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Mirceta M, Shum N, Schmidt MHM, Pearson CE. Fragile sites, chromosomal lesions, tandem repeats, and disease. Front Genet 2022; 13:985975. [PMID: 36468036 PMCID: PMC9714581 DOI: 10.3389/fgene.2022.985975] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/02/2022] [Indexed: 09/16/2023] Open
Abstract
Expanded tandem repeat DNAs are associated with various unusual chromosomal lesions, despiralizations, multi-branched inter-chromosomal associations, and fragile sites. Fragile sites cytogenetically manifest as localized gaps or discontinuities in chromosome structure and are an important genetic, biological, and health-related phenomena. Common fragile sites (∼230), present in most individuals, are induced by aphidicolin and can be associated with cancer; of the 27 molecularly-mapped common sites, none are associated with a particular DNA sequence motif. Rare fragile sites ( ≳ 40 known), ≤ 5% of the population (may be as few as a single individual), can be associated with neurodevelopmental disease. All 10 molecularly-mapped folate-sensitive fragile sites, the largest category of rare fragile sites, are caused by gene-specific CGG/CCG tandem repeat expansions that are aberrantly CpG methylated and include FRAXA, FRAXE, FRAXF, FRA2A, FRA7A, FRA10A, FRA11A, FRA11B, FRA12A, and FRA16A. The minisatellite-associated rare fragile sites, FRA10B, FRA16B, can be induced by AT-rich DNA-ligands or nucleotide analogs. Despiralized lesions and multi-branched inter-chromosomal associations at the heterochromatic satellite repeats of chromosomes 1, 9, 16 are inducible by de-methylating agents like 5-azadeoxycytidine and can spontaneously arise in patients with ICF syndrome (Immunodeficiency Centromeric instability and Facial anomalies) with mutations in genes regulating DNA methylation. ICF individuals have hypomethylated satellites I-III, alpha-satellites, and subtelomeric repeats. Ribosomal repeats and subtelomeric D4Z4 megasatellites/macrosatellites, are associated with chromosome location, fragility, and disease. Telomere repeats can also assume fragile sites. Dietary deficiencies of folate or vitamin B12, or drug insults are associated with megaloblastic and/or pernicious anemia, that display chromosomes with fragile sites. The recent discovery of many new tandem repeat expansion loci, with varied repeat motifs, where motif lengths can range from mono-nucleotides to megabase units, could be the molecular cause of new fragile sites, or other chromosomal lesions. This review focuses on repeat-associated fragility, covering their induction, cytogenetics, epigenetics, cell type specificity, genetic instability (repeat instability, micronuclei, deletions/rearrangements, and sister chromatid exchange), unusual heritability, disease association, and penetrance. Understanding tandem repeat-associated chromosomal fragile sites provides insight to chromosome structure, genome packaging, genetic instability, and disease.
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Affiliation(s)
- Mila Mirceta
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Natalie Shum
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Monika H. M. Schmidt
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Kim E, Rich J, Karoutas A, Tarlykov P, Cochet E, Malysheva D, Mamchaoui K, Ogryzko V, Pirozhkova I. ZNF555 protein binds to transcriptional activator site of 4qA allele and ANT1: potential implication in Facioscapulohumeral dystrophy. Nucleic Acids Res 2015; 43:8227-42. [PMID: 26184877 PMCID: PMC4787827 DOI: 10.1093/nar/gkv721] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 06/27/2015] [Indexed: 01/18/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is an epi/genetic satellite disease associated with at least two satellite sequences in 4q35: (i) D4Z4 macrosatellite and (ii) β-satellite repeats (BSR), a prevalent part of the 4qA allele. Most of the recent FSHD studies have been focused on a DUX4 transcript inside D4Z4 and its tandem contraction in FSHD patients. However, the D4Z4-contraction alone is not pathological, which would also require the 4qA allele. Since little is known about BSR, we investigated the 4qA BSR functional role in the transcriptional control of the FSHD region 4q35. We have shown that an individual BSR possesses enhancer activity leading to activation of the Adenine Nucleotide Translocator 1 gene (ANT1), a major FSHD candidate gene. We have identified ZNF555, a previously uncharacterized protein, as a putative transcriptional factor highly expressed in human primary myoblasts that interacts with the BSR enhancer site and impacts the ANT1 promoter activity in FSHD myoblasts. The discovery of the functional role of the 4qA allele and ZNF555 in the transcriptional control of ANT1 advances our understanding of FSHD pathogenesis and provides potential therapeutic targets.
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Affiliation(s)
- Elena Kim
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Jeremy Rich
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Adam Karoutas
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Pavel Tarlykov
- National Center for Biotechnology, Astana 010000, Kazakhstan
| | - Emilie Cochet
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France Proteomic Platform, IRCIV Gustave Roussy, Villejuif 94408, France
| | - Daria Malysheva
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Kamel Mamchaoui
- Thérapie des maladies du muscle strié, Institut de Myologie, UM76-Pierre et Marie CURIE University/U974-INSERM/UMR7215-CNRS, Paris 75013, France
| | - Vasily Ogryzko
- Proteomic Platform, IRCIV Gustave Roussy, Villejuif 94408, France INSERM, CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
| | - Iryna Pirozhkova
- CNRS, University Paris-Sud, UMR-8126, Gustave Roussy, Villejuif 94408, France
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Himeda CL, Jones TI, Jones PL. Facioscapulohumeral muscular dystrophy as a model for epigenetic regulation and disease. Antioxid Redox Signal 2015; 22:1463-82. [PMID: 25336259 PMCID: PMC4432493 DOI: 10.1089/ars.2014.6090] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Aberrant epigenetic regulation is an integral aspect of many diseases and complex disorders. Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, is caused by disrupted genetic and epigenetic regulation of a macrosatellite repeat. FSHD provides a powerful model to investigate disease-relevant epigenetic modifiers and general mechanisms of epigenetic regulation that govern gene expression. RECENT ADVANCES In the context of a genetically permissive allele, the one aspect of FSHD that is consistent across all known cases is the aberrant epigenetic state of the disease locus. In addition, certain mutations in the chromatin regulator SMCHD1 (structural maintenance of chromosomes hinge-domain protein 1) are sufficient to cause FSHD2 and enhance disease severity in FSHD1. Thus, there are multiple pathways to generate the epigenetic dysregulation required for FSHD. CRITICAL ISSUES Why do some individuals with the genetic requirements for FSHD develop disease pathology, while others remain asymptomatic? Similarly, disease progression is highly variable among individuals. What are the relative contributions of genetic background and environmental factors in determining disease manifestation, progression, and severity in FSHD? What is the interplay between epigenetic factors regulating the disease locus and which, if any, are viable therapeutic targets? FUTURE DIRECTIONS Epigenetic regulation represents a potentially powerful therapeutic target for FSHD. Determining the epigenetic signatures that are predictive of disease severity and identifying the spectrum of disease modifiers in FSHD are vital to the development of effective therapies.
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Affiliation(s)
- Charis L Himeda
- The Wellstone Program and the Departments of Cell and Developmental Biology and Neurology, University of Massachusetts Medical School , Worcester, Massachusetts
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Thijssen PE, Balog J, Yao Z, Pham TP, Tawil R, Tapscott SJ, Van der Maarel SM. DUX4 promotes transcription of FRG2 by directly activating its promoter in facioscapulohumeral muscular dystrophy. Skelet Muscle 2014; 4:19. [PMID: 25789155 PMCID: PMC4364343 DOI: 10.1186/2044-5040-4-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 10/13/2014] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The most common form of facioscapulohumeral muscular dystrophy (FSHD) is caused by a genetic contraction of the polymorphic D4Z4 macrosatellite repeat array in the subtelomeric region of chromosome 4q. In some studies, genes centromeric to the D4Z4 repeat array have been reported to be over-expressed in FSHD, including FRG1 and FRG2, presumably due to decreased long-distance repression by the shorter array through a mechanism similar to position-effect variegation. Differential regulation of FRG1 in FSHD has never been unequivocally proven, however, FRG2 has been reproducibly shown to be induced in primary FSHD-derived muscle cells when differentiated in vitro. The molecular function of FRG2 and a possible contribution to FSHD pathology remain unclear. Recent evidence has identified the mis-expression of DUX4, located within the D4Z4 repeat unit, in skeletal muscle as the cause of FSHD. DUX4 is a double homeobox transcription factor that has been shown to be toxic when expressed in muscle cells. METHODS We used a combination of expression analysis by qRT/PCR and RNA sequencing to determine the transcriptional activation of FRG2 and DUX4. We examined this in both differentiating control and FSHD derived muscle cell cultures or DUX4 transduced control cell lines. Next, we used ChIP-seq analysis and luciferase reporter assays to determine the potential DUX4 transactivation effect on the FRG2 promoter. RESULTS We show that DUX4 directly activates the expression of FRG2. Increased expression of FRG2 was observed following expression of DUX4 in myoblasts and fibroblasts derived from control individuals. Moreover, we identified DUX4 binding sites at the FRG2 promoter by chromatin immunoprecipitation followed by deep sequencing and confirmed the direct regulation of DUX4 on the FRG2 promoter by luciferase reporter assays. Activation of luciferase was dependent on both DUX4 expression and the presence of the DUX4 DNA binding motifs in the FRG2 promoter. CONCLUSION We show that the FSHD-specific upregulation of FRG2 is a direct consequence of the activity of DUX4 protein rather than representing a regional de-repression secondary to fewer D4Z4 repeats.
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Affiliation(s)
- Peter E Thijssen
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Zizhen Yao
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle WA 98109, USA
| | - Tan Phát Pham
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Rabi Tawil
- Neuromuscular Disease Unit, Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle WA 98109, USA
| | - Silvère M Van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
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Ebert G, Steininger A, Weißmann R, Boldt V, Lind-Thomsen A, Grune J, Badelt S, Heßler M, Peiser M, Hitzler M, Jensen LR, Müller I, Hu H, Arndt PF, Kuss AW, Tebel K, Ullmann R. Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. BMC Genomics 2014; 15:537. [PMID: 24973960 PMCID: PMC4092221 DOI: 10.1186/1471-2164-15-537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/17/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology. RESULTS Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the aetiology of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. CONCLUSIONS Our study suggests a link of nuclear architecture and the propagation of SDs across chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome.
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Affiliation(s)
- Grit Ebert
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Anne Steininger
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Robert Weißmann
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Vivien Boldt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Allan Lind-Thomsen
- />Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Jana Grune
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Stefan Badelt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Institute for Theoretical Chemistry, University of Vienna, Waehringer Straße 17, A-1090 Vienna, Austria
| | - Melanie Heßler
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Matthias Peiser
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Manuel Hitzler
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Lars R Jensen
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Ines Müller
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Hao Hu
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Peter F Arndt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Andreas W Kuss
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Katrin Tebel
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Reinhard Ullmann
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
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Cabianca DS, Casa V, Gabellini D. A novel molecular mechanism in human genetic disease: a DNA repeat-derived lncRNA. RNA Biol 2012; 9:1211-7. [PMID: 23047063 DOI: 10.4161/rna.21922] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Two thirds of the human genome is composed of repetitive sequences. Despite their prevalence, DNA repeats are largely ignored. The vast majority of our genome is transcribed to produce non protein-coding RNAs. Among these, long non protein-coding RNAs represent the most prevalent and functionally diverse class. The relevance of the non protein-coding genome to human disease has mainly been studied regarding the altered microRNA expression and function in human cancer. On the contrary, the elucidation of the involvement of long non-coding RNAs in disease is only in its infancy. We have recently found that a chromatin associated, long non protein-coding RNA regulates a Polycomb/Trithorax epigenetic switch at the basis of the repeat associated facioscapulohumeral muscular dystrophy, a common muscle disorder. Based on this, we propose that long non-coding RNAs produced by repetitive sequences contribute in shaping the epigenetic landscape in normal human physiology and in disease.
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Affiliation(s)
- Daphne S Cabianca
- Dulbecco Telethon Institute and Division of Regenerative Medicine, Stem cells, and Gene therapy, San Raffaele Scientific Institute, Milan, Italy
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The epigenetics of facioscapulohumeral muscular dystrophy. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Krueger C, King MR, Krueger F, Branco MR, Osborne CS, Niakan KK, Higgins MJ, Reik W. Pairing of homologous regions in the mouse genome is associated with transcription but not imprinting status. PLoS One 2012; 7:e38983. [PMID: 22802932 PMCID: PMC3389011 DOI: 10.1371/journal.pone.0038983] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 05/17/2012] [Indexed: 01/09/2023] Open
Abstract
Although somatic homologous pairing is common in Drosophila it is not generally observed in mammalian cells. However, a number of regions have recently been shown to come into close proximity with their homologous allele, and it has been proposed that pairing might be involved in the establishment or maintenance of monoallelic expression. Here, we investigate the pairing properties of various imprinted and non-imprinted regions in mouse tissues and ES cells. We find by allele-specific 4C-Seq and DNA FISH that the Kcnq1 imprinted region displays frequent pairing but that this is not dependent on monoallelic expression. We demonstrate that pairing involves larger chromosomal regions and that the two chromosome territories come close together. Frequent pairing is not associated with imprinted status or DNA repair, but is influenced by chromosomal location and transcription. We propose that homologous pairing is not exclusive to specialised regions or specific functional events, and speculate that it provides the cell with the opportunity of trans-allelic effects on gene regulation.
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Affiliation(s)
- Christel Krueger
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- * E-mail: (CK); (WR)
| | - Michelle R. King
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Miguel R. Branco
- Genome Function Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, London, United Kingdom
| | - Cameron S. Osborne
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Kathy K. Niakan
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Anne McLaren Laboratory for Regenerative Medicine, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Higgins
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CK); (WR)
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Zeng W, de Greef JC, Chen YY, Chien R, Kong X, Gregson HC, Winokur ST, Pyle A, Robertson KD, Schmiesing JA, Kimonis VE, Balog J, Frants RR, Ball AR, Lock LF, Donovan PJ, van der Maarel SM, Yokomori K. Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet 2009; 5:e1000559. [PMID: 19593370 PMCID: PMC2700282 DOI: 10.1371/journal.pgen.1000559] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 06/12/2009] [Indexed: 12/11/2022] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant muscular dystrophy in which no mutation of pathogenic gene(s) has been identified. Instead, the disease is, in most cases, genetically linked to a contraction in the number of 3.3 kb D4Z4 repeats on chromosome 4q. How contraction of the 4qter D4Z4 repeats causes muscular dystrophy is not understood. In addition, a smaller group of FSHD cases are not associated with D4Z4 repeat contraction (termed "phenotypic" FSHD), and their etiology remains undefined. We carried out chromatin immunoprecipitation analysis using D4Z4-specific PCR primers to examine the D4Z4 chromatin structure in normal and patient cells as well as in small interfering RNA (siRNA)-treated cells. We found that SUV39H1-mediated H3K9 trimethylation at D4Z4 seen in normal cells is lost in FSHD. Furthermore, the loss of this histone modification occurs not only at the contracted 4q D4Z4 allele, but also at the genetically intact D4Z4 alleles on both chromosomes 4q and 10q, providing the first evidence that the genetic change (contraction) of one 4qD4Z4 allele spreads its effect to other genomic regions. Importantly, this epigenetic change was also observed in the phenotypic FSHD cases with no D4Z4 contraction, but not in other types of muscular dystrophies tested. We found that HP1gamma and cohesin are co-recruited to D4Z4 in an H3K9me3-dependent and cell type-specific manner, which is disrupted in FSHD. The results indicate that cohesin plays an active role in HP1 recruitment and is involved in cell type-specific D4Z4 chromatin regulation. Taken together, we identified the loss of both histone H3K9 trimethylation and HP1gamma/cohesin binding at D4Z4 to be a faithful marker for the FSHD phenotype. Based on these results, we propose a new model in which the epigenetic change initiated at 4q D4Z4 spreads its effect to other genomic regions, which compromises muscle-specific gene regulation leading to FSHD pathogenesis.
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Affiliation(s)
- Weihua Zeng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Jessica C. de Greef
- Leiden University Medical Center, Center for Human and Clinical Genetics, Leiden, The Netherlands
| | - Yen-Yun Chen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Richard Chien
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Heather C. Gregson
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Sara T. Winokur
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - April Pyle
- Institute for Stem Cell Biology and Medicine, Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Keith D. Robertson
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
| | - John A. Schmiesing
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Virginia E. Kimonis
- Division of Medical Genetics and Metabolism, Department of Pediatrics, University of California Irvine Medical Center, Orange, California, United States of America
| | - Judit Balog
- Leiden University Medical Center, Center for Human and Clinical Genetics, Leiden, The Netherlands
| | - Rune R. Frants
- Leiden University Medical Center, Center for Human and Clinical Genetics, Leiden, The Netherlands
| | - Alexander R. Ball
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Leslie F. Lock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | - Peter J. Donovan
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
| | | | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, United States of America
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10
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De Vos WH, Hoebe RA, Joss GH, Haffmans W, Baatout S, Van Oostveldt P, Manders EMM. Controlled light exposure microscopy reveals dynamic telomere microterritories throughout the cell cycle. Cytometry A 2009; 75:428-39. [PMID: 19097172 DOI: 10.1002/cyto.a.20699] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Telomeres are complex end structures that confer functional integrity and positional stability to human chromosomes. Despite their critical importance, there is no clear view on telomere organization in cycling human cells and their dynamic behavior throughout the cell cycle. We investigated spatiotemporal organization of telomeres in living human ECV-304 cells stably expressing telomere binding proteins TRF1 and TRF2 fused to mCitrine using four dimensional microscopy. We thereby made use of controlled light exposure microscopy (CLEM), a novel technology that strongly reduces photodamage by limiting excitation in parts of the image where full exposure is not needed. We found that telomeres share small territories where they dynamically associate. These territories are preferentially positioned at the interface of chromatin domains. TRF1 and TRF2 are abundantly present in these territories but not firmly bound. At the onset of mitosis, the bulk of TRF protein dissociates from telomere regions, territories disintegrate and individual telomeres become faintly visible. The combination of stable cell lines, CLEM and cytometry proved essential in providing novel insights in compartment-based nuclear organization and may serve as a model approach for investigating telomere-driven genome-instability and studying long-term nuclear dynamics.
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Affiliation(s)
- Winnok H De Vos
- Department of Molecular Biotechnology, Faculty of Bio-engineering Sciences, Ghent University, Coupure links 653, Ghent 9000, Belgium.
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11
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de Greef JC, Frants RR, van der Maarel SM. Epigenetic mechanisms of facioscapulohumeral muscular dystrophy. Mutat Res 2008; 647:94-102. [PMID: 18723032 PMCID: PMC2650037 DOI: 10.1016/j.mrfmmm.2008.07.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 07/18/2008] [Accepted: 07/23/2008] [Indexed: 04/08/2023]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) seems to be caused by a complex epigenetic disease mechanism as a result of contraction of the polymorphic macrosatellite repeat D4Z4 on chromosome 4qter. Currently, the exact mechanism causing the FSHD phenotype is still not elucidated. In this review, we discuss the genetic and epigenetic changes observed in patients with FSHD and the possible disease mechanisms that may be associated with FSHD pathogenesis.
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Affiliation(s)
- Jessica C. de Greef
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Rune R. Frants
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Silvère M. van der Maarel
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Address correspondence and reprint requests to: Dr. S.M. van der Maarel, Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Bldg. 2, room S-03-042, Postal zone S-4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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12
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Pirozhkova I, Petrov A, Dmitriev P, Laoudj D, Lipinski M, Vassetzky Y. A functional role for 4qA/B in the structural rearrangement of the 4q35 region and in the regulation of FRG1 and ANT1 in facioscapulohumeral dystrophy. PLoS One 2008; 3:e3389. [PMID: 18852887 PMCID: PMC2561064 DOI: 10.1371/journal.pone.0003389] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 09/17/2008] [Indexed: 01/11/2023] Open
Abstract
The number of D4Z4 repeats in the subtelomeric region of chromosome 4q is strongly reduced in patients with Facio-Scapulo-Humeral Dystrophy (FSHD). We performed chromosome conformation capture (3C) analysis to document the interactions taking place among different 4q35 markers. We found that the reduced number of D4Z4 repeats in FSHD myoblasts was associated with a global alteration of the three-dimensional structure of the 4q35 region. Indeed, differently from normal myoblasts, the 4qA/B marker interacted directly with the promoters of the FRG1 and ANT1 genes in FSHD cells. Along with the presence of a newly identified transcriptional enhancer within the 4qA allele, our demonstration of an interaction occurring between chromosomal segments located megabases away on the same chromosome 4q allows to revisit the possible mechanisms leading to FSHD.
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Affiliation(s)
- Iryna Pirozhkova
- Université Paris-Sud 11, CNRS UMR 8126, Interactions moléculaires et cancer, Institut de Cancérologie Gustave-Roussy, Villejuif, France
| | - Andrei Petrov
- Université Paris-Sud 11, CNRS UMR 8126, Interactions moléculaires et cancer, Institut de Cancérologie Gustave-Roussy, Villejuif, France
| | - Petr Dmitriev
- Université Paris-Sud 11, CNRS UMR 8126, Interactions moléculaires et cancer, Institut de Cancérologie Gustave-Roussy, Villejuif, France
| | - Dalila Laoudj
- INSERM, ERI25, F-34000, Montpellier, France, Université Montpellier 1, Montpellier, France
| | - Marc Lipinski
- Université Paris-Sud 11, CNRS UMR 8126, Interactions moléculaires et cancer, Institut de Cancérologie Gustave-Roussy, Villejuif, France
| | - Yegor Vassetzky
- Université Paris-Sud 11, CNRS UMR 8126, Interactions moléculaires et cancer, Institut de Cancérologie Gustave-Roussy, Villejuif, France
- * E-mail:
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13
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Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a dominantly inherited disorder with an initially restricted pattern of weakness. Early involvement of the facial and scapular stabilizer muscles results in a distinctive clinical presentation. Progression is descending, with subsequent involvement of either the distal anterior leg or hip-girdle muscles. There is wide variability in age at onset, disease severity, and side-to-side symmetry, which is evident even within affected members of the same family. Although FSHD is considered a relatively benign dystrophy by some, as many as 20% of patients eventually become wheelchair-bound. Associated nonskeletal muscle manifestations include high-frequency hearing loss as well as retinal telangiectasias, both of which are rarely symptomatic. The causal genetic lesion in FSHD was described over a decade ago, raising hope that knowledge about its molecular and cellular pathophysiology was soon to follow. In the vast majority of cases, FSHD results from a heterozygous partial deletion of a critical number of repetitive elements (D4Z4) on chromosome 4q35; yet, to date, no causal gene has been identified. The accumulating evidence points to a complex, perhaps unique, molecular genetic mechanism. The absence of detectable expressed sequences from D4Z4, the association of FSHD-causing 4q35 deletions with a specific distal genomic sequence (4qA allele), altered DNA methylation patterns on 4q35, as well as other direct and indirect evidence point to epigenetic mechanisms. As a consequence, partial deletion of D4Z4 results in a (local) chromatin change and ultimately results in the loss of appropriate control of gene expression. There is at present no effective treatment for FSHD. A better understanding of the underlying pathophysiology is needed to design targeted interventions. Despite these limitations, however, two randomized controlled clinical trials have been conducted on FSHD. These trials, along with a previous natural history study, have helped to better define outcome measures for future trials in FSHD as well as other dystrophies.
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Affiliation(s)
- Rabi Tawil
- University of Rochester Medical Center, Neuromuscular Disease Center, P.O. Box 673, 601 Elmwood Avenue, Rochester, New York 14642, USA.
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14
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Rijkers T, Deidda G, van Koningsbruggen S, van Geel M, Lemmers RJLF, van Deutekom JCT, Figlewicz D, Hewitt JE, Padberg GW, Frants RR, van der Maarel SM. FRG2, an FSHD candidate gene, is transcriptionally upregulated in differentiating primary myoblast cultures of FSHD patients. J Med Genet 2005; 41:826-36. [PMID: 15520407 PMCID: PMC1735617 DOI: 10.1136/jmg.2004.019364] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Autosomal dominant facioscapulohumeral muscular dystrophy (FSHD) is associated with partial deletion of the subtelomeric D4Z4 repeat array on chromosome 4qter. This chromosomal rearrangement may result in regional chromatin relaxation and transcriptional deregulation of genes nearby. METHODS AND RESULTS Here we describe the isolation and characterisation of FRG2, a member of a chromosomally dispersed gene family, mapping only 37 kb proximal to the D4Z4 repeat array. Homology and motif searches yielded no clues to the function of the predicted protein. FRG2 expression is undetectable in all tissues tested except for differentiating myoblasts of FSHD patients, which display low, yet distinct levels of FRG2 expression, partly from chromosome 4 but predominantly originating from its homologue on chromosome 10. However, in non-FSHD myopathy patients only distantly related FRG2 homologues are transcribed, while differentiating myoblasts from healthy controls fail to express any member of this gene family. Moreover, fibroblasts of FSHD patients and control individuals undergoing forced Ad5-MyoD mediated myogenesis show expression of FRG2 mainly originating from chromosome 10. Luciferase reporter assays show that the FRG2 promoter region can direct high levels of expression but is inhibited by increasing numbers of D4Z4 repeat units. Transient transfection experiments with FRG2 fusion-protein constructs reveal nuclear localisation and apparently FRG2 overexpression causes a wide range of morphological changes. CONCLUSION The localisation of FRG2 genes close to the D4Z4 repeats on chromosome 4 and 10, their transcriptional upregulation specifically in FSHD myoblast cultures, potential involvement in myogenesis, and promoter properties qualify FRG2 as an attractive candidate for FSHD pathogenesis.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cell Differentiation
- Cells, Cultured
- Chromosomes, Human, Pair 10/genetics
- Chromosomes, Human, Pair 4/genetics
- Female
- Genetic Predisposition to Disease
- Humans
- Male
- Molecular Sequence Data
- Muscle Development
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Myoblasts, Skeletal/chemistry
- Myoblasts, Skeletal/cytology
- Myoblasts, Skeletal/metabolism
- Nuclear Proteins
- Promoter Regions, Genetic
- Proteins/analysis
- Proteins/genetics
- Proteins/metabolism
- Transcriptional Activation
- Up-Regulation
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Affiliation(s)
- T Rijkers
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
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15
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van der Maarel SM, Frants RR. The D4Z4 repeat-mediated pathogenesis of facioscapulohumeral muscular dystrophy. Am J Hum Genet 2005; 76:375-86. [PMID: 15674778 PMCID: PMC1196390 DOI: 10.1086/428361] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Indexed: 01/19/2023] Open
Affiliation(s)
- Silvère M van der Maarel
- Leiden University Medical Center, Center for Human and Clinical Genetics, Leiden, The Netherlands.
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16
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Monajembashi S, Rapp A, Schmitt E, Dittmar H, Greulich KO, Hausmann M. Spatial association of homologous pericentric regions in human lymphocyte nuclei during repair. Biophys J 2004; 88:2309-22. [PMID: 15626712 PMCID: PMC1305280 DOI: 10.1529/biophysj.104.048728] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Spatial positioning of pericentric chromosome regions in human lymphocyte cell nuclei was investigated during repair after H(2)O(2)/L-histidine treatment. Fifteen to three-hundred minutes after treatment, these regions of chromosomes 1, 15, and X were labeled by fluorescence in situ hybridization. The relative locus distances (LL-distances), the relative distances to the nuclear center (LC-distances), and the locus-nuclear center-locus angles (LCL-angles) were measured in approximately 5000 nuclei after two-dimensional microscopy. Experimental frequency histograms were compared to control data from untreated stimulated and quiescent (G(0)) nuclei and to a theoretical two-dimensional projection from random points. Based on the frequency distributions of the LL-distances and the LCL-angles, an increase of closely associated labeled regions was found shortly after repair activation. For longer repair times this effect decreased. After 300 min the frequency distribution of the LL-distances was found to be compatible with the random distance distribution again. The LL-distance frequency histograms for quiescent nuclei did not significantly differ from the theoretical random distribution, although this was the case for the stimulated control of chromosomes 15 and X. It may be inferred that, concerning the distances, homologous pericentric regions appear not to be randomly distributed during S-phase, and are subjected to dynamic processes during replication and repair.
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Affiliation(s)
- Shamci Monajembashi
- Department of Single Cell and Single Molecule Techniques, Institute of Molecular Biotechnology, Beutenbergstrasse 11, D-07745Jena, Germany.
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17
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Tam R, Smith KP, Lawrence JB. The 4q subtelomere harboring the FSHD locus is specifically anchored with peripheral heterochromatin unlike most human telomeres. ACTA ACUST UNITED AC 2004; 167:269-79. [PMID: 15504910 PMCID: PMC2172553 DOI: 10.1083/jcb.200403128] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This paper investigates the nuclear localization of human telomeres and, specifically, the 4q35 subtelomere mutated in facioscapulohumeral dystrophy (FSHD). FSHD is a common muscular dystrophy that has been linked to contraction of D4Z4 tandem repeats, widely postulated to affect distant gene expression. Most human telomeres, such as 17q and 17p, avoid the nuclear periphery to reside within the internal, euchromatic compartment. In contrast, 4q35 localizes at the peripheral heterochromatin with 4p more internal, generating a reproducible chromosome orientation that we relate to gene expression profiles. Studies of hybrid and translocation cell lines indicate this localization is inherent to the distal tip of 4q. Investigation of heterozygous FSHD myoblasts demonstrated no significant displacement of the mutant allele from the nuclear periphery. However, consistent association of the pathogenic D4Z4 locus with the heterochromatic compartment supports a potential role in regulating the heterochromatic state and makes a telomere positioning effect more likely. Furthermore, D4Z4 repeats on other chromosomes also frequently organize with the heterochromatic compartment at the nuclear or nucleolar periphery, demonstrating a commonality among chromosomes harboring this subtelomere repeat family.
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Affiliation(s)
- Rose Tam
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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18
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Daniel A, St Heaps L. Chromosome loops arising from intrachromosomal tethering of telomeres occur at high frequency in G1 (non-cycling) mitotic cells: Implications for telomere capture. CELL & CHROMOSOME 2004; 3:3. [PMID: 15453908 PMCID: PMC521695 DOI: 10.1186/1475-9268-3-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Accepted: 09/29/2004] [Indexed: 12/01/2022]
Abstract
Background To investigate potential mechanisms for telomere capture the spatial arrangement of telomeres and chromosomes was examined in G1 (non-cycling) mitotic cells with diploid or triploid genomes. This was examined firstly by directly labelling the respective short arm (p) and long arm subtelomeres (q) with different fluorophores and probing cell preparations using a number of subtelomere probe pairs, those for chromosomes 1, 3, 4, 5, 6, 7, 9, 10, 12, 17, 18, and 20. In addition some interstitial probes (CEN15, PML and SNRPN on chromosome 15) and whole chromosome paint probes (e.g. WCP12) were jointly hybridised to investigate the co-localization of interphase chromosome domains and tethered subtelomeres. Cells were prepared by omitting exposure to colcemid and hypotonic treatments. Results In these cells a specific interphase chromosome topology was detected. It was shown that the p and q telomeres of the each chromosome associate frequently (80% pairing) in an intrachromosomal manner, i.e. looped chromosomes with homologues usually widely spaced within the nucleus. This p-q tethering of the telomeres from the one chromosome was observed with large (chromosomes 3, 4, 5), medium sized (6, 7, 9, 10, 12), or small chromosomes (17, 18, 20). When triploid nuclei were probed there were three tetherings of p-q subtelomere signals representing the three widely separated looped chromosome homologues. The separate subtelomere pairings were shown to coincide with separate chromosome domains as defined by the WCP and interstitial probes. The 20% of apparently unpaired subtelomeric signals in diploid nuclei were partially documented to be pairings with the telomeres of other chromosomes. Conclusions A topology for telomeres was detected where looped chromosome homologues were present at G1 interphase. These homologues were spatially arranged with respect to one-another independently of other chromosomes, i.e. there was no chromosome order on different sides of the cell nuclei and no segregation into haploid sets was detected. The normal function of this high frequency of intrachromosomal loops is unknown but a potential role is likely in the genesis of telomere captures whether of the intrachromosomal type or between non-homologues. This intrachromosomal tethering of telomeres cannot be related to telomeric or subtelomeric sequences since these are shared in varying degree with other chromosomes. In our view, these intrachromosomal telomeric tetherings with the resulting looped chromosomes arranged in a regular topology must be important to normal cell function since non-cycling cells in G1 are far from quiescent, are in fact metabolically active, and these cells represent the majority status since only a small proportion of cells are normally dividing.
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Affiliation(s)
- Art Daniel
- Department of Cytogenetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW 2145, Australia
| | - Luke St Heaps
- Department of Cytogenetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW 2145, Australia
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19
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Abdel-Halim HI, Imam SA, Badr FM, Natarajan AT, Mullenders LHF, Boei JJWA. Ionizing radiation-induced instant pairing of heterochromatin of homologous chromosomes in human cells. Cytogenet Genome Res 2004; 104:193-9. [PMID: 15162037 DOI: 10.1159/000077488] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Accepted: 11/25/2003] [Indexed: 11/19/2022] Open
Abstract
Using fluorescence in situ hybridization with human band-specific DNA probes we examined the effect of ionizing radiation on the intra-nuclear localization of the heterochromatic region 9q12-->q13 and the euchromatic region 8p11.2 of similar sized chromosomes 9 and 8 respectively in confluent (G1) primary human fibroblasts. Microscopic analysis of the interphase nuclei revealed colocalization of the homologous heterochromatic regions from chromosome 9 in a proportion of cells directly after exposure to 4 Gy X-rays. The percentage of cells with paired chromosomes 9 gradually decreased to control levels during a period of one hour. No significant changes in localization were observed for chromosome 8. Using 2-D image analysis, radial and inter-homologue distances were measured for both chromosome bands. In unexposed cells, a random distribution of the chromosomes over the interphase nucleus was found. Directly after irradiation, the average inter-homologue distance decreased for chromosome 9 without alterations in radial distribution. The percentage of cells with inter-homologue distance <3 micro m increased from 11% in control cells to 25% in irradiated cells. In contrast, irradiation did not result in significant changes in the inter-homologue distance for chromosome 8. Colocalization of the heterochromatic regions of homologous chromosomes 9 was not observed in cells irradiated on ice. This observation, together with the time dependency of the colocalization, suggests an underlying active cellular process. The biological relevance of the observed homologous pairing remains unclear. It might be related to a homology dependent repair process of ionizing radiation induced DNA damage that is specific for heterochromatin. However, also other more general cellular responses to radiation-induced stress or change in chromatin organization might be responsible for the observed pairing of heterochromatic regions.
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MESH Headings
- Adult
- Cell Nucleus/ultrastructure
- Cells, Cultured/radiation effects
- Cells, Cultured/ultrastructure
- Chromosome Banding
- Chromosomes, Human, Pair 8/radiation effects
- Chromosomes, Human, Pair 8/ultrastructure
- Chromosomes, Human, Pair 9/radiation effects
- Chromosomes, Human, Pair 9/ultrastructure
- Cold Temperature
- DNA Damage
- Fibroblasts/radiation effects
- Fibroblasts/ultrastructure
- Heterochromatin/radiation effects
- Humans
- Image Processing, Computer-Assisted
- In Situ Hybridization, Fluorescence
- Interphase
- Sequence Homology, Nucleic Acid
- Skin/cytology
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Affiliation(s)
- H I Abdel-Halim
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
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20
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Bickmore WA, van der Maarel SM. Perturbations of chromatin structure in human genetic disease: recent advances. Hum Mol Genet 2003; 12 Spec No 2:R207-13. [PMID: 12915455 DOI: 10.1093/hmg/ddg260] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gene expression studies in mammals and simpler eukaryotes have highlighted the central role that chromatin structure and modifications play in both the activation and repression of transcription. Aberrant chromatin structure can cause human genetic disease. Here we discuss recent progress in understanding the molecular mechanisms that underlie three human genetic diseases linked to perturbations of chromatin structure: ICF syndrome, facioscapulohumeral muscular dystrophy and a case of alpha-thalassaemia.
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21
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Loidl J. Chromosomes of the budding yeast Saccharomyces cerevisiae. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 222:141-96. [PMID: 12503849 DOI: 10.1016/s0074-7696(02)22014-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mitotic chromosomes of the baker's yeast, Saccharomyces cerevisiae, cannot be visualized by standard cytological methods. Only the study of meiotic bivalents and the synaptonemal complex and the visualization of chromosome-sized DNA molecules on pulsed-field gels have provided some insight into chromosome structure and behavior. More recently, advanced techniques such as in situ hybridization, the illumination of chromosomal loci by GFP-tagged DNA-binding proteins, and immunostaining of chromosomal proteins have promoted our knowledge about yeast chromosomes. These novel cytological approaches in combination with the yeast's advanced biochemistry and genetics have produced a great wealth of information on the interplay between molecular and cytological processes and have strengthened the role of yeast as a leading cell biological model organism. Recent cytological studies have revealed much about the chromosomal organization in interphase nuclei and have contributed significantly to our current understanding of chromosome condensation, sister chromatid cohesion, and centromere orientation in mitosis. Moreover, important details about the biochemistry and ultrastructure of meiotic pairing and recombination have been revealed by combined cytological and molecular approaches. This article covers several aspects of yeast chromosome structure, including their organization within interphase nuclei and their behavior during mitosis and meiosis.
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Affiliation(s)
- Josef Loidl
- Institute of Botany, University of Vienna, A-1030 Vienna, Austria
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22
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Mahy NL, Perry PE, Bickmore WA. Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 2002; 159:753-63. [PMID: 12473685 PMCID: PMC2173389 DOI: 10.1083/jcb.200207115] [Citation(s) in RCA: 219] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genes can be transcribed from within chromosome territories; however, the major histocompatibilty complex locus has been reported extending away from chromosome territories, and the incidence of this correlates with transcription from the region. A similar result has been seen for the epidermal differentiation complex region of chromosome 1. These data suggested that chromatin decondensation away from the surface of chromosome territories may result from, and/or may facilitate, transcription of densely packed genes subject to coordinate regulation.To investigate whether localization outside of the visible confines of chromosome territories can also occur for regions that are not coordinately regulated, we have examined the spatial organization of human 11p15.5 and the syntenic region on mouse chromosome 7. This region is gene rich but its genes are not coordinately expressed, rather overall high levels of transcription occur in several cell types. We found that chromatin from 11p15.5 frequently extends away from the chromosome 11 territory. Localization outside of territories was also detected for other regions of high gene density and high levels of transcription. This is shown to be partly dependent on ongoing transcription. We suggest that local gene density and transcription, rather than the activity of individual genes, influences the organization of chromosomes in the nucleus.
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MESH Headings
- Animals
- Cell Nucleus/drug effects
- Cell Nucleus/genetics
- Cells, Cultured
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin/metabolism
- Chromosome Painting
- Chromosomes, Artificial, P1 Bacteriophage/genetics
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 11/metabolism
- Chromosomes, Mammalian/genetics
- Chromosomes, Mammalian/metabolism
- Cosmids/genetics
- DNA/genetics
- DNA/metabolism
- Dactinomycin/pharmacology
- Dichlororibofuranosylbenzimidazole/pharmacology
- Fibroblasts/cytology
- Fibroblasts/drug effects
- Fibroblasts/metabolism
- Genes
- Genetic Markers
- Genome, Human
- Humans
- In Situ Hybridization, Fluorescence/methods
- Lymphocyte Activation
- Lymphocytes/cytology
- Lymphocytes/drug effects
- Lymphocytes/metabolism
- Mice
- Nucleic Acid Synthesis Inhibitors/pharmacology
- Physical Chromosome Mapping
- Synteny
- Telomere/chemistry
- Transcription, Genetic
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23
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Pettenati MJ, Jackle B, Bobby P, Stewart W, Von Kap-Herr C, Mowrey P, Rao PN, May KM. Unexpected retention and concomitant loss of subtelomeric regions in balanced chromosome anomalies by FISH. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 111:48-53. [PMID: 12124733 DOI: 10.1002/ajmg.10535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Florescence in situ hybridization (FISH) using subtelomeric probes has been useful in detecting cryptic telomeric chromosomal rearrangements. We report, for the first time, that cytogenetically visible chromosome rearrangements can occur between the subtelomeric and telomeric region in clinically normal individuals with balanced chromosome anomalies in which one of the breakpoints involves a terminal band region. Using FISH with subtelomeric probes, we observed in three cases with a balanced reciprocal translocations the retention and subsequent loss of subtelomeric regions. In one case with a paracentric inversion, there was a proximal relocation of a subtelomeric region. Because subtelomeric regions serve important roles in chromosome pairing, this retention and concomitant loss or relocation of a subtelomeric region could possibly further disrupt the complex meiotic configurations of these balanced chromosome rearrangements. This may then have an effect on gamete production, placing these individuals at a higher risk for miscarriages and/or abnormal outcomes for individuals with similar chromosome aberrations.
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Affiliation(s)
- Mark J Pettenati
- Department of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA.
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24
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Abstract
Subtelomeres are extraordinarily dynamic and variable regions near the ends of chromosomes. They are defined by their unusual structure: patchworks of blocks that are duplicated near the ends of multiple chromosomes. Duplications among subtelomeres have spawned small gene families, making inter-individual variation in subtelomeres a potential source of phenotypic diversity. The ectopic recombination that occurs between subtelomeres might also have a role in reconstituting telomeres in the absence of telomerase. However, the propensity for subtelomeres to interchange is a double-edged sword, as extensive subtelomeric homology can mediate deleterious rearrangements of the ends of chromosomes to cause human disease.
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Affiliation(s)
- Heather C Mefford
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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25
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Dunham MA, Neumann AA, Fasching CL, Reddel RR. Telomere maintenance by recombination in human cells. Nat Genet 2000; 26:447-50. [PMID: 11101843 DOI: 10.1038/82586] [Citation(s) in RCA: 624] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Telomeres of eukaryotic chromosomes contain many tandem repeats of a G-rich sequence (for example, TTAGGG in vertebrates). In most normal human cells, telomeres shorten with each cell division, and it is proposed that this limits the number of times these cells can replicate. Telomeres may be maintained in germline cells, and in many immortalized cells and cancers, by the telomerase holoenzyme (first discovered in the ciliate Tetrahymena), which uses an RNA subunit as template for synthesis of telomeric DNA by the reverse transcriptase catalytic subunit. Some immortalized human cell lines and some tumours maintain their telomeres in the absence of any detectable telomerase activity by a mechanism referred to as alternative lengthening of telomeres (ALT). Here we show that DNA sequences are copied from telomere to telomere in an immortalized human ALT cell line, indicating that ALT occurs by means of homologous recombination and copy switching.
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Affiliation(s)
- M A Dunham
- Cancer Research Unit, Children's Medical Research Institute, Westmead, Sydney, Australia
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