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Genome Functions and Chromatin Organization in Health and Disease
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Genome Functions and Chromatin Organization in Health and Disease

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 (25 November 2024) | Viewed by 5236

Special Issue Editors

Dr. Concetta Federico

E-Mail Website
Guest Editor
Department of Biological, Geological and Environmental Sciences, University of Catania, 95124 Catania, Italy
Interests: chromosome organization and evolution; DNA polymorphisms in forensic genetics; neurodegeneration; human genetic diseases; environmental mutagenesis
Special Issues, Collections and Topics in MDPI journals
Dr. Sabrina Tosi

E-Mail Website
Guest Editor
Leukaemia and Chromosome Research Laboratory, Department of Life Sciences, Brunel University London, Kingston Ln, Uxbridge, London UB8 3PH, UK
Interests: chromosomal rearrangements; molecular cytogenetics; genome organization; leukaemiaa
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The special issue on “Genome Functions and Chromatin Organization in Health and Disease” delves into the fascinating field of understanding how the organization of the genome and chromatin contribute to maintaining cellular health and how perturbation of such organization impact on disease development.

The 3D genome organization plays a critical role in regulating gene expression and cellular function. Alterations in genome and chromatin organization have been implicated in various diseases, including cancer, neurodegenerative disorders, cardiovascular diseases, and developmental disorders. The proposal welcomes both original articles and reviews that employ cutting-edge technology to investigate the three-dimensional architecture of the genome and the folding patterns of chromatin such as high-throughput sequencing, chromosome conformation capture methods, and advanced imaging technologies that enable the mapping and visualization of genomic interactions and chromatin structure at high resolution.

Articles covering recent advances in the dynamic reorganization of genes, chromatin, and chromosomes within cell nuclei, both in physiological and pathological conditions are of particular interest. Through the study of genome organization and chromatin dynamics, the aim of this special issue is to deepen our understanding of cellular processes, unveil novel therapeutic targets, and ultimately pave the way for advancements in personalized medicine and precision genomics.

Dr. Concetta Federico
Dr. Sabrina Tosi
Guest 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 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

  • genome organization
  • chromatin
  • chromosome rearrangements
  • chromosome repositioning
  • genetic diseases
  • epigenetic alterations

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Published Papers (3 papers)

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Research

17 pages, 3195 KiB  
Article
Molecular Signatures of CB-6644 Inhibition of the RUVBL1/2 Complex in Multiple Myeloma
by Weijun Yi, Sebastian A. Dziadowicz, Rachel S. Mangano, Lei Wang, Joseph McBee, Steven M. Frisch, Lori A. Hazlehurst, Donald A. Adjeroh and Gangqing Hu
Int. J. Mol. Sci. 2024, 25(16), 9022; https://doi.org/10.3390/ijms25169022 - 20 Aug 2024
Viewed by 1651
Abstract
Multiple myeloma is the second most hematological cancer. RUVBL1 and RUVBL2 form a subcomplex of many chromatin remodeling complexes implicated in cancer progression. As an inhibitor specific to the RUVBL1/2 complex, CB-6644 exhibits remarkable anti-tumor activity in xenograft models of Burkitt’s lymphoma and [...] Read more.
Multiple myeloma is the second most hematological cancer. RUVBL1 and RUVBL2 form a subcomplex of many chromatin remodeling complexes implicated in cancer progression. As an inhibitor specific to the RUVBL1/2 complex, CB-6644 exhibits remarkable anti-tumor activity in xenograft models of Burkitt’s lymphoma and multiple myeloma (MM). In this work, we defined transcriptional signatures corresponding to CB-6644 treatment in MM cells and determined underlying epigenetic changes in terms of chromatin accessibility. CB-6644 upregulated biological processes related to interferon response and downregulated those linked to cell proliferation in MM cells. Transcriptional regulator inference identified E2Fs as regulators for downregulated genes and MED1 and MYC as regulators for upregulated genes. CB-6644-induced changes in chromatin accessibility occurred mostly in non-promoter regions. Footprinting analysis identified transcription factors implied in modulating chromatin accessibility in response to CB-6644 treatment, including ATF4/CEBP and IRF4. Lastly, integrative analysis of transcription responses to various chemical compounds of the molecular signature genes from public gene expression data identified CB-5083, a p97 inhibitor, as a synergistic candidate with CB-6644 in MM cells, but experimental validation refuted this hypothesis. Full article
(This article belongs to the Special Issue Genome Functions and Chromatin Organization in Health and Disease)
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19 pages, 1649 KiB  
Article
Preferential Co-Expression and Colocalization of rDNA-Contacting Genes with LincRNAs Suggest Their Involvement in Shaping Inter-Chromosomal Interactions with Nucleoli
by Nickolai A. Tchurikov, Ildar R. Alembekov, Elena S. Klushevskaya, Antonina N. Kretova, Viktoriya N. Lukicheva, Vladimir R. Chechetkin, Galina I. Kravatskaya and Yuri V. Kravatsky
Int. J. Mol. Sci. 2024, 25(12), 6333; https://doi.org/10.3390/ijms25126333 - 7 Jun 2024
Cited by 1 | Viewed by 1290
Abstract
Different developmental genes shape frequent dynamic inter-chromosomal contacts with rDNA units in human and Drosophila cells. In the course of differentiation, changes in these contacts occur, coupled with changes in the expression of hundreds of rDNA-contacting genes. The data suggest a possible role [...] Read more.
Different developmental genes shape frequent dynamic inter-chromosomal contacts with rDNA units in human and Drosophila cells. In the course of differentiation, changes in these contacts occur, coupled with changes in the expression of hundreds of rDNA-contacting genes. The data suggest a possible role of nucleoli in the global regulation of gene expression. However, the mechanism behind the specificity of these inter-chromosomal contacts, which are rebuilt in every cell cycle, is not yet known. Here, we describe the strong association of rDNA-contacting genes with numerous long intergenic non-coding RNAs (lincRNAs) in HEK293T cells and in initial and differentiated K562 cells. We observed that up to 600 different lincRNAs were preferentially co-expressed with multiple overlapping sets of rDNA-contacting developmental genes, and there was a strong correlation between the genomic positions of rDNA-contacting genes and lincRNA mappings. These two findings suggest that lincRNAs might guide the corresponding developmental genes toward rDNA clusters. We conclude that the inter-chromosomal interactions of rDNA-contacting genes with nucleoli might be guided by lincRNAs, which might physically link particular genomic regions with rDNA clusters. Full article
(This article belongs to the Special Issue Genome Functions and Chromatin Organization in Health and Disease)
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12 pages, 6396 KiB  
Article
Alterations in Genome Organization in Lymphoma Cell Nuclei due to the Presence of the t(14;18) Translocation
by Elisa Garimberti, Concetta Federico, Denise Ragusa, Francesca Bruno, Salvatore Saccone, Joanna Mary Bridger and Sabrina Tosi
Int. J. Mol. Sci. 2024, 25(4), 2377; https://doi.org/10.3390/ijms25042377 - 17 Feb 2024
Cited by 3 | Viewed by 1656
Abstract
Chromosomal rearrangements have been shown to alter genome organization, consequently having an impact on gene expression. Studies on certain types of leukemia have shown that gene expression can be exacerbated by the altered nuclear positioning of fusion genes arising from chromosomal translocations. However, [...] Read more.
Chromosomal rearrangements have been shown to alter genome organization, consequently having an impact on gene expression. Studies on certain types of leukemia have shown that gene expression can be exacerbated by the altered nuclear positioning of fusion genes arising from chromosomal translocations. However, studies on lymphoma have been, so far, very limited. The scope of this study was to explore genome organization in lymphoma cells carrying the t(14;18)(q32;q21) rearrangement known to results in over-expression of the BCL2 gene. In order to achieve this aim, we used fluorescence in situ hybridization to carefully map the positioning of whole chromosome territories and individual genes involved in translocation in the lymphoma-derived cell line Pfeiffer. Our data show that, although there is no obvious alteration in the positioning of the whole chromosome territories, the translocated genes may take the nuclear positioning of either of the wild-type genes. Furthermore, the BCL2 gene was looping out in a proportion of nuclei with the t(14;18) translocation but not in control nuclei without the translocation, indicating that chromosome looping may be an essential mechanism for BCL2 expression in lymphoma cells. Full article
(This article belongs to the Special Issue Genome Functions and Chromatin Organization in Health and Disease)
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