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Current Research on Chromatin Structure and Function
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Current Research on Chromatin Structure and Function

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

Deadline for manuscript submissions: closed (30 March 2024) | Viewed by 3967

Special Issue Editor

Dr. Alexey V. Feofanov

E-Mail Website
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

Special Issue Information

Dear Colleagues,

Chromatin is a complex dynamic system formed by DNA and proteins providing compact storage of genetic material and regulated access to it. Despite the progress in understanding the canonical principles of the structural organization of chromatin, a wide variety of possible structural states and their impact on genome functioning demands further thorough research and analysis. This variety is formed by specialized enzymes, architectural and regulatory proteins, non-canonical DNA structures, histone variants and histone modifications.

We invite researchers to present their studies, discuss their data and opinions on the structural states of chromatin and nucleosomes, the dynamics of chromatin at different levels of its structural organization and the mechanisms of regulation of the structure of chromatin and nucleosomes, using the International Journal of Molecular Sciences as a platform for this.

Dr. Alexey V. Feofanov
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

  • nucleosome
  • histone modifications
  • histone variants
  • architectural proteins
  • non-canonical DNA structures
  • cryo-EM
  • X-ray crystallography
  • NMR
  • spFRET
  • force microscopy
  • molecular dynamics
  • molecular modelling

Published Papers (3 papers)

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Research

11 pages, 1423 KiB  
Article
Short Sequence Aligner Benchmarking for Chromatin Research
by John Lawrence Carter, Harlan Stevens, Perry G. Ridge and Steven Michael Johnson
Int. J. Mol. Sci. 2023, 24(18), 14074; https://doi.org/10.3390/ijms241814074 - 14 Sep 2023
Viewed by 1162
Abstract
Much of today’s molecular science revolves around next-generation sequencing. Frequently, the first step in analyzing such data is aligning sequencing reads to a reference genome. This step is often taken for granted, but any analysis downstream of the alignment will be affected by [...] Read more.
Much of today’s molecular science revolves around next-generation sequencing. Frequently, the first step in analyzing such data is aligning sequencing reads to a reference genome. This step is often taken for granted, but any analysis downstream of the alignment will be affected by the aligner’s ability to correctly map sequences. In most cases, for research into chromatin structure and nucleosome positioning, ATAC-seq, ChIP-seq, and MNase-seq experiments use short read lengths. How well aligners manage these reads is critical. Most aligner programs will output mapped reads and unmapped reads. However, from a biological point of view, reads will fall into one of three categories: correctly mapped, incorrectly mapped, and unmapped. While increased sequencing depth can often compensate for unmapped reads, incorrectly and correctly mapped reads appear algorithmically identical but can produce biologically significant alterations in the results. For this reason, we are benchmarking various alignment programs to determine their propensity to incorrectly map short reads. As short-read alignment is an important step in ATAC-seq, ChIP-seq, and MNase-seq experiments, caution should be taken in mapping reads to ensure that the most accurate conclusions can be made from the data generated. Our analysis is intended to help investigators new to the field pick the alignment program best suited for their experimental conditions. In general, the aligners we tested performed well. BWA, Bowtie2, and Chromap were all exceptionally accurate, and we recommend using them. Furthermore, we show that longer read lengths do in fact lead to more accurate mappings. Full article
(This article belongs to the Special Issue Current Research on Chromatin Structure and Function)
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13 pages, 1870 KiB  
Article
Structure and Dynamics of Compact Dinucleosomes: Analysis by Electron Microscopy and spFRET
by Maria E. Stefanova, Olesya I. Volokh, Oleg V. Chertkov, Grigory A. Armeev, Alexey K. Shaytan, Alexey V. Feofanov, Mikhail P. Kirpichnikov, Olga S. Sokolova and Vasily M. Studitsky
Int. J. Mol. Sci. 2023, 24(15), 12127; https://doi.org/10.3390/ijms241512127 - 28 Jul 2023
Viewed by 852
Abstract
Formation of compact dinucleosomes (CODIs) occurs after collision between adjacent nucleosomes at active regulatory DNA regions. Although CODIs are likely dynamic structures, their structural heterogeneity and dynamics were not systematically addressed. Here, single-particle Förster resonance energy transfer (spFRET) and electron microscopy were employed [...] Read more.
Formation of compact dinucleosomes (CODIs) occurs after collision between adjacent nucleosomes at active regulatory DNA regions. Although CODIs are likely dynamic structures, their structural heterogeneity and dynamics were not systematically addressed. Here, single-particle Förster resonance energy transfer (spFRET) and electron microscopy were employed to study the structure and dynamics of CODIs. spFRET microscopy in solution and in gel revealed considerable uncoiling of nucleosomal DNA from the histone octamer in a fraction of CODIs, suggesting that at least one of the nucleosomes is destabilized in the presence of the adjacent closely positioned nucleosome. Accordingly, electron microscopy analysis suggests that up to 30 bp of nucleosomal DNA are involved in transient uncoiling/recoiling on the octamer. The more open and dynamic nucleosome structure in CODIs cannot be stabilized by histone chaperone Spt6. The data suggest that proper internucleosomal spacing is an important determinant of chromatin stability and support the possibility that CODIs could be intermediates of chromatin disruption. Full article
(This article belongs to the Special Issue Current Research on Chromatin Structure and Function)
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25 pages, 3982 KiB  
Communication
PARP3 Affects Nucleosome Compaction Regulation
by Alexander Ukraintsev, Mikhail Kutuzov, Ekaterina Belousova, Marie Joyeau, Victor Golyshev, Alexander Lomzov and Olga Lavrik
Int. J. Mol. Sci. 2023, 24(10), 9042; https://doi.org/10.3390/ijms24109042 - 20 May 2023
Viewed by 1206
Abstract
Genome compaction is one of the important subject areas for understanding the mechanisms regulating genes’ expression and DNA replication and repair. The basic unit of DNA compaction in the eukaryotic cell is the nucleosome. The main chromatin proteins responsible for DNA compaction have [...] Read more.
Genome compaction is one of the important subject areas for understanding the mechanisms regulating genes’ expression and DNA replication and repair. The basic unit of DNA compaction in the eukaryotic cell is the nucleosome. The main chromatin proteins responsible for DNA compaction have already been identified, but the regulation of chromatin architecture is still extensively studied. Several authors have shown an interaction of ARTD proteins with nucleosomes and proposed that there are changes in the nucleosomes’ structure as a result. In the ARTD family, only PARP1, PARP2, and PARP3 participate in the DNA damage response. Damaged DNA stimulates activation of these PARPs, which use NAD+ as a substrate. DNA repair and chromatin compaction need precise regulation with close coordination between them. In this work, we studied the interactions of these three PARPs with nucleosomes by atomic force microscopy, which is a powerful method allowing for direct measurements of geometric characteristics of single molecules. Using this method, we evaluated perturbations in the structure of single nucleosomes after the binding of a PARP. We demonstrated here that PARP3 significantly alters the geometry of nucleosomes, possibly indicating a new function of PARP3 in chromatin compaction regulation. Full article
(This article belongs to the Special Issue Current Research on Chromatin Structure and Function)
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