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Nucleosome Structure, Dynamics and Interactions

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A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell Nuclei: Function, Transport and Receptors".

Deadline for manuscript submissions: closed (20 July 2022) | Viewed by 15727

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Special Issue Editors

Dr. Alexey V. Feofanov

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Guest Editor

1. Bioengineering Department, Biological Faculty, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
2. Laboratory of Optical Microscopy and Spectroscopy of Biomolecules, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
Interests: nucleosome structure; nucleosome-protein interactions; single molecule; spFRET microscopy
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Vasily M. Studitsky

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Guest Editor

1. Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
2. Fox Chase Cancer Center, Philadelphia, PA 19111-2497, USA
Interests: mechanisms of transcription and replication in chromatin; mechanisms of histone chaperone action in chromatin
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The nucleosome is a minimal structural unit of chromatin that modulates the access of various nuclear proteins involved in DNA repair, transcription and replication to DNA. Various DNA transactions are accompanied with changes in the nucleosome structure, varying from local alterations to dramatic unwrapping of DNA from the histone octamer and nucleosome unfolding. Histone variants and post-translational modifications introduce additional diversity into the repertoire of the structural changes. Nucleosomes and nucleosome-bound proteins are targets for various drugs, which differently affect the structure of nucleosome–protein complexes and block unwanted nuclear processes. Structural analysis of nucleosomes and their complexes with nuclear proteins aims to reveal basic principles of DNA functioning in normal and pathological cells.

The aim of this Special Issue is to provide an opportunity for researchers to present their latest results in the field of study of nucleosome structure, dynamics and interactions, and to summarize the most recent developments in the field.

Dr. Alexey V. Feofanov
Dr. Vasily M. Studitsky
Guest Editors

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Keywords

nucleosome
structure
nuclear proteins
dynamics
DNA-targeted drugs
nuclear-protein-targeted drugs

Published Papers (6 papers)

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Research

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14 pages, 2535 KiB

Open AccessArticle

Chromatin Liquid–Liquid Phase Separation (LLPS) Is Regulated by Ionic Conditions and Fiber Length

by Qinming Chen, Lei Zhao, Aghil Soman, Anastasia Yu Arkhipova, Jindi Li, Hao Li, Yinglu Chen, Xiangyan Shi and Lars Nordenskiöld

Cells 2022, 11(19), 3145; https://doi.org/10.3390/cells11193145 - 06 Oct 2022

Cited by 5 | Viewed by 2837

Abstract

The dynamic regulation of the physical states of chromatin in the cell nucleus is crucial for maintaining cellular homeostasis. Chromatin can exist in solid- or liquid-like forms depending on the surrounding ions, binding proteins, post-translational modifications and many other factors. Several recent studies suggested that chromatin undergoes liquid–liquid phase separation (LLPS) in vitro and also in vivo; yet, controversial conclusions about the nature of chromatin LLPS were also observed from the in vitro studies. These inconsistencies are partially due to deviations in the in vitro buffer conditions that induce the condensation/aggregation of chromatin as well as to differences in chromatin (nucleosome array) constructs used in the studies. In this work, we present a detailed characterization of the effects of K⁺, Mg²⁺ and nucleosome fiber length on the physical state and property of reconstituted nucleosome arrays. LLPS was generally observed for shorter nucleosome arrays (15-197-601, reconstituted from 15 repeats of the Widom 601 DNA with 197 bp nucleosome repeat length) at physiological ion concentrations. In contrast, gel- or solid-like condensates were detected for the considerably longer 62-202-601 and lambda DNA (~48.5 kbp) nucleosome arrays under the same conditions. In addition, we demonstrated that the presence of reduced BSA and acetate buffer is not essential for the chromatin LLPS process. Overall, this study provides a comprehensive understanding of several factors regarding chromatin physical states and sheds light on the mechanism and biological relevance of chromatin phase separation in vivo. Full article

(This article belongs to the Special Issue Nucleosome Structure, Dynamics and Interactions)

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16 pages, 2663 KiB

Open AccessArticle

Hmo1 Protein Affects the Nucleosome Structure and Supports the Nucleosome Reorganization Activity of Yeast FACT

by Daria K. Malinina, Anastasiia L. Sivkina, Anna N. Korovina, Laura L. McCullough, Tim Formosa, Mikhail P. Kirpichnikov, Vasily M. Studitsky and Alexey V. Feofanov

Cells 2022, 11(19), 2931; https://doi.org/10.3390/cells11192931 - 20 Sep 2022

Cited by 3 | Viewed by 2296

Abstract

Yeast Hmo1 is a high mobility group B (HMGB) protein that participates in the transcription of ribosomal protein genes and rDNA, and also stimulates the activities of some ATP-dependent remodelers. Hmo1 binds both DNA and nucleosomes and has been proposed to be a functional yeast analog of mammalian linker histones. We used EMSA and single particle Förster resonance energy transfer (spFRET) microscopy to characterize the effects of Hmo1 on nucleosomes alone and with the histone chaperone FACT. Hmo1 induced a significant increase in the distance between the DNA gyres across the nucleosomal core, and also caused the separation of linker segments. This was opposite to the effect of the linker histone H1, which enhanced the proximity of linkers. Similar to Nhp6, another HMGB factor, Hmo1, was able to support large-scale, ATP-independent, reversible unfolding of nucleosomes by FACT in the spFRET assay and partially support FACT function in vivo. However, unlike Hmo1, Nhp6 alone does not affect nucleosome structure. These results suggest physiological roles for Hmo1 that are distinct from Nhp6 and possibly from other HMGB factors and linker histones, such as H1. Full article

(This article belongs to the Special Issue Nucleosome Structure, Dynamics and Interactions)

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20 pages, 6607 KiB

Open AccessArticle

H2A-H2B Histone Dimer Plasticity and Its Functional Implications

by Anastasiia S. Kniazeva, Grigoriy A. Armeev and Alexey K. Shaytan

Cells 2022, 11(18), 2837; https://doi.org/10.3390/cells11182837 - 12 Sep 2022

Cited by 2 | Viewed by 2923

Abstract

The protein core of the nucleosome is composed of an H3-H4 histone tetramer and two H2A-H2B histone dimers. The tetramer organizes the central 60 DNA bp, while H2A-H2B dimers lock the flanking DNA segments. Being positioned at the sides of the nucleosome, H2A-H2B dimers stabilize the overall structure of the nucleosome and modulate its dynamics, such as DNA unwrapping, sliding, etc. Such modulation at the epigenetic level is achieved through post-translational modifications and the incorporation of histone variants. However, the detailed connection between the sequence of H2A-H2B histones and their structure, dynamics and implications for nucleosome functioning remains elusive. In this work, we present a detailed study of H2A-H2B dimer dynamics in the free form and in the context of nucleosomes via atomistic molecular dynamics simulations (based on X. laevis histones). We supplement simulation results by comparative analysis of information in the structural databases. Particularly, we describe a major dynamical mode corresponding to the bending movement of the longest H2A and H2B α-helices. This overall bending dynamics of the H2A-H2B dimer were found to be modulated by its interactions with DNA, H3-H4 tetramer, the presence of DNA twist-defects with nucleosomal DNA and the amino acid sequence of histones. Taken together, our results shed new light on the dynamical mechanisms of nucleosome functioning, such as nucleosome sliding, DNA-unwrapping and their epigenetic modulation. Full article

(This article belongs to the Special Issue Nucleosome Structure, Dynamics and Interactions)

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18 pages, 3052 KiB

Open AccessArticle

Structure of an Intranucleosomal DNA Loop That Senses DNA Damage during Transcription

by Nadezhda S. Gerasimova, Olesya I. Volokh, Nikolay A. Pestov, Grigory A. Armeev, Mikhail P. Kirpichnikov, Alexey K. Shaytan, Olga S. Sokolova and Vasily M. Studitsky

Cells 2022, 11(17), 2678; https://doi.org/10.3390/cells11172678 - 28 Aug 2022

Cited by 5 | Viewed by 2469

Abstract

Transcription through chromatin by RNA polymerase II (Pol II) is accompanied by the formation of small intranucleosomal DNA loops containing the enzyme (i-loops) that are involved in survival of core histones on the DNA and arrest of Pol II during the transcription of damaged DNA. However, the structures of i-loops have not been determined. Here, the structures of the intermediates formed during transcription through a nucleosome containing intact or damaged DNA were studied using biochemical approaches and electron microscopy. After RNA polymerase reaches position +24 from the nucleosomal boundary, the enzyme can backtrack to position +20, where DNA behind the enzyme recoils on the surface of the histone octamer, forming an i-loop that locks Pol II in the arrested state. Since the i-loop is formed more efficiently in the presence of SSBs positioned behind the transcribing enzyme, the loop could play a role in the transcription-coupled repair of DNA damage hidden in the chromatin structure. Full article

(This article belongs to the Special Issue Nucleosome Structure, Dynamics and Interactions)

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17 pages, 3029 KiB

Open AccessArticle

N-Terminal Tails of Histones H2A and H2B Differentially Affect Transcription by RNA Polymerase II In Vitro

by Han-Wen Chang, Alexey V. Feofanov, Alexander V. Lyubitelev, Grigory A. Armeev, Elena Y. Kotova, Fu-Kai Hsieh, Mikhail P. Kirpichnikov, Alexey K. Shaytan and Vasily M. Studitsky

Cells 2022, 11(16), 2475; https://doi.org/10.3390/cells11162475 - 10 Aug 2022

Cited by 2 | Viewed by 1589

Abstract

Histone N-terminal tails and their post-translational modifications affect various biological processes, often in a context-specific manner; the underlying mechanisms are poorly studied. Here, the role of individual N-terminal tails of histones H2A/H2B during transcription through chromatin was analyzed in vitro. spFRET data suggest that the tail of histone H2B (but not of histone H2A) affects nucleosome stability. Accordingly, deletion of the H2B tail (amino acids 1–31, but not 1–26) causes a partial relief of the nucleosomal barrier to transcribing RNA polymerase II (Pol II), likely facilitating uncoiling of DNA from the histone octamer during transcription. Taken together, the data suggest that residues 27–31 of histone H2B stabilize DNA–histone interactions at the DNA region localized ~25 bp in the nucleosome and thus interfere with Pol II progression through the region localized 11–15 bp in the nucleosome. This function of histone H2B requires the presence of the histone H2A N-tail that mediates formation of nucleosome–nucleosome dimers; however, nucleosome dimerization per se plays only a minimal role during transcription. Histone chaperone FACT facilitates transcription through all analyzed nucleosome variants, suggesting that H2A/H2B tails minimally interact with FACT during transcription; therefore, an alternative FACT-interacting domain(s) is likely involved in this process. Full article

(This article belongs to the Special Issue Nucleosome Structure, Dynamics and Interactions)

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Review

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19 pages, 14137 KiB

Open AccessReview

Structural Transition of the Nucleosome during Transcription Elongation

by Tomoya Kujirai, Haruhiko Ehara, Shun-ichi Sekine and Hitoshi Kurumizaka

Cells 2023, 12(10), 1388; https://doi.org/10.3390/cells12101388 - 14 May 2023

Cited by 1 | Viewed by 2741

Abstract

In eukaryotes, genomic DNA is tightly wrapped in chromatin. The nucleosome is a basic unit of chromatin, but acts as a barrier to transcription. To overcome this impediment, the RNA polymerase II elongation complex disassembles the nucleosome during transcription elongation. After the RNA polymerase II passage, the nucleosome is rebuilt by transcription-coupled nucleosome reassembly. Nucleosome disassembly–reassembly processes play a central role in preserving epigenetic information, thus ensuring transcriptional fidelity. The histone chaperone FACT performs key functions in nucleosome disassembly, maintenance, and reassembly during transcription in chromatin. Recent structural studies of transcribing RNA polymerase II complexed with nucleosomes have provided structural insights into transcription elongation on chromatin. Here, we review the structural transitions of the nucleosome during transcription. Full article

(This article belongs to the Special Issue Nucleosome Structure, Dynamics and Interactions)

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