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Nucleosome: From Structural and Functional Aspects to Clinic
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Nucleosome: From Structural and Functional Aspects to Clinic

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

Deadline for manuscript submissions: closed (16 February 2024) | Viewed by 4952

Special Issue Editor

Dr. Natalya Maluchenko

E-Mail Website
Guest Editor
Biology Faculty, Lomonosov Moscow State University, Lenin Hills 1/12, 119234 Moscow, Russia
Interests: nucleosomes; proteins; chromatin

Special Issue Information

Dear Colleagues,

Nucleosomes are the basic structural units of chromatin formed from DNA and histones, revealing the structural features of DNA's stability as genetic material. Despite advances in the understanding of the canonical principles of nucleosome structural organization, the various possible structural states and their implications for genome function require further in-depth study and analysis. In addition, nucleosomes also have important clinical significance. Nucleosomes as structural–functional units of chromatin control the stability of the eukaryotic genome and regulate DNA processes such as transcription, replication, and repair. The influence of nucleosome structure and dynamics produces superior regulation of the expression of related genes and downstream pathways; disturbance and failure of these processes lead to the emergence of various tumor and metabolic diseases. Intervention at the nucleosome level can change the process of diseases earlier and is a feasible option for future diagnosis and treatment. For example, post-translational modifications of nucleosome histones are the most important components of epigenetic regulation systems, and disorder of epigenetic regulation is one of the most important mechanisms of carcinogenesis. Additionally, many nucleosome-binding proteins, such as FACT, PARPs, HDAC, etc., are promising targets for targeted therapy. In this issue, we invite all scientists involved in practical research on nucleosome-binding proteins, various epigenetic factors, and inhibitors to cooperate. This Special Issue aims to collect articles on nucleosomes’ structure and function and their clinical applications.

Dr. Natalya Maluchenko
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.

Published Papers (3 papers)

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Research

14 pages, 2097 KiB  
Article
Competitive Chemical Reaction Kinetic Model of Nucleosome Assembly Using the Histone Variant H2A.Z and H2A In Vitro
by Hongyu Zhao, Xueqin Shao, Mingxin Guo, Yongqiang Xing, Jingyan Wang, Liaofu Luo and Lu Cai
Int. J. Mol. Sci. 2023, 24(21), 15846; https://doi.org/10.3390/ijms242115846 - 31 Oct 2023
Viewed by 902
Abstract
Nucleosomes not only serve as the basic building blocks for eukaryotic chromatin but also regulate many biological processes, such as DNA replication, repair, and recombination. To modulate gene expression in vivo, the histone variant H2A.Z can be dynamically incorporated into the nucleosome. However, [...] Read more.
Nucleosomes not only serve as the basic building blocks for eukaryotic chromatin but also regulate many biological processes, such as DNA replication, repair, and recombination. To modulate gene expression in vivo, the histone variant H2A.Z can be dynamically incorporated into the nucleosome. However, the assembly dynamics of H2A.Z-containing nucleosomes remain elusive. Here, we demonstrate that our previous chemical kinetic model for nucleosome assembly can be extended to H2A.Z-containing nucleosome assembly processes. The efficiency of H2A.Z-containing nucleosome assembly, like that of canonical nucleosome assembly, was also positively correlated with the total histone octamer concentration, reaction rate constant, and reaction time. We expanded the kinetic model to represent the competitive dynamics of H2A and H2A.Z in nucleosome assembly, thus providing a novel method through which to assess the competitive ability of histones to assemble nucleosomes. Based on this model, we confirmed that histone H2A has a higher competitive ability to assemble nucleosomes in vitro than histone H2A.Z. Our competitive kinetic model and experimental results also confirmed that in vitro H2A.Z-containing nucleosome assembly is governed by chemical kinetic principles. Full article
(This article belongs to the Special Issue Nucleosome: From Structural and Functional Aspects to Clinic)
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28 pages, 8459 KiB  
Article
Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study
by Pavel D. Oleinikov, Anastasiia S. Fedulova, Grigoriy A. Armeev, Nikita A. Motorin, Lovepreet Singh-Palchevskaia, Anastasiia L. Sivkina, Pavel G. Feskin, Grigory S. Glukhov, Dmitry A. Afonin, Galina A. Komarova, Mikhail P. Kirpichnikov, Vasily M. Studitsky, Alexey V. Feofanov and Alexey K. Shaytan
Int. J. Mol. Sci. 2023, 24(20), 15194; https://doi.org/10.3390/ijms242015194 - 14 Oct 2023
Cited by 1 | Viewed by 2207
Abstract
In eukaryotic organisms, genomic DNA associates with histone proteins to form nucleosomes. Nucleosomes provide a basis for genome compaction, epigenetic markup, and mediate interactions of nuclear proteins with their target DNA loci. A negatively charged (acidic) patch located on the H2A-H2B histone dimer [...] Read more.
In eukaryotic organisms, genomic DNA associates with histone proteins to form nucleosomes. Nucleosomes provide a basis for genome compaction, epigenetic markup, and mediate interactions of nuclear proteins with their target DNA loci. A negatively charged (acidic) patch located on the H2A-H2B histone dimer is a characteristic feature of the nucleosomal surface. The acidic patch is a common site in the attachment of various chromatin proteins, including viral ones. Acidic patch-binding peptides present perspective compounds that can be used to modulate chromatin functioning by disrupting interactions of nucleosomes with natural proteins or alternatively targeting artificial moieties to the nucleosomes, which may be beneficial for the development of new therapeutics. In this work, we used several computational and experimental techniques to improve our understanding of how peptides may bind to the acidic patch and what are the consequences of their binding. Through extensive analysis of the PDB database, histone sequence analysis, and molecular dynamic simulations, we elucidated common binding patterns and key interactions that stabilize peptide–nucleosome complexes. Through MD simulations and FRET measurements, we characterized changes in nucleosome dynamics conferred by peptide binding. Using fluorescence polarization and gel electrophoresis, we evaluated the affinity and specificity of the LANA1-22 peptide to DNA and nucleosomes. Taken together, our study provides new insights into the different patterns of intermolecular interactions that can be employed by natural and designed peptides to bind to nucleosomes, and the effects of peptide binding on nucleosome dynamics and stability. Full article
(This article belongs to the Special Issue Nucleosome: From Structural and Functional Aspects to Clinic)
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16 pages, 2605 KiB  
Article
Epigallocatechin Gallate Affects the Structure of Chromatosomes, Nucleosomes and Their Complexes with PARP1
by Tatiana V. Andreeva, Natalya V. Maluchenko, Anastasiya V. Efremenko, Alexander V. Lyubitelev, Anna N. Korovina, Dmitry A. Afonin, Mikhail P. Kirpichnikov, Vasily M. Studitsky and Alexey V. Feofanov
Int. J. Mol. Sci. 2023, 24(18), 14187; https://doi.org/10.3390/ijms241814187 - 16 Sep 2023
Viewed by 1117
Abstract
The natural flavonoid epigallocatechin gallate has a wide range of biological activities, including being capable of binding to nucleic acids; however, the mechanisms of the interactions of epigallocatechin gallate with DNA organized in chromatin have not been systematically studied. In this work, the [...] Read more.
The natural flavonoid epigallocatechin gallate has a wide range of biological activities, including being capable of binding to nucleic acids; however, the mechanisms of the interactions of epigallocatechin gallate with DNA organized in chromatin have not been systematically studied. In this work, the interactions of epigallocatechin gallate with chromatin in cells and with nucleosomes and chromatosomes in vitro were studied using fluorescent microscopy and single-particle Förster resonance energy transfer approaches, respectively. Epigallocatechin gallate effectively penetrates into the nuclei of living cells and binds to DNA there. The interaction of epigallocatechin gallate with nucleosomes in vitro induces a large-scale, reversible uncoiling of nucleosomal DNA that occurs without the dissociation of DNA or core histones at sub- and low-micromolar concentrations of epigallocatechin gallate. Epigallocatechin gallate does not reduce the catalytic activity of poly(ADP-ribose) polymerase 1, but causes the modulation of the structure of the enzyme–nucleosome complex. Epigallocatechin gallate significantly changes the structure of chromatosomes, but does not cause the dissociation of the linker histone. The reorganization of nucleosomes and chromatosomes through the use of epigallocatechin gallate could facilitate access to protein factors involved in DNA repair, replication and transcription to DNA and, thus, might contribute to the modulation of gene expression through the use of epigallocatechin gallate, which was reported earlier. Full article
(This article belongs to the Special Issue Nucleosome: From Structural and Functional Aspects to Clinic)
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