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Domain Organization of the Genome - from Random Neighborhood to Joint Regulation

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 July 2021) | Viewed by 14786

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Special Issue Editor

Dr. Tatyana D. Kolesnikova

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Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
Interests: heterochromatin; replication timing; drosophila chromosomes; polytene chromosomes; endocycle; drosophila genome evolution

Special Issue Information

The genomes of higher eukaryotes are highly heterogeneous in nucleotide composition and gene density. Based on analysis of the distribution of chromatin proteins, the genome can be divided into discrete chromatin types. There is also a tendency for the majority of housekeeping genes to lie in the domains of permanently open chromatin and form clusters of permanently active genes, while tissue-specific genes more often lie in closed domains and open chromatin locally where they are expressed. The development of the Hi-C method and other methods of detailed analysis of the three-dimensional organization of the nucleus led to the concept of contact domains (TADs), the boundaries of which are largely interconnected with the chromatin and replication domains. The barriers between contact domains play a dominant role in the organization of epigenetic and replication domains. In recent years, the paradigm has finally changed from considering the genome as a linear system to a three-dimensional view of the genome, where the phase separation of similar chromatin domains plays a global role in genome regulation and nuclear organization. In this issue, I propose to publish works devoted to the study of different types of genome clustering into domains with different properties. I am particularly interested in papers that discuss the mechanisms of boundary formation between domains and the importance of these boundaries for the correct regulation of gene expression. A very intriguing subject is the evolutionary direction, which shows how important such clustering is for the regulation of individual genes, and how the regulation of genes changes when they enter new conditions.

Dr. Tatyana D. Kolesnikova
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. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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 domains
epigenetics
gene density
gene clusters
syntenic blocks
phase separation
nucleolus
topologically associated domains
replication domains
genome evolution
heterochromatin
euchromatin

Published Papers (5 papers)

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Research

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20 pages, 2801 KiB

Open AccessArticle

The Psychoemotional Stress-Induced Changes in the Abundance of SatIII (1q12) and Telomere Repeats, but Not Ribosomal DNA, in Human Leukocytes

by Pavel E. Umriukhin, Elizaveta S. Ershova, Anton D. Filev, Oksana N. Agafonova, Andrey V. Martynov, Natalia V. Zakharova, Roman V. Veiko, Lev N. Porokhovnik, George P. Kostyuk, Sergey I. Kutsev, Natalia N. Veiko and Svetlana V. Kostyuk

Genes 2022, 13(2), 343; https://doi.org/10.3390/genes13020343 - 14 Feb 2022

Cited by 9 | Viewed by 2200

Abstract

INTRODUCTION. As shown earlier, copy number variations (CNV) in the human satellite III (1q12) fragment (f-SatIII) and the telomere repeat (TR) reflects the cell’s response to oxidative stress. The contents of f-SatIII and TR in schizophrenic (SZ) patients were found to be lower than in healthy controls (HC) in previous studies. The major question of this study was: ‘What are the f-SatIII and TR CNV dynamic changes in human leukocytes, depending on psychoemotional stress?’ MATERIALS AND METHODS. We chose a model of psychoemotional stress experienced by second-year medical students during their exams. Blood samples were taken in stressful conditions (exams) and in a control non-stressful period. Biotinylated probes were used for f-SatIII, rDNA, and TR quantitation in leukocyte DNA by non-radioactive quantitative hybridization in SZ patients (n = 97), HC (n = 97), and medical students (n = 17, n = 42). A flow cytometry analysis was used for the oxidative stress marker (NOX4, 8-oxodG, and γH2AX) detection in the lymphocytes of the three groups. RESULTS. Oxidative stress markers increased significantly in the students’ lymphocytes during psychoemotional stress. The TR and f-SatIII, but not the rDNA, contents significantly changed in the DNA isolated from human blood leukocytes. After a restoration period (post-examinational vacations), the f-SatIII content decreased, and the TR content increased. Changes in the blood cells of students during examinational stress were similar to those in SZ patients during an exacerbation of the disease. CONCLUSIONS. Psychoemotional stress in students during exams triggers a universal mechanism of oxidative stress. The oxidative stress causes significant changes in the f-SatIII and TR contents, while the ribosomal repeat content remains stable. A hypothesis is proposed to explain the quantitative polymorphisms of f-SatIII and TR contents under transient (e.g., students’ exams) or chronic (in SZ patients) stress. The changes in the f-SatIII and TR copy numbers are non-specific events, irrespective of the source of stress. Thus, our findings suggest that the psychoemotional stress, common in SZ patients and healthy students during exams, but not in a schizophrenia-specific event, was responsible for the changes in the repeat contents that we observed earlier in SZ patients. Full article

(This article belongs to the Special Issue Domain Organization of the Genome - from Random Neighborhood to Joint Regulation)

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Review

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18 pages, 994 KiB

Open AccessReview

The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model

by Lev N. Porokhovnik, Natalia N. Veiko, Elizaveta S. Ershova and Svetlana V. Kostyuk

Genes 2021, 12(10), 1524; https://doi.org/10.3390/genes12101524 - 28 Sep 2021

Cited by 11 | Viewed by 2686

Abstract

The pericentric satellite III (SatIII or Sat3) and II tandem repeats recently appeared to be transcribed under stress conditions, and the transcripts were shown to play an essential role in the universal stress response. In this paper, we review the role of human-specific SatIII copy number variation (CNV) in normal stress response, aging and pathology, with a focus on 1q12 loci. We postulate a close link between transcription of SatII/III repeats and their CNV. The accrued body of data suggests a hypothetical universal mechanism, which provides for SatIII copy gain during the stress response, alongside with another, more hypothetical reverse mechanism that might reduce the mean SatIII copy number, likely via the selection of cells with excessively large 1q12 loci. Both mechanisms, working alternatively like swings of the pendulum, may ensure the balance of SatIII copy numbers and optimum stress resistance. This model is verified on the most recent data on SatIII CNV in pathology and therapy, aging, senescence and response to genotoxic stress in vitro. Full article

(This article belongs to the Special Issue Domain Organization of the Genome - from Random Neighborhood to Joint Regulation)

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13 pages, 283 KiB

Open AccessReview

Insulators in Plants: Progress and Open Questions

by Amina Kurbidaeva and Michael Purugganan

Genes 2021, 12(9), 1422; https://doi.org/10.3390/genes12091422 - 16 Sep 2021

Cited by 5 | Viewed by 2692

Abstract

The genomes of higher eukaryotes are partitioned into topologically associated domains or TADs, and insulators (also known as boundary elements) are the key elements responsible for their formation and maintenance. Insulators were first identified and extensively studied in Drosophila as well as mammalian genomes, and have also been described in yeast and plants. In addition, many insulator proteins are known in Drosophila, and some have been investigated in mammals. However, much less is known about this important class of non-coding DNA elements in plant genomes. In this review, we take a detailed look at known plant insulators across different species and provide an overview of potential determinants of plant insulator functions, including cis-elements and boundary proteins. We also discuss methods previously used in attempts to identify plant insulators, provide a perspective on their importance for research and biotechnology, and discuss areas of potential future research. Full article

(This article belongs to the Special Issue Domain Organization of the Genome - from Random Neighborhood to Joint Regulation)

12 pages, 265 KiB

Open AccessReview

Genome Reorganization during Erythroid Differentiation

by Anastasia Ryzhkova and Nariman Battulin

Genes 2021, 12(7), 1012; https://doi.org/10.3390/genes12071012 - 30 Jun 2021

Cited by 1 | Viewed by 2505

Abstract

Hematopoiesis is a convenient model to study how chromatin dynamics plays a decisive role in regulation of cell fate. During erythropoiesis a population of stem and progenitor cells becomes increasingly lineage restricted, giving rise to terminally differentiated progeny. The concerted action of transcription factors and epigenetic modifiers leads to a silencing of the multipotent transcriptome and activation of the transcriptional program that controls terminal differentiation. This article reviews some aspects of the biology of red blood cells production with the focus on the extensive chromatin reorganization during differentiation. Full article

(This article belongs to the Special Issue Domain Organization of the Genome - from Random Neighborhood to Joint Regulation)

13 pages, 945 KiB

Open AccessReview

Co-Regulated Genes and Gene Clusters

by Sergey V. Razin, Elena S. Ioudinkova, Omar L. Kantidze and Olga V. Iarovaia

Genes 2021, 12(6), 907; https://doi.org/10.3390/genes12060907 - 11 Jun 2021

Cited by 8 | Viewed by 3968

Abstract

There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes. Full article

(This article belongs to the Special Issue Domain Organization of the Genome - from Random Neighborhood to Joint Regulation)

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