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Genome Organization in Interphase Chromosomes
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Genome Organization in Interphase Chromosomes

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

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 20059

Special Issue Editor

Prof. Dr. Igor Zhimulev

E-Mail Website
Guest Editor
Institute of Molecular and Cellular Biology of the Siberian Branch of the RAS, Novosibirsk, Russia

Special Issue Information

Dear Colleagues,

Interphase chromosomes are the structures where the eukaryotic genome is expressed. Polytene interphase chromosomes demonstrate a characteristic banding pattern of black and gray bands and light interbands. These patterns are the same in both types of chromosomes—in polytene and in cell culture interphase. Genes of development are located within the black bands, while housekeeping genes occupy two structures—that is, interbands (promoter sites) and gray bands (sites of gene bodies), and origins of replication are located predominantly in the interbands. These three types of genes correspond to the their own chromatin states, gene sets, nucleosome modifiers, chromatin remodelers, and protein complexes of transcription enhancers. On the other hand, heterochromatin is an essential part of eukaryotic genomes. It plays important roles in genome stability, transcriptional modification, and chromosome organization.

The aim of this Special Issue "Genome Organization in Interphase Chromosomes " is to consider contemporary data on the full-genome analysis of the genetic organization of chromosome structures, nucleosome distribution, further characterization of chromatin states in different chromatin models, relations of chromatin states with genes, protein complexes regulating transcription and replication in the genome, protein complexes regulating chromatin remodeling, the ability of enhancers to stimulate promoters over long distances and enhancer–promoter interactions only within such domains, as well as the relationship of topologically associated domains (TADs) with chromosome structures and gene/protein complexes.

This review critically examines the current understanding of heterochromatin structure, repetitive DNA, and our understanding of heterochromatin’s evolution and function.

Prof. Dr. Igor Zhimulev
Guest Editor

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Keywords

  • Interphase chromosomes
  • nucleosomes
  • chromatin states
  • houskeeping genes
  • genes of development
  • hetrochromatic part of genome
  • gene promoters
  • insulators
  • enhancers
  • genome domains
  • DNA-proteins complexes

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Published Papers (4 papers)

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Research

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15 pages, 3628 KiB  
Article
In Vivo Silencing of Genes Coding for dTip60 Chromatin Remodeling Complex Subunits Affects Polytene Chromosome Organization and Proper Development in Drosophila melanogaster
by Yuri Prozzillo, Stefano Cuticone, Diego Ferreri, Gaia Fattorini, Giovanni Messina and Patrizio Dimitri
Int. J. Mol. Sci. 2021, 22(9), 4525; https://doi.org/10.3390/ijms22094525 - 26 Apr 2021
Cited by 8 | Viewed by 3357
Abstract
Chromatin organization is developmentally regulated by epigenetic changes mediated by histone-modifying enzymes and chromatin remodeling complexes. In Drosophila melanogaster, the Tip60 chromatin remodeling complex (dTip60) play roles in chromatin regulation, which are shared by evolutionarily-related complexes identified in animal and plants. Recently, [...] Read more.
Chromatin organization is developmentally regulated by epigenetic changes mediated by histone-modifying enzymes and chromatin remodeling complexes. In Drosophila melanogaster, the Tip60 chromatin remodeling complex (dTip60) play roles in chromatin regulation, which are shared by evolutionarily-related complexes identified in animal and plants. Recently, it was found that most subunits previously assigned to the dTip60 complex are shared by two related complexes, DOM-A.C and DOM-B.C, defined by DOM-A and DOM-B isoforms, respectively. In this work, we combined classical genetics, cell biology, and reverse genetics approaches to further investigate the biological roles played during Drosophila melanogaster development by a number of subunits originally assigned to the dTip60 complex. Full article
(This article belongs to the Special Issue Genome Organization in Interphase Chromosomes)
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10 pages, 2471 KiB  
Article
Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes
by Victor G. Levitsky, Tatyana Yu. Zykova, Yuri M. Moshkin and Igor F. Zhimulev
Int. J. Mol. Sci. 2020, 21(23), 9282; https://doi.org/10.3390/ijms21239282 - 5 Dec 2020
Cited by 3 | Viewed by 2544
Abstract
We analyzed the whole-genome experimental maps of nucleosomes in Drosophila melanogaster and classified genes by the expression level in S2 cells (RPKM value, reads per kilobase million) as well as the number of tissues in which a gene was expressed (breadth of expression, [...] Read more.
We analyzed the whole-genome experimental maps of nucleosomes in Drosophila melanogaster and classified genes by the expression level in S2 cells (RPKM value, reads per kilobase million) as well as the number of tissues in which a gene was expressed (breadth of expression, BoE). Chromatin in 5′-regions of genes we classified on four states according to the hidden Markov model (4HMM). Only the Aquamarine chromatin state we considered as Active, while the rest three states we defined as Non-Active. Surprisingly, about 20/40% of genes with 5′-regions mapped to Active/Non-Active chromatin possessed the minimal/at least modest RPKM and BoE. We found that regardless of RPKM/BoE the genes of Active chromatin possessed the regular nucleosome arrangement in 5′-regions, while genes of Non-Active chromatin did not show respective specificity. Only for genes of Active chromatin the RPKM/BoE positively correlates with the number of nucleosome sites upstream/around TSS and negatively with that downstream TSS. We propose that for genes of Active chromatin, regardless of RPKM value and BoE the nucleosome arrangement in 5′-regions potentiates transcription, while for genes of Non-Active chromatin, the transcription machinery does not require the substantial support from nucleosome arrangement to influence gene expression. Full article
(This article belongs to the Special Issue Genome Organization in Interphase Chromosomes)
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Review

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20 pages, 2919 KiB  
Review
Mechanisms of Enhancer-Promoter Interactions in Higher Eukaryotes
by Olga Kyrchanova and Pavel Georgiev
Int. J. Mol. Sci. 2021, 22(2), 671; https://doi.org/10.3390/ijms22020671 - 12 Jan 2021
Cited by 48 | Viewed by 8680
Abstract
In higher eukaryotes, enhancers determine the activation of developmental gene transcription in specific cell types and stages of embryogenesis. Enhancers transform the signals produced by various transcription factors within a given cell, activating the transcription of the targeted genes. Often, developmental genes can [...] Read more.
In higher eukaryotes, enhancers determine the activation of developmental gene transcription in specific cell types and stages of embryogenesis. Enhancers transform the signals produced by various transcription factors within a given cell, activating the transcription of the targeted genes. Often, developmental genes can be associated with dozens of enhancers, some of which are located at large distances from the promoters that they regulate. Currently, the mechanisms underlying specific distance interactions between enhancers and promoters remain poorly understood. This review briefly describes the properties of enhancers and discusses the mechanisms of distance interactions and potential proteins involved in this process. Full article
(This article belongs to the Special Issue Genome Organization in Interphase Chromosomes)
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13 pages, 1257 KiB  
Review
The Role of Nucleoporin Elys in Nuclear Pore Complex Assembly and Regulation of Genome Architecture
by Yuri Y. Shevelyov
Int. J. Mol. Sci. 2020, 21(24), 9475; https://doi.org/10.3390/ijms21249475 - 13 Dec 2020
Cited by 7 | Viewed by 4518
Abstract
For a long time, the nuclear lamina was thought to be the sole scaffold for the attachment of chromosomes to the nuclear envelope (NE) in metazoans. However, accumulating evidence indicates that nuclear pore complexes (NPCs) comprised of nucleoporins (Nups) participate in this process [...] Read more.
For a long time, the nuclear lamina was thought to be the sole scaffold for the attachment of chromosomes to the nuclear envelope (NE) in metazoans. However, accumulating evidence indicates that nuclear pore complexes (NPCs) comprised of nucleoporins (Nups) participate in this process as well. One of the Nups, Elys, initiates NPC reassembly at the end of mitosis. Elys directly binds the decondensing chromatin and interacts with the Nup107–160 subcomplex of NPCs, thus serving as a seeding point for the subsequent recruitment of other NPC subcomplexes and connecting chromatin with the re-forming NE. Recent studies also uncovered the important functions of Elys during interphase where it interacts with chromatin and affects its compactness. Therefore, Elys seems to be one of the key Nups regulating chromatin organization. This review summarizes the current state of our knowledge about the participation of Elys in the post-mitotic NPC reassembly as well as the role that Elys and other Nups play in the maintenance of genome architecture. Full article
(This article belongs to the Special Issue Genome Organization in Interphase Chromosomes)
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