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Bridger JM, Pereira RT, Pina C, Tosi S, Lewis A. Alterations to Genome Organisation in Stem Cells, Their Differentiation and Associated Diseases. Results Probl Cell Differ 2022; 70:71-102. [PMID: 36348105 DOI: 10.1007/978-3-031-06573-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The organisation of the genome in its home, the cell nucleus, is reliant on a number of different aspects to establish, maintain and alter its functional non-random positioning. The genome is dispersed throughout a cell nucleus in specific chromosome territories which are further divided into topologically associated domains (TADs), where regions of the genome from different and the same chromosomes come together. This organisation is both controlled by DNA and chromatin epigenetic modification and the association of the genome with nuclear structures such as the nuclear lamina, the nucleolus and nuclear bodies and speckles. Indeed, sequences that are associated with the first two structures mentioned are termed lamina-associated domains (LADs) and nucleolar-associated domains (NADs), respectively. The modifications and nuclear structures that regulate genome function are altered through a cell's life from stem cell to differentiated cell through to reversible quiescence and irreversible senescence, and hence impacting on genome organisation, altering it to silence specific genes and permit others to be expressed in a controlled way in different cell types and cell cycle statuses. The structures and enzymes and thus the organisation of the genome can also be deleteriously affected, leading to disease and/or premature ageing.
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Affiliation(s)
- Joanna M Bridger
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK.
| | - Rita Torres Pereira
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Cristina Pina
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Sabrina Tosi
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
| | - Annabelle Lewis
- Division of Biosciences, Department of Life Sciences, Centre for Genome Engineering and Maintenance (cenGEM), College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UK
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Jowhar Z, Shachar S, Gudla PR, Wangsa D, Torres E, Russ JL, Pegoraro G, Ried T, Raznahan A, Misteli T. Effects of human sex chromosome dosage on spatial chromosome organization. Mol Biol Cell 2018; 29:2458-2469. [PMID: 30091656 PMCID: PMC6233059 DOI: 10.1091/mbc.e18-06-0359] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/25/2018] [Accepted: 08/01/2018] [Indexed: 01/08/2023] Open
Abstract
Sex chromosome aneuploidies (SCAs) are common genetic syndromes characterized by the presence of an aberrant number of X and Y chromosomes due to meiotic defects. These conditions impact the structure and function of diverse tissues, but the proximal effects of SCAs on genome organization are unknown. Here, to determine the consequences of SCAs on global genome organization, we have analyzed multiple architectural features of chromosome organization in a comprehensive set of primary cells from SCA patients with various ratios of X and Y chromosomes by use of imaging-based high-throughput chromosome territory mapping (HiCTMap). We find that X chromosome supernumeracy does not affect the size, volume, or nuclear position of the Y chromosome or an autosomal chromosome. In contrast, the active X chromosome undergoes architectural changes as a function of increasing X copy number as measured by a decrease in size and an increase in circularity, which is indicative of chromatin compaction. In Y chromosome supernumeracy, Y chromosome size is reduced suggesting higher chromatin condensation. The radial positioning of chromosomes is unaffected in SCA karyotypes. Taken together, these observations document changes in genome architecture in response to alterations in sex chromosome numbers and point to trans-effects of dosage compensation on chromosome organization.
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Affiliation(s)
- Ziad Jowhar
- Cell Biology of Genomes Group, National Institutes of Health, Bethesda, MD 20892
| | - Sigal Shachar
- Cell Biology of Genomes Group, National Institutes of Health, Bethesda, MD 20892
| | - Prabhakar R. Gudla
- High-Throughput Imaging Facility, National Institutes of Health, Bethesda, MD 20892
| | - Darawalee Wangsa
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Erin Torres
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Jill L. Russ
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Institutes of Health, Bethesda, MD 20892
| | - Thomas Ried
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Armin Raznahan
- Human Genetics Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892
| | - Tom Misteli
- Cell Biology of Genomes Group, National Institutes of Health, Bethesda, MD 20892
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Ranade D, Koul S, Thompson J, Prasad KB, Sengupta K. Chromosomal aneuploidies induced upon Lamin B2 depletion are mislocalized in the interphase nucleus. Chromosoma 2017; 126:223-244. [PMID: 26921073 PMCID: PMC5371638 DOI: 10.1007/s00412-016-0580-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 01/28/2016] [Accepted: 02/09/2016] [Indexed: 12/31/2022]
Abstract
Chromosome territories assume non-random positions in the interphase nucleus with gene-rich chromosomes localized toward the nuclear interior and gene-poor chromosome territories toward the nuclear periphery. Lamins are intermediate filament proteins of the inner nuclear membrane required for the maintenance of nuclear structure and function. Here, we show using whole-genome expression profiling that Lamin A/C or Lamin B2 depletion in an otherwise diploid colorectal cancer cell line (DLD1) deregulates transcript levels from specific chromosomes. Further, three-dimensional fluorescence in situ hybridization (3D-FISH) analyses of a subset of these transcriptionally deregulated chromosome territories revealed that the diploid chromosome territories in Lamin-depleted cells largely maintain conserved positions in the interphase nucleus in a gene-density-dependent manner. In addition, chromosomal aneuploidies were induced in ~25 % of Lamin A/C or Lamin B2-depleted cells. Sub-populations of these aneuploid cells consistently showed a mislocalization of the gene-rich aneuploid chromosome 19 territory toward the nuclear periphery, while gene-poor aneuploid chromosome 18 territory was mislocalized toward the nuclear interior predominantly upon Lamin B2 than Lamin A/C depletion. In addition, a candidate gene locus ZNF570 (Chr.19q13.12) significantly overexpressed upon Lamin B2 depletion was remarkably repositioned away from the nuclear lamina. Taken together, our studies strongly implicate an overarching role for Lamin B2 in the maintenance of nuclear architecture since loss of Lamin B2 relieves the spatial positional constraints required for maintaining conserved localization of aneuploid chromosome territories in the interphase nucleus.
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Affiliation(s)
- Devika Ranade
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Shivsmriti Koul
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Joyce Thompson
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Kumar Brajesh Prasad
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India
| | - Kundan Sengupta
- Biology, Indian Institute of Science Education and Research, Pune, Main Building, Homi Bhabha Road, Pashan, Pune, Maharashtra, 411008, India.
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Ioannou D, Millan NM, Jordan E, Tempest HG. A new model of sperm nuclear architecture following assessment of the organization of centromeres and telomeres in three-dimensions. Sci Rep 2017; 7:41585. [PMID: 28139771 PMCID: PMC5282497 DOI: 10.1038/srep41585] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 12/21/2016] [Indexed: 01/01/2023] Open
Abstract
The organization of chromosomes in sperm nuclei has been proposed to possess a unique “hairpin-loop” arrangement, which is hypothesized to aid in the ordered exodus of the paternal genome following fertilization. This study simultaneously assessed the 3D and 2D radial and longitudinal organization of telomeres, centromeres, and investigated whether chromosomes formed the same centromere clusters in sperm cells. Reproducible radial and longitudinal non-random organization was observed for all investigated loci using both 3D and 2D approaches in multiple subjects. We report novel findings, with telomeres and centromeres being localized throughout the nucleus but demonstrating roughly a 1:1 distribution in the nuclear periphery and the intermediate regions with <15% occupying the nuclear interior. Telomeres and centromeres were observed to aggregate in sperm nuclei, forming an average of 20 and 7 clusters, respectively. Reproducible
longitudinal organization demonstrated preferential localization of telomeres and centromeres in the mid region of the sperm cell. Preliminary evidence is also provided to support the hypothesis that specific chromosomes preferentially form the same centromere clusters. The more segmental distribution of telomeres and centromeres as described in this study could more readily accommodate and facilitate the sequential exodus of paternal chromosomes following fertilization.
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Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Nicole M Millan
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Elizabeth Jordan
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Helen G Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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Fritz AJ, Stojkovic B, Ding H, Xu J, Bhattacharya S, Gaile D, Berezney R. Wide-scale alterations in interchromosomal organization in breast cancer cells: defining a network of interacting chromosomes. Hum Mol Genet 2014; 23:5133-46. [PMID: 24833717 DOI: 10.1093/hmg/ddu237] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The interchromosomal spatial positionings of a subset of human chromosomes was examined in the human breast cell line MCF10A (10A) and its malignant counterpart MCF10CA1a (CA1a). The nine chromosomes selected (#1, 4, 11, 12, 15, 16, 18, 21 and X) cover a wide range in size and gene density and compose ∼40% of the total human genome. Radial positioning of the chromosome territories (CT) was size dependent with certain of the CT more peripheral in CA1a. Each CT was in close proximity (interaction) with a similar number of other CT except the inactive CTXi. It had lower levels of interchromosomal partners in 10A which increased strikingly in CA1a. Major alterations from 10A to CA1a were detected in the pairwise interaction profiles which were subdivided into five types of altered interaction profiles: overall increase, overall decrease, switching from 1 to ≥2, vice versa or no change. A global data mining program termed the chromatic median calculated the most probable overall association network for the entire subset of CT. This interchromosomal network was drastically altered in CA1a with only 1 of 20 shared connections. We conclude that CT undergo multiple and preferred interactions with other CT in the cell nucleus and form preferred-albeit probabilistic-interchromosomal networks. This network of interactions is highly altered in malignant human breast cells. It is intriguing to consider the relationship of these alterations to the corresponding changes in the gene expression program of these malignant cancer cells.
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Affiliation(s)
| | - Branislav Stojkovic
- Department of Computer Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Hu Ding
- Department of Computer Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Jinhui Xu
- Department of Computer Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Sambit Bhattacharya
- Department of Computer Sciences, Fayetteville State University, Fayetteville, NC 28301, USA
| | - Daniel Gaile
- Department of Biostatistics, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
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Petrova NV, Velichko AK, Kantidze OL, Razin SV. Heat shock-induced dissociation of TRF2 from telomeres does not initiate a telomere-dependent DNA damage response. Cell Biol Int 2014; 38:675-81. [PMID: 24474557 DOI: 10.1002/cbin.10252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 01/02/2014] [Indexed: 01/12/2023]
Abstract
Telomeric repeat binding factor 2 (TRF2) is a well-studied shelterin complex subunit that plays a major role in the protection of chomosome ends and the prevention of the telomere-associated DNA damage response. We show that heat shock induces the dissociation of TRF2 from telomeres in human primary and cancer cell cultures. TRF2 is not simply degraded in response to heat shock, but redistributed thoughout the nucleoplasm. This TRF2 depletion/redistribution does not initiate the DNA damage response at chomosome termini.
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Affiliation(s)
- Nadezhda V Petrova
- Laboratory of Structural and Functional Organization of Chomosomes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
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Hierarchical radial and polar organisation of chromosomes in human sperm. Chromosome Res 2012; 20:875-87. [DOI: 10.1007/s10577-012-9323-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 01/06/2023]
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Ioannou D, Griffin DK. Male fertility, chromosome abnormalities, and nuclear organization. Cytogenet Genome Res 2010; 133:269-79. [PMID: 21088381 DOI: 10.1159/000322060] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Numerous studies have implicated the role of gross genomic rearrangements in male infertility, e.g., constitutional aneuploidy, translocations, inversions, Y chromosome deletions, elevated sperm disomy, and DNA damage. The primary purpose of this paper is to review male fertility studies associated with such abnormalities. In addition, we speculate whether altered nuclear organization, another chromosomal/whole genome-associated phenomenon, is also concomitant with male factor infertility. Nuclear organization has been studied in a range of systems and implicated in several diseases. For many applications the measurement of the relative position of chromosome territories is sufficient to determine patterns of nuclear organization. Initial evidence has suggested that, unlike in the more usual 'size-related' or 'gene density-related' models, mammalian (including human) sperm heads display a highly organized pattern including a chromocenter with the centromeres located to the center of the nucleus and the telomeres near the periphery. More recent evidence, however, suggests there may be size- and gene density-related components to nuclear organization in sperm. It seems reasonable to hypothesize therefore that alterations in this pattern may be associated with male factor infertility. A small handful of studies have addressed this issue; however, to date it remains an exciting avenue for future research with possible implications for diagnosis and therapy.
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Affiliation(s)
- D Ioannou
- School of Biosciences, University of Kent, Canterbury, UK
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Meaburn KJ, Gudla PR, Khan S, Lockett SJ, Misteli T. Disease-specific gene repositioning in breast cancer. J Cell Biol 2009; 187:801-12. [PMID: 19995938 PMCID: PMC2806312 DOI: 10.1083/jcb.200909127] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 11/06/2009] [Indexed: 11/22/2022] Open
Abstract
Genomes are nonrandomly organized within the three-dimensional space of the cell nucleus. Here, we have identified several genes whose nuclear positions are altered in human invasive breast cancer compared with normal breast tissue. The changes in positioning are gene specific and are not a reflection of genomic instability within the cancer tissue. Repositioning events are specific to cancer and do not generally occur in noncancerous breast disease. Moreover, we show that the spatial positions of genes are highly consistent between individuals. Our data indicate that cancer cells have disease-specific gene distributions. These interphase gene positioning patterns may be used to identify cancer tissues.
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Affiliation(s)
- Karen J. Meaburn
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Prabhakar R. Gudla
- Optical Microscopy and Analysis Laboratory, Advanced Technology Program, Science Applications International Corporation-Frederick, Inc., and National Cancer Institute at Frederick, Frederick, MD 21702
| | - Sameena Khan
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Stephen J. Lockett
- Optical Microscopy and Analysis Laboratory, Advanced Technology Program, Science Applications International Corporation-Frederick, Inc., and National Cancer Institute at Frederick, Frederick, MD 21702
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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Meaburn KJ, Newbold RF, Bridger JM. Positioning of human chromosomes in murine cell hybrids according to synteny. Chromosoma 2008; 117:579-91. [PMID: 18651158 DOI: 10.1007/s00412-008-0175-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 06/06/2008] [Accepted: 07/01/2008] [Indexed: 10/21/2022]
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