chromatin, but its precise mechanism remains incompletely understood. Here, we identify a critical region (amino acids 140–160) within NDF that specifically interacts with phosphorylated RPB1, the largest subunit of elongating RNA Polymerase II (Pol II). [...] Read more.
The Nucleosome Destabilizing Factor (NDF) facilitates transcription through chromatin, but its precise mechanism remains incompletely understood. Here, we identify a critical region (amino acids 140–160) within NDF that specifically interacts with phosphorylated RPB1, the largest subunit of elongating RNA Polymerase II (Pol II). Mutations in this region disrupt Pol II interaction and impair Pol II elongation both in vitro and in cells, yet do not affect NDF’s ability to destabilize nucleosomes, establishing a functional separation between these two activities. Cellular studies reveal that NDF knockout cells display faster Pol II elongation rates but produce fewer nascent transcripts, demonstrating NDF’s primary role in maintaining transcriptional processivity throughout gene bodies. Our findings demonstrate that NDF uses distinct mechanisms to ensure productive transcription elongation rather than simply enhancing elongation speed, offering new insights into how transcription efficiency is maintained in chromatin. Full article
(This article belongs to the Special Issue Recent Advances in Chromatin Structure and Dynamics)
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Review

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22 pages, 1118 KB  
Review
The Biological Function of Genome Organization
by Xin Yang, Hongni Zhu, Yajie Liu, Jinhong Wang, Yi Song, Shasha Liao and Peng Dong
Int. J. Mol. Sci. 2025, 26(18), 9058; https://doi.org/10.3390/ijms26189058 - 17 Sep 2025
Viewed by 378
Abstract
The mammalian genome is hierarchically packaged into distinct functional units, including chromatin loops, topologically associating domains, compartments and chromosome territories. This structural organization is fundamentally important because it orchestrates essential nuclear functions that underpin normal cellular identity and organismal development. In this review, [...] Read more.
The mammalian genome is hierarchically packaged into distinct functional units, including chromatin loops, topologically associating domains, compartments and chromosome territories. This structural organization is fundamentally important because it orchestrates essential nuclear functions that underpin normal cellular identity and organismal development. In this review, we synthesize current understanding of the intricate relationship between genome architecture and its critical biological roles. We discuss how hierarchical structures are dynamically established and maintained by architectural proteins, transcription factors, epigenetic regulators and non-coding RNAs via distinct mechanisms. Importantly, we focus on the functional consequences of three-dimensional (3D) genome organization and discuss how it modulates fundamental biological processes such as transcription, gene co-expression, epigenetic modification, DNA replication and repair. We also examine the dynamics of 3D genome organization during cellular differentiation, early embryonic development and organogenesis, followed by discussing how structural disruptions are mechanistically linked to various human diseases. Understanding the biological function of 3D genome organization is thus not only essential for deciphering fundamental nuclear processes but also holds significant promise for elucidating disease etiologies and developing effective therapeutics. Full article
(This article belongs to the Special Issue Recent Advances in Chromatin Structure and Dynamics)
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13 pages, 625 KB  
Review
Beyond Chaperoning: The Multifaceted Role of FACT in Chromatin Transactions
by Olesya Volokh, Vasily M. Studitsky and Olga S. Sokolova
Int. J. Mol. Sci. 2025, 26(11), 5176; https://doi.org/10.3390/ijms26115176 - 28 May 2025
Viewed by 776
Abstract
Eukaryotic transcription involves a complex interplay of protein factors that dynamically engage with chromatin at distinct stages. Among these, the histone chaperone FACT (Facilitates Chromatin Transcription) plays a unique role in nucleosome disassembly and reassembly during transcription, replication, and repair. While its functional [...] Read more.
Eukaryotic transcription involves a complex interplay of protein factors that dynamically engage with chromatin at distinct stages. Among these, the histone chaperone FACT (Facilitates Chromatin Transcription) plays a unique role in nucleosome disassembly and reassembly during transcription, replication, and repair. While its functional importance is well established, the underlying structural mechanisms involved in these activities remain incompletely understood. The remarkable functional versatility of FACT in regulating genetic information processing likely stems from its distinctive structural and mechanical properties. This review focuses on the structural organization of FACT and analysis of the mechanisms involved in chromatin reorganization by this unusual histone chaperone. Full article
(This article belongs to the Special Issue Recent Advances in Chromatin Structure and Dynamics)
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20 pages, 786 KB  
Review
Phase Separation in Chromatin Organization and Human Diseases
by Ziwei Zhai, Fei Meng, Junqi Kuang and Duanqing Pei
Int. J. Mol. Sci. 2025, 26(11), 5156; https://doi.org/10.3390/ijms26115156 - 28 May 2025
Viewed by 1823
Abstract
Understanding how the genome is organized into multi-level chromatin structures within cells and how these chromatin structures regulate gene transcription influencing animal development and human diseases has long been a major goal in genetics and cell biology. Recent evidence suggests that chromatin structure [...] Read more.
Understanding how the genome is organized into multi-level chromatin structures within cells and how these chromatin structures regulate gene transcription influencing animal development and human diseases has long been a major goal in genetics and cell biology. Recent evidence suggests that chromatin structure formation and remodeling is regulated not only by chromatin loop extrusion but also by phase-separated condensates. Here, we discuss recent findings on the mechanisms of chromatin organization mediated by phase separation, with a focus on the roles of phase-separated condensates in chromatin structural dysregulation in human diseases. Indeed, these mechanistic revelations herald promising therapeutic strategies targeting phase-separated condensates—leveraging their intrinsic biophysical susceptibilities to restore chromatin structure dysregulated by aberrant phase separation. Full article
(This article belongs to the Special Issue Recent Advances in Chromatin Structure and Dynamics)
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