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Chromatin Molecular Complexes-Functional Organization, Protection and Regulation of the Genome
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Chromatin Molecular Complexes-Functional Organization, Protection and Regulation of the Genome

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

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 29721

Special Issue Editor

Dr. Ctirad Hofr

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Guest Editor
LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic

Special Issue Information

Dear Colleagues,

Chromatin interconnects three worlds. The first is the world of DNA, which encodes genes that serve as sources for genotypes. The second is the RNA world, where RNA plays the main role in translating genetic information into phenotypes. The last is the protein world, in which biochemical reactions are made possible, leading to the final stage – gene expression. Molecular scientists have been deciphering mechanisms and interactions between proteins and nucleic acids within chromatin to understand processes that regulate genome maintenance, gene transcription, and expression.

This Special Issue covers molecular complexes that are essential for chromatin function in genome maintenance and gene translation. The issue will contribute to understanding the roles of nucleoproteins, and combined roles of nucleic acids and proteins for cell survival and the proper function of genome maintenance. The fun comes when we try to use our previous knowledge obtained on simpler molecular and biological systems to understand functional and structural relationships within more evolutionally developed and complex biomolecular assemblies.

text

This Special Issue will share new results on essential roles of biomolecular complexes that have been evolutionally the most successful to maintain the continuous flow of genetic information and best survival strategies from ancestors to successors.

Dr. Ctirad Hofr
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
  • nucleoprotein
  • telomere
  • nucleosome
  • transcription factor
  • DNA transcription
  • RNA translation

Published Papers (6 papers)

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Editorial

Jump to: Research, Review

4 pages, 554 KiB  
Editorial
Chromatin Molecular Complexes—Functional Organization, Protection and Regulation of the Genome
by Ctirad Hofr
Int. J. Mol. Sci. 2022, 23(14), 7516; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23147516 - 07 Jul 2022
Viewed by 1057
Abstract
This Special Issue highlights the advantages of using combined approaches to explore chromatin molecular complexes [...] Full article
(This article belongs to the Special Issue Chromatin Molecular Complexes-Functional Organization, Protection and Regulation of the Genome)
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Research

Jump to: Editorial, Review

21 pages, 23254 KiB  
Article
Subunits of the PBAP Chromatin Remodeler Are Capable of Mediating Enhancer-Driven Transcription in Drosophila
by Yulii V. Shidlovskii, Oleg V. Bylino, Alexander V. Shaposhnikov, Zaur M. Kachaev, Lyubov A. Lebedeva, Valeria V. Kolesnik, Diego Amendola, Giovanna De Simone, Nadia Formicola, Paul Schedl, Filomena Anna Digilio and Ennio Giordano
Int. J. Mol. Sci. 2021, 22(6), 2856; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22062856 - 11 Mar 2021
Cited by 7 | Viewed by 3025
Abstract
The chromatin remodeler SWI/SNF is an important participant in gene activation, functioning predominantly by opening the chromatin structure on promoters and enhancers. Here, we describe its novel mode of action in which SWI/SNF factors mediate the targeted action of an enhancer. We studied [...] Read more.
The chromatin remodeler SWI/SNF is an important participant in gene activation, functioning predominantly by opening the chromatin structure on promoters and enhancers. Here, we describe its novel mode of action in which SWI/SNF factors mediate the targeted action of an enhancer. We studied the functions of two signature subunits of PBAP subfamily, BAP170 and SAYP, in Drosophila. These subunits were stably tethered to a transgene reporter carrying the hsp70 core promoter. The tethered subunits mediate transcription of the reporter in a pattern that is generated by enhancers close to the insertion site in multiple loci throughout the genome. Both tethered SAYP and BAP170 recruit the whole PBAP complex to the reporter promoter. However, we found that BAP170-dependent transcription is more resistant to the depletion of other PBAP subunits, suggesting that BAP170 may play a more critical role in establishing enhancer-dependent transcription. Full article
(This article belongs to the Special Issue Chromatin Molecular Complexes-Functional Organization, Protection and Regulation of the Genome)
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17 pages, 2627 KiB  
Article
G-Quadruplex Structures Colocalize with Transcription Factories and Nuclear Speckles Surrounded by Acetylated and Dimethylated Histones H3
by Denisa Komůrková, Alena Svobodová Kovaříková and Eva Bártová
Int. J. Mol. Sci. 2021, 22(4), 1995; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22041995 - 17 Feb 2021
Cited by 10 | Viewed by 3864
Abstract
G-quadruplexes (G4s) are four-stranded helical structures that regulate several nuclear processes, including gene expression and telomere maintenance. We observed that G4s are located in GC-rich (euchromatin) regions and outside the fibrillarin-positive compartment of nucleoli. Genomic regions around G4s were preferentially H3K9 acetylated and [...] Read more.
G-quadruplexes (G4s) are four-stranded helical structures that regulate several nuclear processes, including gene expression and telomere maintenance. We observed that G4s are located in GC-rich (euchromatin) regions and outside the fibrillarin-positive compartment of nucleoli. Genomic regions around G4s were preferentially H3K9 acetylated and H3K9 dimethylated, but H3K9me3 rarely decorated G4 structures. We additionally observed the variability in the number of G4s in selected human and mouse cell lines. We found the highest number of G4s in human embryonic stem cells. We observed the highest degree of colocalization between G4s and transcription factories, positive on the phosphorylated form of RNA polymerase II (RNAP II). Similarly, a high colocalization rate was between G4s and nuclear speckles, enriched in pre-mRNA splicing factor SC-35. PML bodies, the replication protein SMD1, and Cajal bodies colocalized with G4s to a lesser extent. Thus, G4 structures seem to appear mainly in nuclear compartments transcribed via RNAP II, and pre-mRNA is spliced via the SC-35 protein. However, α-amanitin, an inhibitor of RNAP II, did not affect colocalization between G4s and transcription factories as well as G4s and SC-35-positive domains. In addition, irradiation by γ-rays did not change a mutual link between G4s and DNA repair proteins (G4s/γH2AX, G4s/53BP1, and G4s/MDC1), accumulated into DNA damage foci. Described characteristics of G4s seem to be the manifestation of pronounced G4s stability that is likely maintained not only via a high-order organization of these structures but also by a specific histone signature, including H3K9me2, responsible for chromatin compaction. Full article
(This article belongs to the Special Issue Chromatin Molecular Complexes-Functional Organization, Protection and Regulation of the Genome)
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18 pages, 1888 KiB  
Article
Exploring the Interaction between the SWI/SNF Chromatin Remodeling Complex and the Zinc Finger Factor CTCF
by Mariangela Valletta, Rosita Russo, Ilaria Baglivo, Veronica Russo, Sara Ragucci, Annamaria Sandomenico, Emanuela Iaccarino, Menotti Ruvo, Italia De Feis, Claudia Angelini, Sara Iachettini, Annamaria Biroccio, Paolo Vincenzo Pedone and Angela Chambery
Int. J. Mol. Sci. 2020, 21(23), 8950; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21238950 - 25 Nov 2020
Cited by 12 | Viewed by 4199
Abstract
The transcription factor CCCTC-binding factor (CTCF) modulates pleiotropic functions mostly related to gene expression regulation. The role of CTCF in large scale genome organization is also well established. A unifying model to explain relationships among many CTCF-mediated activities involves direct or indirect interactions [...] Read more.
The transcription factor CCCTC-binding factor (CTCF) modulates pleiotropic functions mostly related to gene expression regulation. The role of CTCF in large scale genome organization is also well established. A unifying model to explain relationships among many CTCF-mediated activities involves direct or indirect interactions with numerous protein cofactors recruited to specific binding sites. The co-association of CTCF with other architectural proteins such as cohesin, chromodomain helicases, and BRG1, further supports the interplay between master regulators of mammalian genome folding. Here, we report a comprehensive LC-MS/MS mapping of the components of the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex co-associated with CTCF including subunits belonging to the core, signature, and ATPase modules. We further show that the localization patterns of representative SWI/SNF members significantly overlap with CTCF sites on transcriptionally active chromatin regions. Moreover, we provide evidence of a direct binding of the BRK-BRG1 domain to the zinc finger motifs 4–8 of CTCF, thus, suggesting that these domains mediate the interaction of CTCF with the SWI/SNF complex. These findings provide an updated view of the cooperative nature between CTCF and the SWI/SNF ATP-dependent chromatin remodeling complexes, an important step for understanding how these architectural proteins collaborate to shape the genome. Full article
(This article belongs to the Special Issue Chromatin Molecular Complexes-Functional Organization, Protection and Regulation of the Genome)
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Graphical abstract

19 pages, 2898 KiB  
Article
Site-Specific Phosphorylation of Histone H1.4 Is Associated with Transcription Activation
by Ankita Saha, Christopher H. Seward, Lisa Stubbs and Craig A. Mizzen
Int. J. Mol. Sci. 2020, 21(22), 8861; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21228861 - 23 Nov 2020
Cited by 7 | Viewed by 2767
Abstract
Core histone variants, such as H2A.X and H3.3, serve specialized roles in chromatin processes that depend on the genomic distributions and amino acid sequence differences of the variant proteins. Modifications of these variants alter interactions with other chromatin components and thus the protein’s [...] Read more.
Core histone variants, such as H2A.X and H3.3, serve specialized roles in chromatin processes that depend on the genomic distributions and amino acid sequence differences of the variant proteins. Modifications of these variants alter interactions with other chromatin components and thus the protein’s functions. These inferences add to the growing arsenal of evidence against the older generic view of those linker histones as redundant repressors. Furthermore, certain modifications of specific H1 variants can confer distinct roles. On the one hand, it has been reported that the phosphorylation of H1 results in its release from chromatin and the subsequent transcription of HIV-1 genes. On the other hand, recent evidence indicates that phosphorylated H1 may in fact be associated with active promoters. This conflict suggests that different H1 isoforms and modified versions of these variants are not redundant when together but may play distinct functional roles. Here, we provide the first genome-wide evidence that when phosphorylated, the H1.4 variant remains associated with active promoters and may even play a role in transcription activation. Using novel, highly specific antibodies, we generated the first genome-wide view of the H1.4 isoform phosphorylated at serine 187 (pS187-H1.4) in estradiol-inducible MCF7 cells. We observe that pS187-H1.4 is enriched primarily at the transcription start sites (TSSs) of genes activated by estradiol treatment and depleted from those that are repressed. We also show that pS187-H1.4 associates with ‘early estrogen response’ genes and stably interacts with RNAPII. Based on the observations presented here, we propose that phosphorylation at S187 by CDK9 represents an early event required for gene activation. This event may also be involved in the release of promoter-proximal polymerases to begin elongation by interacting directly with the polymerase or other parts of the transcription machinery. Although we focused on estrogen-responsive genes, taking into account previous evidence of H1.4′s enrichment of promoters of pluripotency genes, and its involvement with rDNA activation, we propose that H1.4 phosphorylation for gene activation may be a more global observation. Full article
(This article belongs to the Special Issue Chromatin Molecular Complexes-Functional Organization, Protection and Regulation of the Genome)
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Review

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28 pages, 2256 KiB  
Review
Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin
by Olivia Morrison and Jitendra Thakur
Int. J. Mol. Sci. 2021, 22(13), 6922; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22136922 - 28 Jun 2021
Cited by 29 | Viewed by 14114
Abstract
Chromatin consists of a complex of DNA and histone proteins as its core components and plays an important role in both packaging DNA and regulating DNA metabolic pathways such as DNA replication, transcription, recombination, and chromosome segregation. Proper functioning of chromatin further involves [...] Read more.
Chromatin consists of a complex of DNA and histone proteins as its core components and plays an important role in both packaging DNA and regulating DNA metabolic pathways such as DNA replication, transcription, recombination, and chromosome segregation. Proper functioning of chromatin further involves a network of interactions among molecular complexes that modify chromatin structure and organization to affect the accessibility of DNA to transcription factors leading to the activation or repression of the transcription of target DNA loci. Based on its structure and compaction state, chromatin is categorized into euchromatin, heterochromatin, and centromeric chromatin. In this review, we discuss distinct chromatin factors and molecular complexes that constitute euchromatin—open chromatin structure associated with active transcription; heterochromatin—less accessible chromatin associated with silencing; centromeric chromatin—the site of spindle binding in chromosome segregation. Full article
(This article belongs to the Special Issue Chromatin Molecular Complexes-Functional Organization, Protection and Regulation of the Genome)
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