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Advances in Cytomolecular Organisation of the Nuclear Genome

A topical collection in International Journal of Molecular Sciences (ISSN 1422-0067). This collection belongs to the section "Molecular Biology".

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Editors

Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
Interests: plant molecular cytogenetics; structure and evolution of karyotypes; arrangement of chromosomes at interphase; nucleolar dominance; cytogenetics of meiosis; application of Brachypodium as a model genus to study various aspects of plant nuclear genome structure; dynamics; (in)stability and evolution at the cytomolecular level
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Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-007 Katowice, Poland
Interests: plant molecular cytogenetics; nucleolar dominance; evolution of repetitive DNA, especially 35S and 5S rDNA; nucleolus structure; polyploidy; plant epigenetics
Special Issues, Collections and Topics in MDPI journals
Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
Interests: plant molecular cytogenetics; arrangement of chromosomes at interphase; Rabl configuration; cytogenetics of meiosis; structure and function of the nucleolus
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

This Topical Collection follows the publication of the first volume on “Cytomolecular Organisation of the Nuclear Genome”, which presented 15 interesting papers.

Modern molecular cytogenetics enables a variety of observations of nuclear genome organisation at the level of the chromosome or in the interphase nucleus. This progress is driven by robust, high-resolution methodology; DNA:DNA fluorescence in situ hybridisation combined using the latest microscopes with image acquisition and processing systems enables  simultaneous two- or three-dimensional, multicolour visualisation of highly repetitive, low-repeat, and single-copy sequences in the genome. Fluorescent antibodies to specific proteins can also be used to selectively localise epigenetically modified components of chromatin, such as methylated DNA and histones. They also have utility in highlighting proteins comprising important biological structures, such as the synaptonemal complex and the enzymatic machinery responsible for genetic recombination events.

This Topical Collection encompasses a wide range of topics connected with various aspects of the organisation of the nuclear genome at the cytomolecular level in eukaryotes, including plants, animals, humans, fungi, and protists. The topics may cover, among other things, analyses of the structure and evolution of karyotypes, the cell cycle and cell division, chromatin arrangement at interphase and nuclear genome instability after mutagenic treatment. Original research on these and other related topics is welcome.

Prof. Dr. Robert Hasterok
Dr. Natalia Borowska-Zuchowska
Dr. Ewa Robaszkiewicz
Collection Editors

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 collection 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

  • cell cycle
  • cell division
  • chromosome aberrations
  • chromosome painting
  • chromosome territories
  • chromosomes
  • cytogenetics
  • epigenetics
  • evolution of repetitive dna
  • fluorescence in situ hybridisation
  • immunolocalisation
  • karyotype structure and evolution
  • interphase nucleus
  • meiosis
  • mitosis
  • molecular cytogenetics
  • nucleolar dominance
  • nucleolus
  • polyploidy
  • Rabl configuration

Published Papers (2 papers)

2023

17 pages, 2316 KiB  
Article
Histone Maps in Gossypium darwinii Reveal Epigenetic Regulation Drives Subgenome Divergence and Cotton Domestication
by Jinlei Han, Guangrun Yu, Xin Zhang, Yan Dai, Hui Zhang, Baohong Zhang and Kai Wang
Int. J. Mol. Sci. 2023, 24(13), 10607; https://doi.org/10.3390/ijms241310607 - 25 Jun 2023
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Abstract
The functional annotation of genomes, including chromatin modifications, is essential to understand the intricate architecture of chromatin and the consequential gene regulation. However, such an annotation remains limited for cotton genomes. Here, we conducted chromatin profiling in a wild allotetraploid cotton Gossypium darwinii [...] Read more.
The functional annotation of genomes, including chromatin modifications, is essential to understand the intricate architecture of chromatin and the consequential gene regulation. However, such an annotation remains limited for cotton genomes. Here, we conducted chromatin profiling in a wild allotetraploid cotton Gossypium darwinii (AD genome) by integrating the data of histone modification, transcriptome, and chromatin accessibility. We revealed that the A subgenome showed a higher level of active histone marks and lower level of repressive histone marks than the D subgenome, which was consistent with the expression bias between the two subgenomes. We show that the bias in transcription and histone modification between the A and D subgenomes may be caused by genes unique to the subgenome but not by homoeologous genes. Moreover, we integrate histone marks and open chromatin to define six chromatin states (S1–S6) across the cotton genome, which index different genomic elements including genes, promoters, and transposons, implying distinct biological functions. In comparison to the domesticated cotton species, we observed that 23.2% of genes in the genome exhibit a transition from one chromatin state to another at their promoter. Strikingly, the S2 (devoid of epigenetic marks) to S3 (enriched for the mark of open chromatin) was the largest transition group. These transitions occurred simultaneously with changes in gene expression, which were significantly associated with several domesticated traits in cotton. Collectively, our study provides a useful epigenetic resource for research on allopolyploid plants. The domestication–induced chromatin dynamics and associated genes identified here will aid epigenetic engineering, improving polyploid crops. Full article
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19 pages, 4012 KiB  
Article
The Influence of Edaphic Factors on DNA Damage and Repair in Wild Wheat Triticum dicoccoides Körn. (Poaceae, Triticeae)
by Olga Raskina, Boris Shklyar and Eviatar Nevo
Int. J. Mol. Sci. 2023, 24(7), 6847; https://doi.org/10.3390/ijms24076847 - 06 Apr 2023
Viewed by 1534
Abstract
A complex DNA repair network maintains genome integrity and genetic stability. In this study, the influence of edaphic factors on DNA damage and repair in wild wheat Triticum dicoccoides was addressed. Plants inhabiting two abutting microsites with dry terra rossa and humid basalt [...] Read more.
A complex DNA repair network maintains genome integrity and genetic stability. In this study, the influence of edaphic factors on DNA damage and repair in wild wheat Triticum dicoccoides was addressed. Plants inhabiting two abutting microsites with dry terra rossa and humid basalt soils were studied. The relative expression level of seven genes involved in DNA repair pathways—RAD51, BRCA1, LigIV, KU70, MLH1, MSH2, and MRE11—was assessed using quantitative real-time PCR (qPCR). Immunolocalization of RAD51, LigIV, γH2AX, RNA Polymerase II, and DNA-RNA hybrid [S9.6] (R-loops) in somatic interphase nuclei and metaphase chromosomes was carried out in parallel. The results showed a lower expression level of genes involved in DNA repair and a higher number of DNA double-strand breaks (DSBs) in interphase nuclei in plants growing in terra rossa soil compared with plants in basalt soil. Further, the number of DSBs and R-loops in metaphase chromosomes was also greater in plants growing on terra rossa soil. Finally, RAD51 and LigIV foci on chromosomes indicate ongoing DSB repair during the M-phase via the Homologous Recombination and Non-Homologous End Joining pathways. Together, these results show the impact of edaphic factors on DNA damage and repair in the wheat genome adapted to contrasting environments. Full article
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Figure 1

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