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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 October 2025 | Viewed by 1501

Special Issue Editor


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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

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Keywords

  • chromatin structure and dynamics
  • genome architecture
  • epigenetic regulation

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Published Papers (3 papers)

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Research

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21 pages, 9235 KiB  
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 334
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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13 pages, 625 KiB  
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 175
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 KiB  
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 449
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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