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Sullivan LL, Maloney KA, Towers AJ, Gregory SG, Sullivan BA. Human centromere repositioning within euchromatin after partial chromosome deletion. Chromosome Res 2016; 24:451-466. [PMID: 27581771 DOI: 10.1007/s10577-016-9536-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
Centromeres are defined by a specialized chromatin organization that includes nucleosomes that contain the centromeric histone variant centromere protein A (CENP-A) instead of canonical histone H3. Studies in various organisms have shown that centromeric chromatin (i.e., CENP-A chromatin or centrochromatin) exhibits plasticity, in that it can assemble on different types of DNA sequences. However, once established on a chromosome, the centromere is maintained at the same position. In humans, this location is the highly homogeneous repetitive DNA alpha satellite. Mislocalization of centromeric chromatin to atypical locations can lead to genome instability, indicating that restriction of centromeres to a distinct genomic position is important for cell and organism viability. Here, we describe a rearrangement of Homo sapiens chromosome 17 (HSA17) that has placed alpha satellite DNA next to euchromatin. We show that on this mutant chromosome, CENP-A chromatin has spread from the alpha satellite into the short arm of HSA17, establishing a ∼700 kb hybrid centromeric domain that spans both repetitive and unique sequences and changes the expression of at least one gene over which it spreads. Our results illustrate the plasticity of human centromeric chromatin and suggest that heterochromatin normally constrains CENP-A chromatin onto alpha satellite DNA. This work highlights that chromosome rearrangements, particularly those that remove the pericentromere, create opportunities for centromeric nucleosomes to move into non-traditional genomic locations, potentially changing the surrounding chromatin environment and altering gene expression.
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Affiliation(s)
- Lori L Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, DUMC 3054, Durham, NC, 27710, USA
| | - Kristin A Maloney
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, DUMC 3054, Durham, NC, 27710, USA.,Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Aaron J Towers
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, 27710, USA.,Quintiles, 4820 Emperor Blvd., Durham, NC, 27703, USA
| | - Simon G Gregory
- Department of Medicine, Duke Molecular Physiology Institute, 300 N. Duke Street, Durham, NC, 27701, USA.,Division of Human Genetics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, DUMC 3054, Durham, NC, 27710, USA. .,Quintiles, 4820 Emperor Blvd., Durham, NC, 27703, USA.
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Aldrup-MacDonald ME, Kuo ME, Sullivan LL, Chew K, Sullivan BA. Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles. Genome Res 2016; 26:1301-1311. [PMID: 27510565 PMCID: PMC5052062 DOI: 10.1101/gr.206706.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/08/2016] [Indexed: 01/27/2023]
Abstract
Alpha satellite is a tandemly organized type of repetitive DNA that comprises 5% of the genome and is found at all human centromeres. A defined number of 171-bp monomers are organized into chromosome-specific higher-order repeats (HORs) that are reiterated thousands of times. At least half of all human chromosomes have two or more distinct HOR alpha satellite arrays within their centromere regions. We previously showed that the two alpha satellite arrays of Homo sapiens Chromosome 17 (HSA17), D17Z1 and D17Z1-B, behave as centromeric epialleles, that is, the centromere, defined by chromatin containing the centromeric histone variant CENPA and recruitment of other centromere proteins, can form at either D17Z1 or D17Z1-B. Some individuals in the human population are functional heterozygotes in that D17Z1 is the active centromere on one homolog and D17Z1-B is active on the other. In this study, we aimed to understand the molecular basis for how centromere location is determined on HSA17. Specifically, we focused on D17Z1 genomic variation as a driver of epiallele formation. We found that D17Z1 arrays that are predominantly composed of HOR size and sequence variants were functionally less competent. They either recruited decreased amounts of the centromere-specific histone variant CENPA and the HSA17 was mitotically unstable, or alternatively, the centromere was assembled at D17Z1-B and the HSA17 was stable. Our study demonstrates that genomic variation within highly repetitive, noncoding DNA of human centromere regions has a pronounced impact on genome stability and basic chromosomal function.
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Affiliation(s)
- Megan E Aldrup-MacDonald
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Molly E Kuo
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Lori L Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Kimberline Chew
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; Division of Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
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Storlazzi CT, Albano F, Dencić-Fekete M, Djordjević V, Rocchi M. Late-appearing pseudocentric fission event during chronic myeloid leukemia progression. ACTA ACUST UNITED AC 2007; 174:61-7. [PMID: 17350469 DOI: 10.1016/j.cancergencyto.2006.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 11/13/2006] [Accepted: 11/21/2006] [Indexed: 11/28/2022]
Abstract
Pseudocentric fission is a rare event consisting of the splitting of one functional centromere into two new products, of which only one can give rise to a functionally competent kinetochore. We report here a pseudocentric fission event within the D5Z2 alphoid subset disrupting the centromeric region of chromosome 5 in a case of chronic myeloid leukemia (CML) after treatment with imatinib and interferon. The breakage generated unequal partitioning of alpha-satellite sequences between the two fission products. One product was inserted within the long arm of chromosome 12 at band 14.3, becoming the only functional centromere of chromosome der(5). The other fission product was rearranged to form a sandwich-like dicentric--but functionally monocentric--chromosome der(6), made up of material from chromosomes 5, 12, and 6. The intercentric distance on der(6) was shown to be largely >20 Mb. To our knowledge, this is the first pseudocentric fission event described in CML. Moreover, our results confirm the susceptibility to breakage of the centromeric region of chromosome 5.
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Affiliation(s)
- Clelia Tiziana Storlazzi
- Department of Genetics and Microbiology, University of Bari, Via Amendola 165/A, 70126 Bari, Italy.
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Rudd MK, Schueler MG, Willard HF. Sequence organization and functional annotation of human centromeres. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 68:141-9. [PMID: 15338612 DOI: 10.1101/sqb.2003.68.141] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- M K Rudd
- Institute for Genome Sciences & Policy, Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, USA
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Zahed L, Oreibi G, Azar C, Salti I. Ring chromosome 18q and jumping translocation 18p in an adult male with hypergonadotrophic hypogonadism. ACTA ACUST UNITED AC 2004; 129A:25-8. [PMID: 15266611 DOI: 10.1002/ajmg.a.30099] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Constitutional jumping translocations (JT) are rare, especially in phenotypically normal individuals. We report on an adult male with partial hypogonadism as the sole phenotypic abnormality with an unusual chromosome abnormality. In this patient, centric fission of chromosome 18 lead to formation of a ring 18q chromosome, while 18p formed a JT through centromere-telomere fusion with chromosome 8q (66%) or 20q (13%). In 21% of cells, the 18p fragment was missing. Fluorescent in situ hybridization revealed the presence of interstitial telomeres at the junction site of the fusion and unequal distribution of the alphoid sequences through the centric fission, leaving a small, yet functional centromere within the ring. We discuss the phenotype of the patient in light of this unusual karyotype.
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Affiliation(s)
- L Zahed
- Cytogenetics Laboratory, Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon.
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Podgornaya OI, Voronin AP, Enukashvily NI, Matveev IV, Lobov IB. Structure-specific DNA-binding proteins as the foundation for three-dimensional chromatin organization. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 224:227-96. [PMID: 12722952 DOI: 10.1016/s0074-7696(05)24006-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Any functions of tandem repetitive sequences need proteins that specifically bind to them. Telomere-binding TRF2/MTBP attaches telomeres to the nuclear envelope in interphase due to its rod-domain-like motif. Interphase nuclei organized as a number of sponge-like ruffly round chromosome territories that could be rotated from outside. SAF-A/hnRNP-U and p68-helicase are proteins suitable to do that. Their location in the interchromosome territory space, ATPase domains, and the ability to be bound by satellite DNAs (satDNA) make them part of the wires used to help chromosome territory rotates. In case of active transcription p68-helicase can be involved in the formation of local "gene expression matrices" and due to its satDNA-binding specificity cause the rearrangement of the local chromosome territory. The marks of chromatin rearrangement, which have to be heritable, could be provided by SAF-A/hnRNP-U. During telophase unfolding the proper chromatin arrangement is restored according to these marks. The structural specificity of both proteins to the satDNAs provides a regulative but relatively stable mode of binding. The structural specificity of protein binding could help to find the "magic" centromeric sequence. With future investigations of proteins with the structural specificity of binding during early embryogenesis, when heterochromatin formation goes on, the molecular mechanisms of the "gene gating" hypothesis (Blobel, 1985) will be confirmed.
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Affiliation(s)
- O I Podgornaya
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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Sullivan BA, Blower MD, Karpen GH. Determining centromere identity: cyclical stories and forking paths. Nat Rev Genet 2001; 2:584-96. [PMID: 11483983 DOI: 10.1038/35084512] [Citation(s) in RCA: 238] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The centromere is the genetic locus required for chromosome segregation. It is the site of spindle attachment to the chromosomes and is crucial for the transfer of genetic information between cell and organismal generations. Although the centromere was first recognized more than 120 years ago, little is known about what determines its site(s) of activity, and how it contributes to kinetochore formation and spindle attachment. Recent work in this field has supported the hypothesis that most eukaryotic centromeres are determined epigenetically rather than by primary DNA sequence. Here, we review recent studies that have elucidated the organization and functions of centromeric chromatin, and evaluate present-day models for how centromere identity and propagation are determined.
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Affiliation(s)
- B A Sullivan
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, California 92037, USA
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Wang JCC, Mamunes P, Kou SY, Schmidt J, Mao R, Hsu WT. Centromeric dna break in a 10;16 reciprocal translocation associated with trisomy 16 confined placental mosaicism and maternal uniparental disomy for chromosome 16. ACTA ACUST UNITED AC 1998. [DOI: 10.1002/(sici)1096-8628(19981204)80:4<418::aid-ajmg22>3.0.co;2-c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Stavropoulou C, Mignon C, Delobel B, Moncla A, Depetris D, Croquette MF, Mattei MG. Severe phenotype resulting from an active ring X chromosome in a female with a complex karyotype: characterisation and replication study. J Med Genet 1998; 35:932-8. [PMID: 9832041 PMCID: PMC1051487 DOI: 10.1136/jmg.35.11.932] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
We report on the characterisation of a complex chromosome rearrangement, 46,X,del(Xq)/47,X,del(Xq),+r(X), in a female newborn with multiple malformations. Cytogenetic and molecular methods showed that the del(Xq) contains the XIST locus and is non-randomly inactivated in all metaphases. The tiny r(X) chromosome gave a positive FISH signal with UBE1, ZXDA, and MSN cosmid probes, but not with a XIST cosmid probe. Moreover, it has an active status, as shown by a very short (three hour) terminal BrdU pulse followed by fluorescent anti-BrdU antibody staining. The normal X is of paternal origin and both rearranged chromosomes originate from the same maternal chromosome. We suggest that both abnormal chromosomes result from the three point breakage of a maternal isodicentric idic(X)(q21.1). Finally, the phenotype of our patient is compared to other published cases and, despite the absence of any 45,X clone, it appears very similar to those with a 45,X/46,X,r(X) karyotype where the tiny r(X) is active.
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Affiliation(s)
- C Stavropoulou
- INSERM U491, Faculté de Médecine Timone, Marseille, France
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Shepard W, Cruse WB, Fourme R, de la Fortelle E, Prangé T. A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution. Structure 1998; 6:849-61. [PMID: 9687367 DOI: 10.1016/s0969-2126(98)00087-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND The replication origin of the single-stranded (ss)DNA bacteriophage G4 has been proposed to fold into a hairpin loop containing the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs in conserved repetitive sequences of centromeric DNA. ssDNA analogues of these sequences often show exceptional stability which is associated with hairpin loops or unusual duplexes, and may be important in DNA replication and centromere function. Nuclear magnetic resonance (NMR) studies indicate that the GCGAAAGC sequence forms a hairpin loop in solution, while centromere-like repeats dimerise into unusual duplexes. The factors stabilising these unusual secondary structure elements in ssDNA, however, are poorly understood. RESULTS The nonamer d(GCGAAAGCT) was crystallised as a bromocytosine derivative in the presence of cobalt hexammine. The crystal structure, solved by the multiple wavelength anomalous dispersion (MAD) method at the bromine K-edge, reveals an unexpected zipper-like motif in the middle of a standard B-DNA duplex. Four central adenines, flanked by two sheared G.A mismatches, are intercalated and stacked on top of each other without any interstrand Watson-Crick base pairing. The cobalt hexammine cation appears to participate only in crystal cohesion. CONCLUSIONS The GAAA consensus sequence can dimerise into a stable zipper-like duplex as well as forming a hairpin loop. The arrangement closes the minor groove and exposes the intercalated, unpaired, adenines to the solvent and DNA-binding proteins. Such a motif, which can transform into a hairpin, should be considered as a structural option in modelling DNA and as a potential binding site, where it could have a role in DNA replication, nuclease resistance, ssDNA genome packaging and centromere function.
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Affiliation(s)
- W Shepard
- LURE, Université Paris-Sud, Orsay, France.
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Abstract
Successful construction of artificial chromosomes is an important step for studies to elucidate the DNA elements necessary for chromosome structure and function. A roadblock to developing a tractable system in multicellular organisms, including humans, is the poorly understood nature of centromeres. Progress, has been made in defining the satellite DNA that appears to contribute to the centromere in both humans and Drosophila and large arrays of alpha satellite DNA have been used to construct first-generation human artificial chromosomes. Non-satellite DNA sequences are also capable of forming 'neo-centromeres' under some circumstances, however, raising questions about the sequence-dependence of centromere and kinetochore assembly. Taken together with new information on the nature of protein components of the kinetochore, these data support a model in which functional kinetochores are assembled on centromeric chromatin, the competence of which is established epigenetically. The development of human artificial chromosome systems should facilitate investigation of the DNA and chromatin requirements for active centromere assembly.
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Affiliation(s)
- H F Willard
- Department of Genetics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.
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Fetni R, Richer CL, Malfoy B, Dutrillaux B, Lemieux N. Cytologic characterization of two distinct alpha satellite DNA domains on human chromosome 7, using double-labeling hybridizations in fluorescence and electron microscopy on a melanoma cell line. CANCER GENETICS AND CYTOGENETICS 1997; 96:17-22. [PMID: 9209464 DOI: 10.1016/s0165-4608(96)00282-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The most prominent class of centromeric DNA sequences belongs to the alpha satellite family of tandemly repeated DNA. The human chromosome 7 has been shown to contain two distinct alpha satellite arrays: D7Z1 and D7Z2, separated by 1 Mb. The order of these arrays was analyzed in normal blood cells and in the melanoma cell line IPC182 with two approaches using in situ hybridization: (1) Relative mapping on high-resolution chromosomes in fluorescence and electron microscopy (EM); and (2) simultaneous visualization of the two sequences using fluorochromes of different colors or gold particles of different sizes. The location within the centromeric area of chromosome 7, on the side of the short arm for D7Z2 and near the long arm for D7Z1 is confirmed. In addition, the hybridization signal of D7Z2 is confined to two small areas of the centromeric region in external positions, whereas the D7Z1 signal covers the entire width of the primary constriction. In situ hybridization with D7Z1 and D7Z2, performed on the melanoma cell line IPC 182, allowed characterization of two isochromosomes, i(7)(q10) and idic(7)(q11), as well as the der(7)t(7;12) observed in this cell line. The three-derived chromosomes appeared to result from different breakpoints, but only D7Z1 was conserved in all cases, suggesting the importance of this sequence for the centromeric function.
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Affiliation(s)
- R Fetni
- Département de Pathologie, Faculté de Médecine, Université de Montréal, Québec, Canada
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Schuffenhauer S, Kobelt A, Daumer-Haas C, Löffler C, Müller G, Murken J, Meitinger T. Interstitial deletion 5p accompanied by dicentric ring formation of the deleted segment resulting in trisomy 5p13-cen. AMERICAN JOURNAL OF MEDICAL GENETICS 1996; 65:56-9. [PMID: 8914742 DOI: 10.1002/(sici)1096-8628(19961002)65:1<56::aid-ajmg9>3.0.co;2-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Karyotypes with an interstitial deletion and a marker chromosome formed from the deleted segment are rare. We identified such a rearrangement in a newborn infant, who presented with macrocephaly, asymmetric square skull, minor facial anomalies, omphalocele, inguinal hernias, hypospadias, and club feet. The karyotype 46,XY,del(5) (pter --> p13::cen --> qter)/47,XY,+dicr(5)(:p13 --> cen::p13 --> cen), del(5)(pter --> p13::cen --> qter) was identified by banding studies and FISH analysis in the peripheral lymphocytes. One breakpoint on the del(5) maps distal to GDNF, and FISH analysis using an alpha-satellite probe suggests that the proximal breakpoint maps within the centromere. The dicentric r(5) consists of two copies of the segment deleted in the del(5), resulting in trisomy of proximal 5p (5p13-cen). The phenotype of the propositus is compared with other trisomy 5p cases and possible mechanisms for the generation of this unique chromosomal rearrangement are discussed.
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Affiliation(s)
- S Schuffenhauer
- Abteilung für Pädiatrische Genetik der Kinderpoliklinik, Ludwig-Maximilians-Universität München, Germany
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Qumsiyeh MB, Tomasi A, Taslimi M. Prenatal detection of short arm deletion and isochromosome 18 formation investigated by molecular techniques. J Med Genet 1995; 32:991-3. [PMID: 8825933 PMCID: PMC1051786 DOI: 10.1136/jmg.32.12.991] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A patient was referred for amniocentesis because of advanced maternal age and polyhydramnios. The fetal karyotype was a mosaic 46,XX,del(18)(p11.1)/46,XX,-18,+i(18q)de novo. The deletion appeared to encompass the whole short arm as evidenced by G banding and in situ hybridisation. However, telomere sequences were found on both ends of the deleted chromosome as well as the isochromosome. The normal 18 and the isochromosome showed more alphoid sequences than the del(18). Subsequent passages of the cell lines showed an increase in the frequency of the isochromosome from 20% to about 30%. Possible mechanisms are discussed.
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Affiliation(s)
- M B Qumsiyeh
- Cytogenetics Laboratory, Duke University Medical Center, Durham, NC 27710, USA
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Nath J, Tucker JD, Hando JC. Y chromosome aneuploidy, micronuclei, kinetochores and aging in men. Chromosoma 1995; 103:725-31. [PMID: 7664620 DOI: 10.1007/bf00344234] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This investigation was conducted to determine the relationship between Y chromosome loss and increased micronucleus formation with age. We also investigated the status of kinetochore proteins in the micronuclei. Umbilical cord blood samples were obtained from 18 newborn males, and peripheral blood was obtained from 35 adult males ranging in age from 22 to 79 years. Isolated lymphocytes from all 53 donors were cultured and blocked with cytochalasin B. Two thousand binucleate cells per donor were scored using a modified micronucleus assay to determine the kinetochore status of each micronucleus. This assay showed 23.8% of the micronuclei to be kinetochore-positive, while 76.2% of the micronuclei were kinetochore-negative. Cells were then hybridized with a 3.56-kb biotinylated Y chromosome-specific probe. All micronucleate cells were relocated and their Y probe status was determined. A significant increase in Y-bearing micronuclei with age was observed. Metaphase cells from the same samples were analyzed for the presence or absence of Y chromosome. The relationship between Y chromosome-positive micronuclei and Y chromosome-negative metaphase cells was highly significant, suggesting that Y chromosome-deficient metaphase cells result from cells which had previously lost a Y chromosome due to micronucleation. The cause of micronucleus formation from a lagging Y chromosome appears probably to be either a faulty or a diminished amount of kinetochore protein.
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Affiliation(s)
- J Nath
- Genetics and Developmental Biology Program, College of Agriculture and Forestry, West Virginia University, P.O. Box 6108, Morgantown, WV 26506-6108, USA
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Rajcan-Separovic E, Wang HS, Speevak MD, Janes L, Korneluk RG, Wakasa K, Ikeda JE. Identification of the origin of double minutes in normal human cells by laser-based chromosome microdissection approach. Hum Genet 1995; 96:39-43. [PMID: 7607652 DOI: 10.1007/bf00214184] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Single copies of tiny chromosome fragments, appearing as double minutes, were observed in a high proportion of cells from amniotic fluid cultures of two mothers undergoing prenatal testing because of advanced age. We applied a laser-based chromosome microdissection method to diagnose the origin of the double minutes. The diagnostic procedures consisted of microdissection of double minutes from a single cell, polymerase chain reaction (PCR) amplification of the dissected DNA, and subsequent fluorescence in situ hybridization (FISH) using the PCR products as a probe pool. Metaphase chromosomes from the patients' cells and from a karyotypically normal individual were probed. Using this strategy, we were able to determine that the double minutes originated from the centromere of chromosome 13 or 21 in one case, and from the chromosome 12 centromere in the other. The characterization of such double minutes helps both in the delineation of the nature of these epichromosomal bodies in normal individuals as well as in the clarification of genetic counselling issues.
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Affiliation(s)
- E Rajcan-Separovic
- GenoSPHERE Project, University of Ottawa, Faculty of Medicine, Ontario, Canada
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Tümer Z, Berg A, Mikkelsen M. Analysis of a whole arm translocation between chromosomes 18 and 20 using fluorescence in situ hybridization: detection of a break in the centromeric alpha-satellite sequences. Hum Genet 1995; 95:299-302. [PMID: 7868122 DOI: 10.1007/bf00225197] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Using classical cytogenetic techniques, we detected a male patient with monosomy 18p/trisomy 20p, originating from a paternal reciprocal translocation of the short arms of chromosomes 18 and 20. To characterize the breakpoints further and to determine the centromeric origin of the chromosomes involved, we analyzed the metaphase chromosomes by fluorescence in situ hybridization using alpha-satellite DNA probes specific to chromosomes 18 and 20. With this approach, we showed that alpha-satellite centromeric fragments were involved in the translocation event and that the chromosome-18-specific centromeric sequences were split into two. Analysis of 14 family members from four generations revealed nine phenotypically normal individuals carrying this reciprocal translocation. These results suggest that breaks in alpha-satellite DNA fragments neither impair the centromeric function nor have clinical effects.
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Affiliation(s)
- Z Tümer
- John F. Kennedy Institute, Glostrup, Denmark
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Gravholt CH, Caprani M, Friedrich U. Fluorescence in situ hybridization reveals a break in the alpha-satellite DNA of chromosome 1 in a family with a balanced whole-arm translocation. Hum Genet 1994; 94:504-8. [PMID: 7959684 DOI: 10.1007/bf00211015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have characterized a whole-arm translocation involving chromosomes 1 and 19 by traditional cytogenetic methods and fluorescence in situ hybridization with chromosome-specific alpha-satellite and whole-chromosome painting probes, and different satellite III DNA probes. We have identified a break in the alpha-satellite DNA region of chromosome 1, with division of this material into two alpha-satellite DNA blocks. This leaves one translocation chromosome with truncated alpha-satellite DNA from chromosome 1 and the other translocation chromosome with all the alpha-satellite DNA from chromosome 19 and truncated alpha-satellite DNA from chromosome 1. We speculate whether the recombination event observed has taken place in tetraplex structures of satellite III DNA interspersed between alpha-satellite DNA.
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Affiliation(s)
- C H Gravholt
- Department of Biological Psychiatry, Psychiatric Hospital in Aarhus, Risskov, Denmark
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20
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Abstract
The DNA sequences that are necessary for the formation of a functional mammalian chromosome are thought to be the origins of replication, the telomeres and the centromere. Telomere structure is now well understood, with the functional element characterized as the motif (TTAGGG)n. The structures of the DNA regions that contain origins of replication and a centromere are known, but the functionally important elements within these regions are still only poorly defined.
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Affiliation(s)
- C Tyler-Smith
- Department of Biochemistry, University of Oxford, UK
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21
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Wevrick R, Willard VP, Willard HF. Structure of DNA near long tandem arrays of alpha satellite DNA at the centromere of human chromosome 7. Genomics 1992; 14:912-23. [PMID: 1478672 DOI: 10.1016/s0888-7543(05)80112-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The centromeric regions of human chromosomes contain long tracts of tandemly repeated DNA, of which the most extensively characterized is alpha satellite. In a screen for additional centromeric DNA sequences, four phage clones were obtained which contain alpha satellite as well as other sequences not usually found associated with tandemly repeated alpha satellite DNA, including L1 repetitive elements, an Alu element, and a novel AT-rich repeated sequence. The alpha satellite DNA contained within these clones does not demonstrate the higher-order repeat structure typical of tandemly repeated alpha satellite. Two of the clones contain inversions; instead of the usual head-to-tail arrangement of alpha satellite monomers, the direction of the monomers changes partway through each clone. The presence of both inversions was confirmed in human genomic DNA by polymerase chain reaction amplification of the inverted regions. One phage clone contains a junction between alpha satellite DNA and a novel low-copy repeated sequence. The junction between the two types of DNA is abrupt and the junction sequence is characterized by the presence of runs of A's and T's, yielding an overall base composition of 65% AT with local areas > 80% AT. The AT-rich sequence is found in multiple copies on chromosome 7 and homologous sequences are found in (peri)centromeric locations on other human chromosomes, including chromosomes 1, 2, and 16. As such, the AT-rich sequence adjacent to alpha satellite DNA provides a tool for the further study of the DNA from this region of the chromosome. The phage clones examined are located within the same 3.3-Mb SstII restriction fragment on chromosome 7 as the two previously described alpha satellite arrays, D7Z1 and D7Z2. These new clones demonstrate that centromeric repetitive DNA, at least on chromosome 7, may be more heterogeneous in composition and organization than had previously been thought.
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Affiliation(s)
- R Wevrick
- Department of Genetics, Stanford University, California 94305
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22
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Mah DC, Shihab-el-Deen A, Price GB, Zannis-Hadjopoulos M. ORS12, a mammalian autonomously replicating DNA sequence, is present at the centromere of CV-1 cell chromosomes. Exp Cell Res 1992; 203:435-42. [PMID: 1459204 DOI: 10.1016/0014-4827(92)90018-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
ors12, an 812-bp-long sequence, previously isolated by extrusion of nascent DNA from replication bubbles active at the onset of S phase (G. Kaufmann, M. Zannis-Hadzopoulus, and R. G. Martin Mol. Cell. Biol. 5, 721-727, 1985), has been shown to function as an origin of DNA replication in autonomously replicating plasmids (L. Frappier and M. Zannis-Hadjopoulos Proc. Natl. Acad. Sci. USA 84, 6668-6672, 1987) and in a cell-free system (C. E. Pearson, L. Frappier, and M. Zannis-Hadzopoulos Biochim. Biophys. Acta 1090, 156-166, 1991). A portion of ors12 (nucleotides 1-168) consists of the highly reiterated alpha-satellite sequence (B. S. Rao et al. Gene 87, 233-242, 1990). We have estimated the copy number of the non-alpha-satellite portion of ors12 in CV-1 cells to be < 9 copies per haploid genome and have used it as a probe to generate a genomic map of ors12 on CV-1 DNA. In situ hybridization of CV-1 metaphase chromosomes, using a biotinylated probe of the entire ors12 sequence, positively identified the centromeres of all chromosomes. However, when the non-alpha-satellite portion of ors12 was used as a probe, it positively identified the centromeric region of only six chromosomes, namely, B4, C11, D14, D24, E25, and E27, as well as that of a marker chromosome. The results suggest that ors12 represents a centromeric putative replication origin that is present on a subset of CV-1 chromosomes and is activated at the onset of S phase.
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Affiliation(s)
- D C Mah
- McGill Cancer Centre, Department of Medicine, McGill University, Montréal Québec, Canada
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23
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Gray JW, Kallioniemi A, Kallioniemi O, Pallavicini M, Waldman F, Pinkel D. Molecular cytogenetics: Diagnosis and prognostic assessment. Curr Opin Biotechnol 1992; 3:623-31. [PMID: 1369118 DOI: 10.1016/0958-1669(92)90006-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This review describes molecular cytogenetic techniques for detection and characterization of genetic aberrations associated with human disease. The techniques of fluorescence in situ hybridization, primed in situ labeling and comparative genome hybridization are described, as are probes for repeated sequences, whole chromosomes and specific loci. Also reviewed are applications of these technologies to pre- and neonatal diagnosis and to the characterization of human malignancies.
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Affiliation(s)
- J W Gray
- Department of Laboratory Medicine, University of California, San Francisco 94143-0808
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24
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Cantú ES, Khan TA, Pai GS. Fluorescence in situ hybridization (FISH) of a whole-arm translocation involving chromosomes 18 and 20 with alpha-satellite DNA probes: detection of a centromeric DNA break? AMERICAN JOURNAL OF MEDICAL GENETICS 1992; 44:340-4. [PMID: 1488982 DOI: 10.1002/ajmg.1320440314] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Fluorescence in situ hybridization (FISH) with alpha-satellite DNA probes was used to study whole-arm chromosome translocation products in a family in which the propositus was shown to have a monosomy 18p/trisomy 20p imbalance. By this approach, we show that the chromosome 18 alpha-satellite DNA block is split into 2 smaller units, whereas the chromosome 20 breakpoint is not included within the alpha-satellite DNA region. We found no evidence to suggest that this split alpha-satellite DNA region has reduced or impaired the function of the centromere or that it contributed to the phenotype of the propositus. The FISH technique critically demonstrated the involvement of a whole-arm translocation in this case and provided accurate identification of breakpoints, which was not possible with standard banding techniques.
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MESH Headings
- Abnormalities, Multiple/genetics
- Centromere/ultrastructure
- Chromosomes, Human, Pair 18
- Chromosomes, Human, Pair 20
- DNA Probes
- DNA, Satellite
- Dosage Compensation, Genetic
- Face/abnormalities
- Failure to Thrive/genetics
- Heart Defects, Congenital/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Infant, Newborn
- Male
- Translocation, Genetic
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Affiliation(s)
- E S Cantú
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston 29425
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25
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Friedman JM, Harrod MJ, Howard-Peebles PN. Complementary duplication and deletion of 17 (pcen----p11.2): a family with a supernumerary chromosome comprised of an interstitially deleted segment. AMERICAN JOURNAL OF MEDICAL GENETICS 1992; 44:37-40. [PMID: 1519647 DOI: 10.1002/ajmg.1320440109] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A sister and brother were investigated because both were developmentally delayed although they had somewhat different physical anomalies. The girl was found to have an interstitial deletion of chromosome 17. Her karyotype was 46,XX,del(17) (pter----p11.2::cen----qter). Her brother had normal chromosomes in peripheral lymphocytes. Cytogenetic investigation of the mother showed the presence of the same deletion as in her daughter and a small supernumerary chromosome. The supernumerary chromosome appeared to contain the material deleted from the short arm of 17 since the mother's phenotype was normal. Study of skin fibroblasts in her son showed that he was mosaic for a normal cell line and one that contained the extra small chromosome; thus, he had mosaic partial trisomy 17(cen----p11.2). The origin of the centromere and telomere(s) of the small supernumerary chromosome in this family presents an interesting problem.
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Affiliation(s)
- J M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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26
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Abstract
Centromeres and telomeres are both composed of specific DNA sequences and unique chromosomal proteins. Isolation and characterization of some of these sequences and proteins has greatly increased our knowledge of centromere and telomere structure. This information is allowing us to determine how centromeres and telomeres perform their various roles in a cell.
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Affiliation(s)
- C M Price
- Department of Chemistry, University of Nebraska, Lincoln 68588
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27
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Greig GM, Willard HF. Beta satellite DNA: characterization and localization of two subfamilies from the distal and proximal short arms of the human acrocentric chromosomes. Genomics 1992; 12:573-80. [PMID: 1559708 DOI: 10.1016/0888-7543(92)90450-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
beta satellite is a repetitive DNA family that consists of approximately 68-bp monomers tandemly repeated in arrays of at least several hundred kilobases. In this report we describe and characterize two subfamilies located exclusively on the human acrocentric chromosomes. The first subfamily is defined by a homogeneous approximately 2.0-kb higher-order repeat unit and is located primarily distal to the ribosomal RNA gene cluster, based both on fluorescence in situ hybridization to metaphase chromosomes and on filter hybridization analysis of translocation chromosomes isolated in somatic cell hybrids. In contrast, the second subfamily is located both distal and proximal to the ribosomal RNA gene cluster on the same acrocentric chromosomes. The DNA sequences of a number of monomers from these two subfamilies are compared to each other and to other beta satellite monomers to assess both inter- and intrasubfamily sequence relationships for these monomers.
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Affiliation(s)
- G M Greig
- Department of Genetics, Stanford University, California 94305
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28
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Abstract
Alpha satellite is one of the most thoroughly studied repetitive DNA families and is a paradigm for understanding other satellite DNA and multigene families. Alpha satellite illustrates both intra- and interchromosomal modes of evolution. Recent advances in understanding the structure and evolution of human and other primate alpha satellites are summarized in this review.
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Affiliation(s)
- H F Willard
- Department of Genetics, Stanford University, California 94305
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29
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Imai HT. Mutability of constitutive heterochromatin (C-bands) during eukaryotic chromosomal evolution and their cytological meaning. IDENGAKU ZASSHI 1991; 66:635-61. [PMID: 1777253 DOI: 10.1266/jjg.66.635] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A quantitative analysis of the alterations of constitutive heterochromatin in eukaryotic chromosomal evolution was attempted using the accumulated C-banding data available for mammals, amphibians, fish, ants, grasshoppers, and plants. It was found that these eukaryotes could be classified into two types by their C-banding patterns: 1) Type I included mammals, fish, and ants, and 2) Type II included amphibians, grasshoppers, and plants. C-bands were rather scarce in Type I eukaryote chromosomes and were found around the pericentromeric region when present at all, whereas the predominance of interstitial or terminal C-bands was found in Type II eukaryote chromosomes. The Type I and II C-banding patterns can best be interpreted by assuming that in the former group of eukaryotes the saltatory increase in constitutive heterochromatin occurs preferentially at the pericentromeric regions of telocentric chromosomes induced by centric fission, with C-bands being eliminated almost completely by centric fusion and/or pericentric inversion. On the other hand, C-bands appear in the Type II eukaryotes both interstitially and in the telomeric regions of chromosomes, and there may be no effective mechanism to eliminate these bands once they are integrated.
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Affiliation(s)
- H T Imai
- National Institute of Genetics, Shizuoka-ken, Japan
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