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Chen JM, Cooper DN, Férec C, Kehrer-Sawatzki H, Patrinos GP. Genomic rearrangements in inherited disease and cancer. Semin Cancer Biol 2010; 20:222-33. [PMID: 20541013 DOI: 10.1016/j.semcancer.2010.05.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 04/22/2010] [Accepted: 05/19/2010] [Indexed: 10/19/2022]
Abstract
Genomic rearrangements in inherited disease and cancer involve gross alterations of chromosomes or large chromosomal regions and can take the form of deletions, duplications, insertions, inversions or translocations. The characterization of a considerable number of rearrangement breakpoints has now been accomplished at the nucleotide sequence level, thereby providing an invaluable resource for the detailed study of the mutational mechanisms which underlie genomic recombination events. A better understanding of these mutational mechanisms is vital for improving the design of mutation detection strategies. At least five categories of mutational mechanism are known to give rise to genomic rearrangements: (i) homologous recombination including non-allelic homologous recombination (NAHR), gene conversion, single strand annealing (SSA) and break-induced replication (BIR), (ii) non-homologous end joining (NHEJ), (iii) microhomology-mediated replication-dependent recombination (MMRDR), (iv) long interspersed element-1 (LINE-1 or L1)-mediated retrotransposition and (v) telomere healing. Focussing on the first three of these general mechanisms, we compare and contrast their hallmark characteristics, and discuss the role of various local DNA sequence features (e.g. recombination-promoting motifs, repetitive sequences and sequences capable of non-B DNA formation) in mediating the recombination events that underlie gross genomic rearrangements. Finally, we explore how studies both at the level of the gene (using the neurofibromatosis type-1 gene as an example) and the whole genome (using data derived from cancer genome sequencing studies) are shaping our understanding of the impact of genomic rearrangements as a cause of human genetic disease.
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Affiliation(s)
- Jian-Min Chen
- Etablissement Français du Sang (EFS) - Bretagne, Brest, France.
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102
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Modeling of chromosome intermingling by partially overlapping uniform random polygons. J Math Biol 2010; 62:371-89. [DOI: 10.1007/s00285-010-0338-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2009] [Revised: 02/28/2010] [Indexed: 12/15/2022]
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103
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Genome destabilization by homologous recombination in the germ line. Nat Rev Mol Cell Biol 2010; 11:182-95. [PMID: 20164840 DOI: 10.1038/nrm2849] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Meiotic recombination, which promotes proper homologous chromosome segregation at the first meiotic division, normally occurs between allelic sequences on homologues. However, recombination can also take place between non-allelic DNA segments that share high sequence identity. Such non-allelic homologous recombination (NAHR) can markedly alter genome architecture during gametogenesis by generating chromosomal rearrangements. Indeed, NAHR-mediated deletions, duplications, inversions and other alterations have been implicated in numerous human genetic disorders. Studies in yeast have provided insights into the molecular mechanisms of meiotic NAHR as well as the cellular strategies that limit it.
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104
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Martin LD, Belch AR, Pilarski LM. Promiscuity of translocation partners in multiple myeloma. J Cell Biochem 2010; 109:1085-94. [DOI: 10.1002/jcb.22499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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105
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DNA repair: easy to visualize, difficult to elucidate. Trends Cell Biol 2009; 19:617-29. [DOI: 10.1016/j.tcb.2009.08.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 08/24/2009] [Accepted: 08/26/2009] [Indexed: 11/19/2022]
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106
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Brandt VL, Roth DB. Recent insights into the formation of RAG-induced chromosomal translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 650:32-45. [PMID: 19731799 DOI: 10.1007/978-1-4419-0296-2_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Chromosomal translocations are found in many types of tumors, where they may be either a cause or a result of malignant transformation. In lymphoid neoplasms, however, it is dear that pathogenesis is initiated by any of a number of recurrent DNA rearrangements. These particular translocations typically place an oncogene under the regulatory control of an Ig or TCR gene promoter, dysregulating cell growth, differentiation, or apoptosis. Given that physiological DNA rearrangements (V(D)J and class switch recombination) are integral to lymphocyte development, it is critical to understand how genomic stability is maintained during these processes. Recent advances in our understanding of DNA damage signaling and repair have provided clues to the kinds of mechanisms that lead to V(D)J-mediated translocations. In turn, investigations into the regulation of V(D)J joining have illuminated a formerly obscure pathway of DNA repair known as alternative NHEJ, which is error-prone and frequently involved in translocations. In this chapter we consider recent advances in our understanding of the functions of the RAG proteins, RAG interactions with DNA repair pathways, damage signaling and chromosome biology, all of which shed light on how mistakes at different stages of V(D)J recombination might lead to leukemias and lymphomas.
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Affiliation(s)
- Vicky L Brandt
- Department of Pathology and Program in Molecular Pathogenesis, The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
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107
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Lissoni S, Baronchelli S, Villa N, Lucchini V, Betri E, Cavalli P, Dalprà L. Chromosome territories, X;Y translocation and Premature Ovarian Failure: is there a relationship? Mol Cytogenet 2009; 2:19. [PMID: 19781104 PMCID: PMC2761935 DOI: 10.1186/1755-8166-2-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 09/27/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Premature ovarian failure (POF) is a secondary hypergonadotrophic amenorrhea occurring before the age of 40 and affecting 1-3% of females. Chromosome anomalies account for 6-8% of POF cases, but only few cases are associated with translocations involving X and Y chromosomes.This study shows the cytogenetic and molecular analysis of a POF patient came to our attention as she developed a left ovary choriocarcinoma at the age of 10 and at 14 years of age she presented secondary amenorrhea with elevated levels of gonadotropins. RESULTS Breakpoint position on X and Y chromosomes was investigated using Fluorescent In Situ Hybridisation (FISH) with a panel of specific BAC probes, microsatellite analysis and evaluation of copy number changes and loss of heterozigosity by Affymetrix(R) GeneChip platform (Santa Clara, CA, USA). Patient's karyotype resulted 46, X, der(Y)t(X;Y)(q13.1;q11.223). X inactivation study was assessed by RBA banding and showed preferential inactivation of derivative chromosome. The reciprocal spatial disposition of sexual chromosome territories was investigated using whole chromosome painting and centromeres probes: patient's results didn't show a significant difference in comparison to normal controls. CONCLUSION The peculiar clinical case come to our attention highlighted the complexity of POF aetiology and of the translocation event, even if our results seem to exclude any effect on nuclear organisation. POF phenotype could be partially explained by skewed X chromosome inactivation that influences gene expression.
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Affiliation(s)
- Sara Lissoni
- Department of Neuroscience and Biomedical Technologies, University of Milan-Bicocca, via Cadore 48, 20052, Monza, Italy.
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108
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Wang JH, Gostissa M, Yan CT, Goff P, Hickernell T, Hansen E, Difilippantonio S, Wesemann DR, Zarrin AA, Rajewsky K, Nussenzweig A, Alt FW. Mechanisms promoting translocations in editing and switching peripheral B cells. Nature 2009; 460:231-6. [PMID: 19587764 DOI: 10.1038/nature08159] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 05/25/2009] [Indexed: 01/08/2023]
Abstract
Variable, diversity and joining gene segment (V(D)J) recombination assembles immunoglobulin heavy or light chain (IgH or IgL) variable region exons in developing bone marrow B cells, whereas class switch recombination (CSR) exchanges IgH constant region exons in peripheral B cells. Both processes use directed DNA double-strand breaks (DSBs) repaired by non-homologous end-joining (NHEJ). Errors in either V(D)J recombination or CSR can initiate chromosomal translocations, including oncogenic IgH locus (Igh) to c-myc (also known as Myc) translocations of peripheral B cell lymphomas. Collaboration between these processes has also been proposed to initiate translocations. However, the occurrence of V(D)J recombination in peripheral B cells is controversial. Here we show that activated NHEJ-deficient splenic B cells accumulate V(D)J-recombination-associated breaks at the lambda IgL locus (Igl), as well as CSR-associated Igh breaks, often in the same cell. Moreover, Igl and Igh breaks are frequently joined to form translocations, a phenomenon associated with specific Igh-Igl co-localization. Igh and c-myc also co-localize in these cells; correspondingly, the introduction of frequent c-myc DSBs robustly promotes Igh-c-myc translocations. Our studies show peripheral B cells that attempt secondary V(D)J recombination, and determine a role for mechanistic factors in promoting recurrent translocations in tumours.
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109
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Zeitz MJ, Mukherjee L, Bhattacharya S, Xu J, Berezney R. A probabilistic model for the arrangement of a subset of human chromosome territories in WI38 human fibroblasts. J Cell Physiol 2009; 221:120-9. [PMID: 19507193 DOI: 10.1002/jcp.21842] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
There is growing evidence that chromosome territories have a probabilistic non-random arrangement within the cell nucleus of mammalian cells. Other than their radial positioning, however, our knowledge of the degree and specificity of chromosome territory associations is predominantly limited to studies of pair-wise associations. In this study we have investigated the association profiles of eight human chromosome pairs (numbers 1, 2, 3, 4, 6, 7, 8, 9) in the cell nuclei of G(0)-arrested WI38 diploid lung fibroblasts. Associations between heterologous chromosome combinations ranged from 52% to 78% while the homologous chromosome pairs had much lower levels of association (3-25%). A geometric computational method termed the Generalized Median Graph enabled identification of the most probable arrangement of these eight chromosome pairs. Approximately 41% of the predicted associations are present in any given nucleus. The association levels of several chromosome pairs were very similar in a series of lung fibroblast cell lines but strikingly different in skin and colon derived fibroblast cells. We conclude that a large subset of human chromosomes has a preferred probabilistic arrangement in WI38 cells and that the resulting chromosomal associations show tissue origin specificity.
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Affiliation(s)
- Michael J Zeitz
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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110
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Abstract
Transcription is a fundamental step in gene expression, yet it remains poorly understood at a cellular level. Visualization of transcription sites and active genes has led to the suggestion that transcription occurs at discrete sites in the nucleus, termed transcription factories, where multiple active RNA polymerases are concentrated and anchored to a nuclear substructure. However, this concept is not universally accepted. This Review discusses the experimental evidence in support of the transcription factory model and the evidence that argues against such a spatially structured view of transcription. The transcription factory model has implications for the regulation of transcription initiation and elongation, for the organization of genes in the genome, for the co-regulation of genes and for genome instability.
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Affiliation(s)
- Heidi Sutherland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Crewe Road, Edinburgh EH4 2XU, UK
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111
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Gandhi MS, Stringer JR, Nikiforova MN, Medvedovic M, Nikiforov YE. Gene position within chromosome territories correlates with their involvement in distinct rearrangement types in thyroid cancer cells. Genes Chromosomes Cancer 2009; 48:222-8. [PMID: 19025793 DOI: 10.1002/gcc.20639] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Chromosomal rearrangements in human cancers are of two types, interchromosomal, which are rearrangements that involve exchange between loci located on different chromosomes, and intrachromosomal, which are rearrangements that involve loci located on the same chromosome. The type of rearrangement that typically activates a specific oncogene may be influenced by its nuclear location and that of its partner. In interphase nuclei, each chromosome occupies a distinct three-dimensional (3D) territory that tends to not overlap the territories of other chromosomes. It is also known that after double strand breaks in the genome, mobility of free DNA ends is limited. These considerations suggest that loci located deep within a chromosomal territory might not participate in interchromosomal rearrangements as readily as in intrachromosomal rearrangements. To test this hypothesis, we used fluorescence in situ hybridization with 3D high-resolution confocal microscopy to analyze the positions of six oncogenes known to be activated by recombination in human cancer cells. We found that loci involved in interchromosomal rearrangements were located closer to the periphery of chromosome territories as compared with the loci that were involved in intrachromosomal inversions. The results of this study provide evidence suggesting that nuclear architecture and location of specific genetic loci within chromosome territories may influence their participation in intrachromosomal or interchromosomal rearrangements in human thyroid cells.
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Affiliation(s)
- Manoj S Gandhi
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261, USA
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112
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Misteli T, Soutoglou E. The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat Rev Mol Cell Biol 2009; 10:243-54. [PMID: 19277046 PMCID: PMC3478884 DOI: 10.1038/nrm2651] [Citation(s) in RCA: 346] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA repair and maintenance of genome stability are crucial to cellular and organismal function, and defects in these processes have been implicated in cancer and ageing. Detailed molecular, biochemical and genetic analyses have outlined the molecular framework involved in cellular DNA-repair pathways, but recent cell-biological approaches have revealed important roles for the spatial and temporal organization of the DNA-repair machinery during the recognition of DNA lesions and the assembly of repair complexes. It has also become clear that local higher-order chromatin structure, chromatin dynamics and non-random global genome organization are key factors in genome maintenance. These cell-biological features of DNA repair illustrate an emerging role for nuclear architecture in multiple aspects of genome maintenance.
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Affiliation(s)
- Tom Misteli
- National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Evi Soutoglou
- Department of Cancer Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 596, ILLKIRCH Cedex, CU de Strasbourg, France
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113
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Gene deregulation and spatial genome reorganization near breakpoints prior to formation of translocations in anaplastic large cell lymphoma. Proc Natl Acad Sci U S A 2009; 106:5831-6. [PMID: 19321746 DOI: 10.1073/pnas.0900912106] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the identification and characterization of translocations have rapidly increased, little is known about the mechanisms of how translocations occur in vivo. We used anaplastic large cell lymphoma (ALCL) with and without the characteristic t(2;5)(p23;q35) translocation to study the mechanisms of formation of translocations and of ALCL transformation. We report deregulation of several genes located near the ALCL translocation breakpoint, regardless of whether the tumor contains the t(2;5). The affected genes include the oncogenic transcription factor Fra2 (located on 2p23), the HLH protein Id2 (2p25), and the oncogenic tyrosine kinase CSF1-receptor (5q33.1). Their up-regulation promotes cell survival and repression of T cell-specific gene expression programs that are characteristic for ALCL. The deregulated genes are in spatial proximity within the nuclear space of t(2;5)-negative ALCL cells, facilitating their translocation on induction of double-strand breaks. These data suggest that deregulation of breakpoint-proximal genes occurs before the formation of translocations, and that aberrant transcriptional activity of genomic regions is linked to their propensity to undergo chromosomal translocations. Also, our data demonstrate that deregulation of breakpoint-proximal genes has a key role in ALCL.
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114
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Ortiz de Mendíbil I, Vizmanos JL, Novo FJ. Signatures of selection in fusion transcripts resulting from chromosomal translocations in human cancer. PLoS One 2009; 4:e4805. [PMID: 19279687 PMCID: PMC2653638 DOI: 10.1371/journal.pone.0004805] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 01/30/2009] [Indexed: 11/27/2022] Open
Abstract
Background The recurrence and non-random distribution of translocation breakpoints in human tumors are usually attributed to local sequence features present in the vicinity of the breakpoints. However, it has also been suggested that functional constraints might contribute to delimit the position of translocation breakpoints within the genes involved, but a quantitative analysis of such contribution has been lacking. Methodology We have analyzed two well-known signatures of functional selection, such as reading-frame compatibility and non-random combinations of protein domains, on an extensive dataset of fusion proteins resulting from chromosomal translocations in cancer. Conclusions Our data provide strong experimental support for the concept that the position of translocation breakpoints in the genome of cancer cells is determined, to a large extent, by the need to combine certain protein domains and to keep an intact reading frame in fusion transcripts. Additionally, the information that we have assembled affords a global view of the oncogenic mechanisms and domain architectures that are used by fusion proteins. This can be used to assess the functional impact of novel chromosomal translocations and to predict the position of breakpoints in the genes involved.
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Affiliation(s)
| | | | - Francisco J. Novo
- Department of Genetics, University of Navarra, Pamplona, Spain
- * E-mail:
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115
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Live cell microscopy analysis of radiation-induced DNA double-strand break motion. Proc Natl Acad Sci U S A 2009; 106:3172-7. [PMID: 19221031 DOI: 10.1073/pnas.0810987106] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We studied the spatiotemporal organization of DNA damage processing by live cell microscopy analysis in human cells. In unirradiated U2OS osteosarcoma and HeLa cancer cells, a fast confined and Brownian-like motion of DNA repair protein foci was observed, which was not altered by radiation. By analyzing the motional activity of GFP-53BP1 foci in live cells up to 12-h after irradiation, we detected an additional slower mobility of damaged chromatin sites showing a mean square displacement of approximately 0.6 microm(2)/h after exposure to densely- or sparsely-ionizing radiation, most likely driven by normal diffusion of chromatin. Only occasionally, larger translational motion connected to morphological changes of the whole nucleus could be observed. In addition, there was no general tendency to form repair clusters in the irradiated cells. We conclude that long-range displacements of damaged chromatin domains do not generally occur during DNA double-strand break repair after introduction of multiple damaged sites by charged particles. The occasional and in part transient appearance of cluster formation of radiation-induced foci may represent a higher mobility of chromatin along the ion trajectory. These observations support the hypothesis that spatial proximity of DNA breaks is required for the formation of radiation-induced chromosomal exchanges.
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116
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Tchélidzé P, Chatron-Colliet A, Thiry M, Lalun N, Bobichon H, Ploton D. Tomography of the cell nucleus using confocal microscopy and medium voltage electron microscopy. Crit Rev Oncol Hematol 2009; 69:127-43. [DOI: 10.1016/j.critrevonc.2008.07.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 07/18/2008] [Indexed: 12/18/2022] Open
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117
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Cvačková Z, Mašata M, Staněk D, Fidlerová H, Raška I. Chromatin position in human HepG2 cells: although being non-random, significantly changed in daughter cells. J Struct Biol 2009; 165:107-17. [PMID: 19056497 PMCID: PMC2658736 DOI: 10.1016/j.jsb.2008.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 10/24/2008] [Accepted: 10/27/2008] [Indexed: 12/22/2022]
Abstract
Mammalian chromosomes occupy chromosome territories within nuclear space the positions of which are generally accepted as non-random. However, it is still controversial whether position of chromosome territories/chromatin is maintained in daughter cells. We addressed this issue and investigated maintenance of various chromatin regions of unknown composition as well as nucleolus-associated chromatin, a significant part of which is composed of nucleolus organizer region-bearing chromosomes. The photoconvertible histone H4-Dendra2 was used to label such regions in transfected HepG2 cells, and its position was followed up to next interphase. The distribution of labeled chromatin in daughter cells exhibited a non-random character. However, its distribution in a vast majority of daughter cells extensively differed from the original ones and the labeled nucleolus-associated chromatin differently located into the vicinity of different nucleoli. Therefore, our results were not consistent with a concept of preservation chromatin position. This conclusion was supported by the finding that the numbers of nucleoli significantly differed between the two daughter cells. Our results support a view that while the transfected daughter HepG2 cells maintain some features of the parental cell chromosome organization, there is also a significant stochastic component associated with reassortment of chromosome territories/chromatin that results in their positional rearrangements.
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Affiliation(s)
| | | | | | | | - Ivan Raška
- Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, and Department of Cell Biology, Institute of Physiology, Academy of Sciences of the Czech Republic, v.v.i., Albertov 4, 128 00 Prague 2, Czech Republic
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118
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Horbinski C, Carter EM, Heard PL, Sathanoori M, Hu J, Vockley J, Gunn S, Hale DE, Surti U, Cody JD. Molecular and clinical characterization of a recurrent cryptic unbalanced t(4q;18q) resulting in an 18q deletion and 4q duplication. Am J Med Genet A 2008; 146A:2898-904. [PMID: 18932219 DOI: 10.1002/ajmg.a.32557] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Recurrent constitutional non-Robertsonian translocations are very rare. We present the third instance of cryptic, unbalanced translocation between 4q and 18q. This individual had an apparently normal karyotype; however, after subtelomere fluorescence in situ hybridization (FISH), he was found to have a cryptic unbalanced translocation between 4q and 18q [ish der(18)t(4;18)(q35;q23)(4qtel+,18qtel-)]. Oligonucleotide array comparative genomic hybridization (aCGH) refined the breakpoints in this child and in the previously reported child and indicated that the breakpoints were within 20 kb of each other, suggesting that this translocation is, indeed, recurrent. A comparison of the clinical presentation of these individuals identified features that are characteristic of both 18q- and 4q+ as well as features that are not associated with either condition, such as a prominent metopic ridge, bitemporal narrowing, prominent, and thick eyebrows. Individuals with features suggestive of this 4q;18q translocation but a normal karyotype warrant aCGH or subtelomere studies.
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Affiliation(s)
- Craig Horbinski
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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119
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Abstract
Zusammenfassung
Fluoreszenz-in-situ-Hybridisierung an dreidimensional konservierten Zellkernen (3D-FISH) ist eine effiziente Methode für Untersuchungen zur 3D-Anordnung von Chromatin im Zellkern. Die Zellkernarchitektur stellt eine Ebene epigenetischer Mechanismen der Genregulation dar. 3D-FISH-Untersuchungen belegten eine große Variabilität in den Nachbarschaftsbeziehungen individueller Chromosomenterritorien im Zellkern. Im Gegensatz hierzu konnte eine distinkte radiale, von der Gendichte abhängige Anordnung von Chromatin gezeigt werden, die evolutionär hochkonserviert ist. Genreiches Material ist bevorzugt in der Kernmitte, genarmes in der Kernperipherie angeordnet. Die Frage einer räumlichen Assoziation kotranskriptionell exprimierter Gene (so genannte „expression hubs”) wird derzeit kontrovers diskutiert.
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120
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True LD, Jordan CD. The cancer nuclear microenvironment: interface between light microscopic cytology and molecular phenotype. J Cell Biochem 2008; 104:1994-2003. [PMID: 18041766 DOI: 10.1002/jcb.21478] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A definitive diagnosis of cancer may be rendered by microscopic assessment of only a few cells in an appropriate clinical setting due to the distinctive nuclear structure of most cancer cells in comparison to nuclei of normal human cells. The molecular architecture of non-neoplastic human nuclei--of the nuclear matrix and of matrix-associated proteins and nucleic acids--is being characterized in exquisite molecular detail. What is missing is the application of the findings and tools of molecular biology to understanding the cytological structure of cancer nuclei. This article delves into the basis of nuclear structure at different levels of resolution--light microscopic, electron microscopic, and molecular.
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Affiliation(s)
- Lawrence D True
- Department of Pathology, University of Washington, Seattle, Washington 98119, USA.
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121
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Hermans KG, van der Korput HA, van Marion R, van de Wijngaart DJ, Ziel-van der Made A, Dits NF, Boormans JL, van der Kwast TH, van Dekken H, Bangma CH, Korsten H, Kraaij R, Jenster G, Trapman J. Truncated ETV1, fused to novel tissue-specific genes, and full-length ETV1 in prostate cancer. Cancer Res 2008; 68:7541-9. [PMID: 18794142 DOI: 10.1158/0008-5472.can-07-5930] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, we describe the properties of novel ETV1 fusion genes, encoding N-truncated ETV1 (dETV1), and of full-length ETV1, overexpressed in clinical prostate cancer. We detected overexpression of novel ETV1 fusion genes or of full-length ETV1 in 10% of prostate cancers. Novel ETV1 fusion partners included FOXP1, an EST (EST14), and an endogenous retroviral repeat sequence (HERVK17). Like TMPRSS2, EST14 and HERVK17 were prostate-specific and androgen-regulated expressed. This unique expression pattern of most ETV1 fusion partners seems an important determinant in prostate cancer development. In transient reporter assays, full-length ETV1 was a strong transactivator, whereas dETV1 was not. However, several of the biological properties of dETV1 and full-length ETV1 were identical. On stable overexpression, both induced migration and invasion of immortalized nontumorigenic PNT2C2 prostate epithelial cells. In contrast to dETV1, full-length ETV1 also induced anchorage-independent growth of these cells. PNT2C2 cells stably transfected with dETV1 or full-length ETV1 expression constructs showed small differences in induced expression of target genes. Many genes involved in tumor invasion/metastasis, including uPA/uPAR and MMPs, were up-regulated in both cell types. Integrin beta3 (ITGB3) was clearly up-regulated by full-length ETV1 but much less by dETV1. Based on the present data and on previous findings, a novel concept of the role of dETV1 and of full-length ETV1 overexpression in prostate cancer is proposed.
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Affiliation(s)
- Karin G Hermans
- Department of Pathology, Josephine Nefkens Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
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Ronneberger O, Baddeley D, Scheipl F, Verveer PJ, Burkhardt H, Cremer C, Fahrmeir L, Cremer T, Joffe B. Spatial quantitative analysis of fluorescently labeled nuclear structures: problems, methods, pitfalls. Chromosome Res 2008; 16:523-62. [PMID: 18461488 DOI: 10.1007/s10577-008-1236-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The vast majority of microscopic data in biology of the cell nucleus is currently collected using fluorescence microscopy, and most of these data are subsequently subjected to quantitative analysis. The analysis process unites a number of steps, from image acquisition to statistics, and at each of these steps decisions must be made that may crucially affect the conclusions of the whole study. This often presents a really serious problem because the researcher is typically a biologist, while the decisions to be taken require expertise in the fields of physics, computer image analysis, and statistics. The researcher has to choose between multiple options for data collection, numerous programs for preprocessing and processing of images, and a number of statistical approaches. Written for biologists, this article discusses some of the typical problems and errors that should be avoided. The article was prepared by a team uniting expertise in biology, microscopy, image analysis, and statistics. It considers the options a researcher has at the stages of data acquisition (choice of the microscope and acquisition settings), preprocessing (filtering, intensity normalization, deconvolution), image processing (radial distribution, clustering, co-localization, shape and orientation of objects), and statistical analysis.
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Affiliation(s)
- O Ronneberger
- Department of Pattern Recognition and Image Processing, University of Freiburg, 79110, Freiburg, Germany
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123
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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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124
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Gudla PR, Nandy K, Collins J, Meaburn KJ, Misteli T, Lockett SJ. A high-throughput system for segmenting nuclei using multiscale techniques. Cytometry A 2008; 73:451-66. [PMID: 18338778 DOI: 10.1002/cyto.a.20550] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Automatic segmentation of cell nuclei is critical in several high-throughput cytometry applications whereas manual segmentation is laborious and irreproducible. One such emerging application is measuring the spatial organization (radial and relative distances) of fluorescence in situ hybridization (FISH) DNA sequences, where recent investigations strongly suggest a correlation between nonrandom arrangement of genes to carcinogenesis. Current automatic segmentation methods have varying performance in the presence of nonuniform illumination and clustering, and boundary accuracy is seldom assessed, which makes them suboptimal for this application. The authors propose a modular and model-based algorithm for extracting individual nuclei. It uses multiscale edge reconstruction for contrast stretching and edge enhancement as well as a multiscale entropy-based thresholding for handling nonuniform intensity variations. Nuclei are initially oversegmented and then merged based on area followed by automatic multistage classification into single nuclei and clustered nuclei. Estimation of input parameters and training of the classifiers is automatic. The algorithm was tested on 4,181 lymphoblast nuclei with varying degree of background nonuniformity and clustering. It extracted 3,515 individual nuclei and identified single nuclei and individual nuclei in clusters with 99.8 +/- 0.3% and 95.5 +/- 5.1% accuracy, respectively. Segmented boundaries of the individual nuclei were accurate when compared with manual segmentation with an average RMS deviation of 0.26 microm (approximately 2 pixels). The proposed segmentation method is efficient, robust, and accurate for segmenting individual nuclei from fluorescence images containing clustered and isolated nuclei. The algorithm allows complete automation and facilitates reproducible and unbiased spatial analysis of DNA sequences.
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Affiliation(s)
- Prabhakar R Gudla
- Image Analysis Laboratory, Advanced Technology Program, SAIC-Frederick, NCI-Frederick, Frederick, Maryland 21702, USA.
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125
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Nuclear functions in space and time: Gene expression in a dynamic, constrained environment. FEBS Lett 2008; 582:1960-70. [DOI: 10.1016/j.febslet.2008.04.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 04/16/2008] [Indexed: 11/19/2022]
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126
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Folle GA. Nuclear architecture, chromosome domains and genetic damage. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2008; 658:172-83. [DOI: 10.1016/j.mrrev.2007.08.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 08/20/2007] [Accepted: 08/20/2007] [Indexed: 12/18/2022]
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127
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128
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Meaburn KJ, Misteli T. Locus-specific and activity-independent gene repositioning during early tumorigenesis. ACTA ACUST UNITED AC 2008; 180:39-50. [PMID: 18195100 PMCID: PMC2213600 DOI: 10.1083/jcb.200708204] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mammalian genome is highly organized within the cell nucleus. The nuclear position of many genes and genomic regions changes during physiological processes such as proliferation, differentiation, and disease. It is unclear whether disease-associated positioning changes occur specifically or are part of more global genome reorganization events. Here, we have analyzed the spatial position of a defined set of cancer-associated genes in an established mammary epithelial three-dimensional cell culture model of the early stages of breast cancer. We find that the genome is globally reorganized during normal and tumorigenic epithelial differentiation. Systematic mapping of changes in spatial positioning of cancer-associated genes reveals gene-specific positioning behavior and we identify several genes that are specifically repositioned during tumorigenesis. Alterations of spatial positioning patterns during differentiation and tumorigenesis were unrelated to gene activity. Our results demonstrate the existence of activity-independent genome repositioning events in the early stages of tumor formation.
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Affiliation(s)
- Karen J Meaburn
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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129
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Huh YH, Kim KD, Yoo SH. Comparison of and chromogranin effect on inositol 1,4,5-trisphosphate sensitivity of cytoplasmic and nucleoplasmic inositol 1,4,5-trisphosphate receptor/Ca2+ channels. Biochemistry 2007; 46:14032-43. [PMID: 17997581 DOI: 10.1021/bi701364p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nucleus also contains the inositol 1,4,5-trisphosphate receptor (IP3R)/Ca2+ channels in the nucleoplasm proper independent of the nuclear envelope or the cytoplasm. The nuclear IP3R/Ca2+ channels were shown to be present in small IP3-dependent nucleoplasmic Ca2+ store vesicles, yet no information is available regarding the IP3 sensitivity of nuclear IP3R/Ca2+ channels. Here, we show that nuclear IP3R/Ca2+ channels are 3-4-fold more sensitive to IP3 than cytoplasmic ones in both neuroendocrine PC12 cells and nonneuroendocrine NIH3T3 cells. Given the presence of phosphoinositides and phospholipase C and the importance of IP3-mediated Ca2+ signaling in the nucleus, the high IP3 sensitivity of nuclear IP3R/Ca2+ channels seemed to reflect the physiological needs of the nucleus to finely control the IP3-dependent Ca2+ concentrations. It was further shown that the IP3R/Ca2+ channels of secretory cells are 7-8-fold more sensitive to IP3 than those of nonsecretory cells. This difference appeared to result from the presence of secretory cell marker protein chromogranins (thus secretory granules) in secretory cells; expression of chromogranins in NIH3T3 cells increased the IP3 sensitivity of both nuclear and cytoplasmic IP3R/Ca2+ channels by approximately 4-6-fold. In contrast, suppression of chromogranin A expression in PC12 cells changed the EC50 of IP3 sensitivity for cytoplasmic IP3R/Ca2+ channels from 17 to 47 nM, whereas suppression of chromogranin B expression changed the EC50 of cytoplasmic IP3R/Ca2+ channels from 17 to 102 nM and the nuclear ones from 4.3 to 35 nM. Given that secretion is the major function of secretory cells and is under a tight control of intracellular Ca2+ concentrations, the high IP3 sensitivity appears to reflect the physiological roles of secretory cells.
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Affiliation(s)
- Yang Hoon Huh
- Department of Biochemistry, Inha University College of Medicine, Jung Gu, Incheon 400-712, Korea
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130
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Brianna Caddle L, Grant JL, Szatkiewicz J, van Hase J, Shirley BJ, Bewersdorf J, Cremer C, Arneodo A, Khalil A, Mills KD. Chromosome neighborhood composition determines translocation outcomes after exposure to high-dose radiation in primary cells. Chromosome Res 2007; 15:1061-73. [PMID: 18060570 DOI: 10.1007/s10577-007-1181-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 09/26/2007] [Accepted: 09/26/2007] [Indexed: 01/05/2023]
Abstract
Radiation exposure is an occupational hazard for military personnel, some health care professionals, airport security screeners, and medical patients, with some individuals at risk for acute, high-dose exposures. Therefore, the biological effects of radiation, especially the potential for chromosome damage, are major occupational and health concerns. However, the biophysical mechanisms of chromosome instability subsequent to radiation-induced DNA damage are poorly understood. It is clear that interphase chromosomes occupy discrete structural and functional subnuclear domains, termed chromosome territories (CT), which may be organized into 'neighborhoods' comprising groups of specific CTs. We directly evaluated the relationship between chromosome positioning, neighborhood composition, and translocation partner choice in primary lymphocytes, using a cell-based system in which we could induce multiple, concentrated DNA breaks via high-dose irradiation. We critically evaluated mis-rejoining profiles and tested whether breaks occurring nearby were more likely to fuse than breaks occurring at a distance. We show that CT neighborhoods comprise heterologous chromosomes, within which inter-CT distances directly relate to translocation partner choice. These findings demonstrate that interphase chromosome arrangement is a principal factor in genomic instability outcomes in primary lymphocytes, providing a structural context for understanding the biological effects of radiation exposure, and the molecular etiology of tumor-specific translocation patterns.
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131
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Guffei A, Lichtensztejn Z, Gonçalves dos Santos Silva A, Louis SF, Caporali A, Mai S. c-Myc-dependent formation of Robertsonian translocation chromosomes in mouse cells. Neoplasia 2007; 9:578-88. [PMID: 17710161 PMCID: PMC1941693 DOI: 10.1593/neo.07355] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 05/31/2007] [Accepted: 06/01/2007] [Indexed: 12/29/2022] Open
Abstract
Robertsonian (Rb) translocation chromosomes occur in human and murine cancers and involve the aberrant joining of two acrocentric chromosomes in humans and two telocentric chromosomes in mice. Mechanisms leading to their generation remain elusive, but models for their formation have been proposed. They include breakage of centromeric sequences and their subsequent fusions, centric misdivision, misparing between highly repetitive sequences of p-tel or p-arm repeats, and recombinational joining of centromeres and/or centromeric fusions. Here, we have investigated the role of the oncoprotein c-Myc in the formation of Rb chromosomes in mouse cells harboring exclusively telocentric chromosomes. In mouse plasmacytoma cells with constitutive c-Myc deregulation and in immortalized mouse lymphocytes with conditional c-Myc expression, we show that positional remodeling of centromeres in interphase nuclei coincides with the formation of Rb chromosomes. Furthermore, we demonstrate that c-Myc deregulation in a myc box II-dependent manner is sufficient to induce Rb translocation chromosomes. Because telomeric signals are present at all joined centromeres of Rb chromosomes, we conclude that c-Myc mediates Rb chromosome formation in mouse cells by telomere fusions at centromeric termini of telocentric chromosomes. Our findings are relevant to the understanding of nuclear chromosome remodeling during the initiation of genomic instability and tumorigenesis.
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Affiliation(s)
- Amanda Guffei
- Manitoba Institute of Cell Biology, The University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Zelda Lichtensztejn
- Manitoba Institute of Cell Biology, The University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Amanda Gonçalves dos Santos Silva
- Manitoba Institute of Cell Biology, The University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada
- Disciplina de Imunologia, Departamento de Microbiologia, Imunologia, e Parasitologia, Universidade Federal de São Paulo, São Paulo, SP 04023-062, Brazil
| | - Sherif F Louis
- Manitoba Institute of Cell Biology, The University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Andrea Caporali
- Manitoba Institute of Cell Biology, The University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada
- Dipartimento di Medicina Sperimentale, Sezione di Biochimica, Biochimica Clinica e Biochimica dell'Esercizio Fisico, Università degli Studi di Parma, Parma 43100, Italy
| | - Sabine Mai
- Manitoba Institute of Cell Biology, The University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada
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132
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Soutoglou E, Misteli T. Mobility and immobility of chromatin in transcription and genome stability. Curr Opin Genet Dev 2007; 17:435-42. [PMID: 17905579 PMCID: PMC2118061 DOI: 10.1016/j.gde.2007.08.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 07/16/2007] [Accepted: 08/17/2007] [Indexed: 01/07/2023]
Abstract
Chromatin is increasingly recognized as a highly dynamic entity. Chromosome sites in lower and higher eukaryotes undergo frequent, rapid, and constrained local motion and occasional slow, long-range movements. Recent observations have revealed some of the functional relevance of chromatin mobility. Paradoxically, both the mobility and immobility of chromatin appear to have functional consequences: Local diffusional motion of chromatin is important in gene regulation, but global chromatin immobility plays a key role in maintenance of genomic stability.
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Affiliation(s)
- Evi Soutoglou
- National Cancer Institute, NIH, Bethesda, MD 20892, United States
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133
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Soutoglou E, Dorn JF, Sengupta K, Jasin M, Nussenzweig A, Ried T, Danuser G, Misteli T. Positional stability of single double-strand breaks in mammalian cells. Nat Cell Biol 2007; 9:675-82. [PMID: 17486118 PMCID: PMC2442898 DOI: 10.1038/ncb1591] [Citation(s) in RCA: 393] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 03/30/2007] [Indexed: 11/09/2022]
Abstract
Formation of cancerous translocations requires the illegitimate joining of chromosomes containing double-strand breaks (DSBs). It is unknown how broken chromosome ends find their translocation partners within the cell nucleus. Here, we have visualized and quantitatively analysed the dynamics of single DSBs in living mammalian cells. We demonstrate that broken ends are positionally stable and unable to roam the cell nucleus. Immobilization of broken chromosome ends requires the DNA-end binding protein Ku80, but is independent of DNA repair factors, H2AX, the MRN complex and the cohesion complex. DSBs preferentially undergo translocations with neighbouring chromosomes and loss of local positional constraint correlates with elevated genomic instability. These results support a contact-first model in which chromosome translocations predominantly form among spatially proximal DSBs.
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Affiliation(s)
- Evi Soutoglou
- National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jonas F. Dorn
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kundan Sengupta
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Maria Jasin
- Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Andre Nussenzweig
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Thomas Ried
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD 20892, USA
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134
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Abstract
The Ringberg Colloquium on Self-Organization and Morphogenesis in Biological Systems took place between December 3-6, 2006 in a castle near Munich, Germany. Researchers from different areas of cell and developmental biology exchanged ideas about how biological systems are organized and dynamic at the same time. A dominant theme was that local interactions between molecules or cells can generate global order.
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Affiliation(s)
- Benjamin S Glick
- Department of Molecular Genetics and Cell Biology, Institute for Biophysical Dynamics, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
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