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Glunčić M, Vlahović I, Rosandić M, Paar V. Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution. Life Sci Alliance 2022; 6:6/1/e202101306. [PMID: 36261226 PMCID: PMC9584774 DOI: 10.26508/lsa.202101306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
Previously it was found that the neuroblastoma breakpoint family (NBPF) gene repeat units of ∼1.6 kb have an important role in human brain evolution and function. The higher order organization of these repeat units has been discovered by both methods, the higher order repeat (HOR)-searching method and the HLS searching method. Using the HOR searching method with global repeat map algorithm, here we identified the tandemly organized NBPF HORs in the human and nonhuman primate NCBI reference genomes. We identified 50 tandemly organized canonical 3mer NBPF HOR copies (Olduvai triplets), but none in nonhuman primates chimpanzee, gorilla, orangutan, and Rhesus macaque. This discontinuous jump in tandemly organized HOR copy number is in sharp contrast to the known gradual increase in the number of Olduvai domains (NBPF monomers) from nonhuman primates to human, especially from ∼138 in chimpanzee to ∼300 in human genome. Using the same global repeat map algorithm method we have also determined the 3mer tandems of canonical 3mer HOR copies in 20 randomly chosen human genomes (10 male and 10 female). In all cases, we found the same 3mer HOR copy numbers as in the case of the reference human genome, with no mutation. On the other hand, some point mutations with respect to reference genome are found for some NBPF monomers which are not tandemly organized in canonical HORs.
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Affiliation(s)
- Matko Glunčić
- Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Marija Rosandić
- University Hospital Centre Zagreb (ret), Zagreb, Croatia,Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Vladimir Paar
- Faculty of Science, University of Zagreb, Zagreb, Croatia,Croatian Academy of Sciences and Arts, Zagreb, Croatia
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2
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Jeffery D, Lochhead M, Almouzni G. CENP-A: A Histone H3 Variant with Key Roles in Centromere Architecture in Healthy and Diseased States. Results Probl Cell Differ 2022; 70:221-261. [PMID: 36348109 DOI: 10.1007/978-3-031-06573-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Centromeres are key architectural components of chromosomes. Here, we examine their construction, maintenance, and functionality. Focusing on the mammalian centromere- specific histone H3 variant, CENP-A, we highlight its coevolution with both centromeric DNA and its chaperone, HJURP. We then consider CENP-A de novo deposition and the importance of centromeric DNA recently uncovered with the added value from new ultra-long-read sequencing. We next review how to ensure the maintenance of CENP-A at the centromere throughout the cell cycle. Finally, we discuss the impact of disrupting CENP-A regulation on cancer and cell fate.
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Affiliation(s)
- Daniel Jeffery
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Marina Lochhead
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Geneviève Almouzni
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France.
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3
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Suzuki Y, Morishita S. The time is ripe to investigate human centromeres by long-read sequencing†. DNA Res 2021; 28:6381569. [PMID: 34609504 PMCID: PMC8502840 DOI: 10.1093/dnares/dsab021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/28/2021] [Indexed: 01/05/2023] Open
Abstract
The complete sequencing of human centromeres, which are filled with highly repetitive elements, has long been challenging. In human centromeres, α-satellite monomers of about 171 bp in length are the basic repeating units, but α-satellite monomers constitute the higher-order repeat (HOR) units, and thousands of copies of highly homologous HOR units form large arrays, which have hampered sequence assembly of human centromeres. Because most HOR unit occurrences are covered by long reads of about 10 kb, the recent availability of much longer reads is expected to enable observation of individual HOR occurrences in terms of their single-nucleotide or structural variants. The time has come to examine the complete sequence of human centromeres.
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Affiliation(s)
- Yuta Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8568, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8568, Japan
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4
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Suzuki Y, Myers EW, Morishita S. Rapid and ongoing evolution of repetitive sequence structures in human centromeres. SCIENCE ADVANCES 2020; 6:6/50/eabd9230. [PMID: 33310858 PMCID: PMC7732198 DOI: 10.1126/sciadv.abd9230] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/30/2020] [Indexed: 06/12/2023]
Abstract
Our understanding of centromere sequence variation across human populations is limited by its extremely long nested repeat structures called higher-order repeats that are challenging to sequence. Here, we analyzed chromosomes 11, 17, and X using long-read sequencing data for 36 individuals from diverse populations including a Han Chinese trio and 21 Japanese. We revealed substantial structural diversity with many previously unidentified variant higher-order repeats specific to individuals characterizing rapid, haplotype-specific evolution of human centromeric arrays, while frequent single-nucleotide variants are largely conserved. We found a characteristic pattern shared among prevalent variants in human and chimpanzee. Our findings pave the way for studying sequence evolution in human and primate centromeres.
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Affiliation(s)
- Yuta Suzuki
- The University of Tokyo, Graduate School of Frontier Sciences, Department of Computational Biology and Medical Sciences, Kashiwa, Chiba 277-8568, Japan.
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Shinichi Morishita
- The University of Tokyo, Graduate School of Frontier Sciences, Department of Computational Biology and Medical Sciences, Kashiwa, Chiba 277-8568, Japan.
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5
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Discovery of 33mer in chromosome 21 - the largest alpha satellite higher order repeat unit among all human somatic chromosomes. Sci Rep 2019; 9:12629. [PMID: 31477765 PMCID: PMC6718397 DOI: 10.1038/s41598-019-49022-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 08/13/2019] [Indexed: 11/10/2022] Open
Abstract
The centromere is important for segregation of chromosomes during cell division in eukaryotes. Its destabilization results in chromosomal missegregation, aneuploidy, hallmarks of cancers and birth defects. In primate genomes centromeres contain tandem repeats of ~171 bp alpha satellite DNA, commonly organized into higher order repeats (HORs). In spite of crucial importance, satellites have been understudied because of gaps in sequencing - genomic “black holes”. Bioinformatical studies of genomic sequences open possibilities to revolutionize understanding of repetitive DNA datasets. Here, using robust (Global Repeat Map) algorithm we identified in hg38 sequence of human chromosome 21 complete ensemble of alpha satellite HORs with six long repeat units (≥20 mers), five of them novel. Novel 33mer HOR has the longest HOR unit identified so far among all somatic chromosomes and novel 23mer reverse HOR is distant far from the centromere. Also, we discovered that for hg38 assembly the 33mer sequences in chromosomes 21, 13, 14, and 22 are 100% identical but nearby gaps are present; that seems to require an additional more precise sequencing. Chromosome 21 is of significant interest for deciphering the molecular base of Down syndrome and of aneuploidies in general. Since the chromosome identifier probes are largely based on the detection of higher order alpha satellite repeats, distinctions between alpha satellite HORs in chromosomes 21 and 13 here identified might lead to a unique chromosome 21 probe in molecular cytogenetics, which would find utility in diagnostics. It is expected that its complete sequence analysis will have profound implications for understanding pathogenesis of diseases and development of new therapeutic approaches.
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6
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Kjeldsen E, Kallenbach M. Duplication of isodicentric chromosome 13, idic(13)(p11.2), leading to pentasomy 13q in acute myeloid leukemia without maturation. Cytogenet Genome Res 2013; 140:21-8. [PMID: 23615042 DOI: 10.1159/000350694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Isodicentric chromosome 13, idic(13)(p11.2), is a very rare chromosomal aberration in acute myeloid leukemia (AML). We describe here a novel case of AML without maturation, where the leukemic cells harbored double idic(13)(p11.2) and a normal chromosome 13 resulting in pentasomy 13q. Analyses were done on aspirated bone marrow cells from diagnosis. We utilized G-banding analysis, 24-color karyotyping and additional FISH analyses with various locus-specific probes to characterize the chromosomal complement. Oligonucleotide-based 180K aCGH analysis was done to search for submicroscopic imbalances. The karyotype was 47,XY,idic(13)(p11.2)x2[23]/46,XY[2]. Pantelomeric FISH analysis indicated critically short telomeres. Oligo-based aCGH analysis confirmed high copy gain of chromosome 13q and did not disclose other genomic imbalances. Reviewing the literature, this may be the second case of pentasomy 13q, since idic(13)(p11.2), when analyzed by conventional cytogenetics, is indistinguishable from i(13)(q10). Both cases were associated with immature AML and a poor outcome. We propose that idic(13)(p11.2) is a new recurrent abnormality in AML without maturation and suggest that pentasomy 13q is an early event in pathogenesis of AML through amplification of genes located on 13q.
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Affiliation(s)
- E Kjeldsen
- Cancer Cytogenetics Laboratory, Department of Hematology, Aarhus University Hospital, DK-8000 Aarhus, Denmark.
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7
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Rosandić M, Glunčić M, Paar V, Basar I. The role of alphoid higher order repeats (HORs) in the centromere folding. J Theor Biol 2008; 254:555-60. [DOI: 10.1016/j.jtbi.2008.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2007] [Revised: 05/13/2008] [Accepted: 06/06/2008] [Indexed: 10/21/2022]
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8
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Paar V, Basar I, Rosandić M, Glunčić M. Consensus higher order repeats and frequency of string distributions in human genome. Curr Genomics 2007; 8:93-111. [PMID: 18660848 PMCID: PMC2435359 DOI: 10.2174/138920207780368169] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 01/26/2007] [Accepted: 01/30/2007] [Indexed: 02/01/2023] Open
Abstract
Key string algorithm (KSA) could be viewed as robust computational generalization of restriction enzyme method. KSA enables robust and effective identification and structural analyzes of any given genomic sequences, like in the case of NCBI assembly for human genome. We have developed a method, using total frequency distribution of all r-bp key strings in dependence on the fragment length l, to determine the exact size of all repeats within the given genomic sequence, both of monomeric and HOR type. Subsequently, for particular fragment lengths equal to each of these repeat sizes we compute the partial frequency distribution of r-bp key strings; the key string with highest frequency is a dominant key string, optimal for segmentation of a given genomic sequence into repeat units. We illustrate how a wide class of 3-bp key strings leads to a key-string-dependent periodic cell which enables a simple identification and consensus length determinations of HORs, or any other highly convergent repeat of monomeric or HOR type, both tandem or dispersed. We illustrated KSA application for HORs in human genome and determined consensus HORs in the Build 35.1 assembly. In the next step we compute suprachromosomal family classification and CENP-B box / pJalpha distributions for HORs. In the case of less convergent repeats, like for example monomeric alpha satellite (20-40% divergence), we searched for optimal compact key string using frequency method and developed a concept of composite key string (GAAAC--CTTTG) or flexible relaxation (28 bp key string) which provides both monomeric alpha satellites as well as alpha monomer segmentation of internal HOR structure. This method is convenient also for study of R-strand (direct) / S-strand (reverse complement) alpha monomer alternations. Using KSA we identified 16 alternating regions of R-strand and S-strand monomers in one contig in choromosome 7. Use of CENP-B box and/or pJalpha motif as key string is suitable both for identification of HORs and monomeric pattern as well as for studies of CENP-B box / pJalpha distribution. As an example of application of KSA to sequences outside of HOR regions we present our finding of a tandem with highly convergent 3434-bp Long monomer in chromosome 5 (divergence less then 0.3%).
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Affiliation(s)
- Vladimir Paar
- Faculty of Science, University of Zagreb, Bijenička 32, 10000 Zagreb, Croatia
| | - Ivan Basar
- Faculty of Science, University of Zagreb, Bijenička 32, 10000 Zagreb, Croatia
| | - Marija Rosandić
- Department of Internal Medicine,
University Hospital Rebro, Kišpatićeva 12, 10000 Zagreb, Croatia
| | - Matko Glunčić
- Faculty of Science, University of Zagreb, Bijenička 32, 10000 Zagreb, Croatia
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9
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Babcock M, Yatsenko S, Stankiewicz P, Lupski JR, Morrow BE. AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12. Genome Res 2007; 17:451-60. [PMID: 17284672 PMCID: PMC1832092 DOI: 10.1101/gr.5651507] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Low copy repeats (LCRs; segmental duplications) constitute approximately 5% of the sequenced human genome. Nonallelic homologous recombination events between LCRs during meiosis can lead to chromosomal rearrangements responsible for many genomic disorders. The 22q11.2 region is susceptible to recurrent and nonrecurrent deletions, duplications as well as translocations that are mediated by LCRs termed LCR22s. One particular DNA structural element, a palindromic AT-rich repeat (PATRR) present within LCR22-3a, is responsible for translocations. Similar AT-rich repeats are present within the two largest LCR22s, LCR22-2 and LCR22-4. We provide direct sequence evidence that the AT-rich repeats have altered LCR22 organization during primate evolution. The AT-rich repeats are surrounded by a subtype of human satellite I (HSAT I), and an AluSc element, forming a 2.4-kb tripartite structure. Besides 22q11.2, FISH and PCR mapping localized the tripartite repeat within heterochromatic, unsequenced regions of the genome, including the pericentromeric regions of the acrocentric chromosomes and the heterochromatic portion of Yq12 in humans. The repeat is also present on autosomes but not on chromosome Y in other hominoid species, suggesting that it has duplicated on Yq12 after speciation of humans from its common ancestor. This demonstrates that AT-rich repeats have shaped or altered the structure of the genome during evolution.
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Affiliation(s)
- Melanie Babcock
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Svetlana Yatsenko
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Pawel Stankiewicz
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - James R. Lupski
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bernice E. Morrow
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Corresponding author.E-mail ; fax (718) 430-8778
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10
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Abstract
In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with alpha-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.
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Affiliation(s)
- Adolf Baumgartner
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, California, CA 94720, USA
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11
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Roizès G. Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning. Nucleic Acids Res 2006; 34:1912-24. [PMID: 16598075 PMCID: PMC1447651 DOI: 10.1093/nar/gkl137] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequence analysis of alphoid repeats from human chromosomes 17, 21 and 13 reveals recurrent diagnostic variant nucleotides. Their combinations define haplotypes, with higher order repeats (HORs) containing identical or closely-related haplotypes tandemly arranged into separate domains. The haplotypes found on homologues can be totally different, while HORs remain 99.8% homogeneous both intrachromosomally and between homologues. These results support the hypothesis, never before demonstrated, that unequal crossovers between sister chromatids accumulate to produce homogenization and amplification into tandem alphoid repeats. I propose that the molecular basis of this involves the diagnostic variant nucleotides, which enable pairing between HORs with identical or closely-related haplotypes. Domains are thus periodically renewed to maintain high intrachromosomal and interhomologue homogeneity. The capacity of a domain to form an active centromere is maintained as long as neither retrotransposons nor significant numbers of mutations affect it. In the presented model, a chromosome with an altered centromere can be transiently rescued by forming a neocentromere, until a restored, fully-competent domain is amplified de novo or rehomogenized through the accumulation of unequal crossovers.
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Affiliation(s)
- Gérard Roizès
- Institut de Génétique Humaine, UPR 1142, CNRS, 141 Rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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12
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Ando S, Yang H, Nozaki N, Okazaki T, Yoda K. CENP-A, -B, and -C chromatin complex that contains the I-type alpha-satellite array constitutes the prekinetochore in HeLa cells. Mol Cell Biol 2002; 22:2229-41. [PMID: 11884609 PMCID: PMC133672 DOI: 10.1128/mcb.22.7.2229-2241.2002] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CENP-A is a component of centromeric chromatin and defines active centromere regions by forming centromere-specific nucleosomes. We have isolated centromeric chromatin containing the CENP-A nucleosome, CENP-B, and CENP-C from HeLa cells using anti-CENP-A and/or anti-CENP-C antibodies and shown that the CENP-A/B/C complex is predominantly formed on alpha-satellite DNA that contains the CENP-B box (alphaI-type array). Mapping of hypersensitive sites for micrococcal nuclease (MNase) digestion indicated that CENP-A nucleosomes were phased on the alphaI-type array as a result of interactions between CENP-B and CENP-B boxes, implying a repetitive configuration for the CENP-B/CENP-A nucleosome complex. Molecular mass analysis by glycerol gradient sedimentation showed that MNase digestion released a CENP-A/B/C chromatin complex of three to four nucleosomes into the soluble fraction, suggesting that CENP-C is a component of the repetitive CENP-B/CENP-A nucleosome complex. Quantitative analysis by immunodepletion of CENP-A nucleosomes showed that most of the CENP-C and approximately half the CENP-B took part in formation of the CENP-A/B/C chromatin complex. A kinetic study of the solubilization of CENPs showed that MNase digestion first released the CENP-A/B/C chromatin complex into the soluble fraction, and later removed CENP-B and CENP-C from the complex. This result suggests that CENP-A nucleosomes form a complex with CENP-B and CENP-C through interaction with DNA. On the basis of these results, we propose that the CENP-A/B/C chromatin complex is selectively formed on the I-type alpha-satellite array and constitutes the prekinetochore in HeLa cells.
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Affiliation(s)
- Satoshi Ando
- Bioscience Center, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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13
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Pellestor F, Imbert I, Andréo B. Rapid chromosome detection by PRINS in human sperm. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 107:109-14. [PMID: 11807883 DOI: 10.1002/ajmg.10101] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Primed in situ (PRINS) labeling may be used for direct estimation of disomy rate in human sperm. We combined the PRINS procedure with a rapid and efficient NaOH pretreatment allowing simultaneous decondensation and denaturation of sperm nuclei. This enabled double labeling of human sperm within a 2-hr time span. Chromosome-specific primers have been defined for most human chromosomes, including those most frequently involved in aneuploidy. Using the dual-color PRINS method, we estimated incidences of disomy for 15 autosomes and the sex chromosomes in sperm samples from 6 normal fertile men. The frequency of disomy ranged from 0.28% to 0.36%. There were no significant interchromosomal differences in disomy rate, but chromosome 21 displayed a higher incidence of nondisjunction than did the other chromosomes.
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Affiliation(s)
- Franck Pellestor
- CNRS UPR 1142, Institute of Human Genetics, Montpellier, France.
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14
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Chinnappan D, Philip A, Wu X, Pan A, Wyandt HE. Acquired Robertsonian translocations in two leukemia patients. CANCER GENETICS AND CYTOGENETICS 2001; 131:104-8. [PMID: 11750049 DOI: 10.1016/s0165-4608(01)00478-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Robertsonian translocations were observed in two leukemia patients. The first case was a patient with chronic lymphocytic leukemia, who was found to have a rare Robertsonian translocation der(14;15)(q10;q10). The second case, a patient with acute myeloid leukemia, had multiple Robertsonian translocations: der(15)t(13;15)(q11.1;p11.1), der(14;22)(q10;q10), and dic(21;22)(p11.1;p11.1). Acquired multiple Robertsonian translocations have not been reported previously in leukemia.
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MESH Headings
- Acute Disease
- Aged
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 15
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Myeloid/genetics
- Male
- Middle Aged
- Translocation, Genetic
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Affiliation(s)
- D Chinnappan
- Department of Biochemistry, Boston University School of Medicine, 715 Albany Street, Boston, MA 02118, USA
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15
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Bandyopadhyay R, McQuillan C, Page SL, Choo KH, Shaffer LG. Identification and characterization of satellite III subfamilies to the acrocentric chromosomes. Chromosome Res 2001; 9:223-33. [PMID: 11330397 DOI: 10.1023/a:1016648404388] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The centromeres and the short arms of the five pairs of acrocentric chromosomes in humans are composed of tandemly ordered repetitive DNA. Previous studies have suggested that the exchanges between acrocentric chromosomes have resulted in concerted evolution of different DNA sequences in their short arms. The acrocentric chromosomes are clinically relevant since they are involved in Robertsonian translocation formation and non-disjunction resulting in aneuploidy. Here we have identified seven new satellite III repetitive DNA subfamilies, determined their nucleotide sequences and established their chromosomal distributions on the short arms of the acrocentric chromosomes. Knowledge of these related sequences may help to elucidate the molecular basis of Robertsonian translocation formation.
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Affiliation(s)
- R Bandyopadhyay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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16
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Lo AW, Craig JM, Saffery R, Kalitsis P, Irvine DV, Earle E, Magliano DJ, Choo K. A 330 kb CENP-A binding domain and altered replication timing at a human neocentromere. EMBO J 2001; 20:2087-96. [PMID: 11296241 PMCID: PMC125239 DOI: 10.1093/emboj/20.8.2087] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Centromere protein A (CENP-A) is an essential centromere-specific histone H3 homologue. Using combined chromatin immunoprecipitation and DNA array analysis, we have defined a 330 kb CENP-A binding domain of a 10q25.3 neocentromere found on the human marker chromosome mardel(10). This domain is situated adjacent to the 80 kb region identified previously as the neocentromere site through lower-resolution immunofluorescence/FISH analysis of metaphase chromosomes. The 330 kb CENP-A binding domain shows a depletion of histone H3, providing evidence for the replacement of histone H3 by CENP-A within centromere-specific nucleosomes. The DNA within this domain has a high AT-content comparable to that of alpha-satellite, a high prevalence of LINEs and tandem repeats, and fewer SINEs and potential genes than the surrounding region. FISH analysis indicates that the normal 10q25.3 genomic region replicates around mid-S phase. Neocentromere formation is accompanied by a replication time lag around but not within the CENP-A binding region, with this lag being significantly more prominent to one side. The availability of fully sequenced genomic markers makes human neocentromeres a powerful model for dissecting the functional domains of complex higher eukaryotic centromeres.
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Affiliation(s)
- Anthony W.I. Lo
- The Murdoch Childrens Research Institute, Royal Children’s Hospital, Flemington Road, Melbourne, Victoria 3052, Australia
Present address: Radiation Oncology Research Laboratory, University of California San Francisco, MCB 200, 1855 Folsom Street, San Francisco, CA 94103-0806, USA Corresponding author e-mail: A.W.I.Lo and J.M.Craig contributed equally to this work
| | | | | | | | | | | | | | - K.H.Andy Choo
- The Murdoch Childrens Research Institute, Royal Children’s Hospital, Flemington Road, Melbourne, Victoria 3052, Australia
Present address: Radiation Oncology Research Laboratory, University of California San Francisco, MCB 200, 1855 Folsom Street, San Francisco, CA 94103-0806, USA Corresponding author e-mail: A.W.I.Lo and J.M.Craig contributed equally to this work
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17
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Mashkova TD, Oparina NY, Lacroix MH, Fedorova LI, G Tumeneva I, Zinovieva OL, Kisselev LL. Structural rearrangements and insertions of dispersed elements in pericentromeric alpha satellites occur preferably at kinkable DNA sites. J Mol Biol 2001; 305:33-48. [PMID: 11114245 DOI: 10.1006/jmbi.2000.4270] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Centromeric region of human chromosome 21 comprises two long alphoid DNA arrays: the well homogenized and CENP-B box-rich alpha21-I and the alpha21-II, containing a set of less homogenized and CENP-B box-poor subfamilies located closer to the short arm of the chromosome. Continuous alphoid fragment of 100 monomers bordering the non-satellite sequences in human chromosome 21 was mapped to the pericentromeric short arm region by fluorescence in situ hybridization (alpha21-II locus). The alphoid sequence contained several rearrangements including five large deletions within monomers and insertions of three truncated L1 elements. No binding sites for centromeric protein CENP-B were found. We analyzed sequences with alphoid/non-alphoid junctions selectively screened from current databases and revealed various rearrangements disrupting the regular tandem alphoid structure, namely, deletions, duplications, inversions, expansions of short oligonucleotide motifs and insertions of different dispersed elements. The detailed analysis of more than 1100 alphoid monomers from junction regions showed that the vast majority of structural alterations and joinings with non-alphoid DNAs occur in alpha satellite families lacking CENP-B boxes. Most analyzed events were found in sequences located toward the edges of the centromeric alphoid arrays. Different dispersed elements were inserted into alphoid DNA at kinkable dinucleotides (TG, CA or TA) situated between pyrimidine/purine tracks. DNA rearrangements resulting from different processes such as recombination and replication occur at kinkable DNA sites alike insertions but irrespectively of the occurrence of pyrimidine/purine tracks. It seems that kinkable dinucleotides TG, CA and TA are part of recognition signals for many proteins involved in recombination, replication, and insertional events. Alphoid DNA is a good model for studying these processes.
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MESH Headings
- Alu Elements/genetics
- Autoantigens
- Base Sequence
- Binding Sites
- Centromere/chemistry
- Centromere/genetics
- Centromere/metabolism
- Centromere Protein B
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Deletion
- Chromosome Inversion
- Chromosomes, Human, Pair 21/chemistry
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 21/metabolism
- Computational Biology
- Crossing Over, Genetic/genetics
- DNA Replication/genetics
- DNA, Satellite/chemistry
- DNA, Satellite/genetics
- DNA, Satellite/metabolism
- DNA-Binding Proteins
- Databases as Topic
- Dinucleotide Repeats/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Lymphocytes
- Mutagenesis, Insertional/genetics
- Mutation/genetics
- Nucleic Acid Conformation
- Polymerase Chain Reaction
- Recombination, Genetic/genetics
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Affiliation(s)
- T D Mashkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Str., Moscow, 117984, Russia.
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18
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O'Keefe CL, Matera AG. Alpha satellite DNA variant-specific oligoprobes differing by a single base can distinguish chromosome 15 homologs. Genome Res 2000; 10:1342-50. [PMID: 10984452 DOI: 10.1101/gr.10.9.1342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ability to distinguish homologous chromosomes is a powerful cytogenetic tool. However, traditional techniques can only distinguish extreme physical variants and are highly dependent on sample preparation. We have previously reported oligonucleotide probes, specific for human chromosome 17 alpha satellite DNA sequence variants, that distinguish cytogenetically normal homologous chromosomes by FISH. Here we report the development of similar oligoprobes, differing at a single nucleotide position, that not only distinguish homologous chromosomes 15 but can be used to follow the transmission of a chromosome from parents to their offspring. We also identified a novel array-size polymorphism in another family. The alphoid array of one chromosome is quite small and below the detection threshold for our oligoprobes, although it is detectable by conventional FISH probes. This size polymorphism provides an additional FISH-based method for distinguishing homologs. Most importantly, this work illustrates the potential applicability of the technique to the entire human chromosome complement.
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Affiliation(s)
- C L O'Keefe
- Department of Genetics, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio 44106-4955 USA
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19
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Wang SY, Cruts M, Del-Favero J, Zhang Y, Tissir F, Potier MC, Patterson D, Nizetic D, Bosch A, Chen H, Bennett L, Estivill X, Kessling A, Antonarakis SE, van Broeckhoven C. A high-resolution physical map of human chromosome 21p using yeast artificial chromosomes. Genome Res 1999; 9:1059-73. [PMID: 10568746 PMCID: PMC310823 DOI: 10.1101/gr.9.11.1059] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The short arm of human chromosome 21 (21p) contains many different types of repetitive sequences and is highly homologous to the short arms of other acrocentric chromosomes. Owing to its repetitive nature and the lack of chromosome 21p-specific molecular markers, most physical maps of chromosome 21 exclude this region. We constructed a physical map of chromosome 21p using sequence tagged site (STS) content mapping of yeast artificial chromosomes (YACs). To this end, 39 STSs located on the short arm or near the centromere of chromosome 21 were constructed, including four polymorphic simple tandem repeats (STRs) and two expressed sequence tags (ESTs). Thirty YACs were selected from the St. Louis YAC library, the chromosome 21-enriched ICRF YAC library, and the CEPH YAC and megaYAC libraries. These were assembled in a YAC contig map ranging from the centromere to the rDNA gene cluster at 21p12. The total size of the region covered by YACs is estimated between 2.9 and 5 Mb. The integrity of the YAC contig was confirmed by restriction enzyme fingerprinting and fluorescence in situ hybridization (FISH). One gap with an estimated size of 400 kb remained near the telomeric end of the contig. This YAC contig map of the short arm of human chromosome 21 constitutes a basic framework for further structural and functional studies of chromosome 21p.
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Affiliation(s)
- S Y Wang
- Flanders Interuniversity Institute for Biotechnology (VIB), Born-Bunge Foundation (BBS), Department of Biochemistry, University of Antwerp (UIA), B-2610 Antwerpen, Belgium
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20
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Maratou K, Siddique Y, Kessling AM, Davies GE. Novel methodology for the detection of chromosome 21-specific alpha-satellite DNA sequences. Genomics 1999; 57:429-32. [PMID: 10329010 DOI: 10.1006/geno.1999.5786] [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: 11/22/2022]
Abstract
We present a novel method, based on the hybridization of allele-specific oligonucleotide probes, that allows the specific detection of chromosome 21 alpha-satellite sequences. Absence of informative polymorphic markers from the centromeric region of chromosome 21 has constituted one of the difficulties in studying the centromere of this chromosome. The alpha-satellite subfamilies from chromosomes 21 and 13 are almost identical in sequence and thus cannot be distinguished using conventional hybridization techniques. Analysis using nuclear families showed that the centromeric polymorphism, detected using our specific probe and pulsed-field gel restriction analysis, segregates in a Mendelian fashion and exhibits a high degree of polymorphism among unrelated individuals. The alphoid DNA of chromosome 21 is highly polymorphic, useful not only as a definitive anchor for the genetic map, but also for studies of chromosome 21 nondisjunction, including the unequivocal assignment of meiotic origin.
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Affiliation(s)
- K Maratou
- Department of Medical and Community Genetics, Imperial College of Science, Technology and Medicine, London, HA1 3UJ, United Kingdom
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21
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Yoda K, Ando S, Okuda A, Kikuchi A, Okazaki T. In vitro assembly of the CENP-B/alpha-satellite DNA/core histone complex: CENP-B causes nucleosome positioning. Genes Cells 1998; 3:533-48. [PMID: 9797455 DOI: 10.1046/j.1365-2443.1998.00210.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND We have studied the nucleosome structure formed from alpha-satellite DNA bound with CENP-B and core histones, in order to develop a previous proposal that the CENP-B dimer may play a critical role in the assembly of higher order structures of the human centromere by juxtaposing CENP-B boxes in long alpha-satellite arrays. RESULTS The dimeric structure of CENP-B was sufficiently stable to bundle together two 3.5 kbp DNA fragments when each DNA contained a CENP-B box. When the same length of DNA included two CENP-B boxes, the intra-molecular interaction with the CENP-B dimer predominated, resulting in the formation of loop structures. The in vitro assembly of CENP-B/alpha-satellite DNA/core histone complexes with the aid of nucleosome assembly protein-1 (NAP-1) permitted an investigation into the nucleosome arrangement in alpha-satellite DNA with CENP-B bound to CENP-B boxes. Footprint analyses with micrococcal nuclease (MNase) revealed that CENP-B causes nucleosome positioning between pairs of CENP-B boxes with unique hypersensitive sites created on both sides. CONCLUSION We propose that CENP-B functions as a structural factor in the centromere region in order to establish a unique, centromere specific pattern of nucleosome positioning.
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Affiliation(s)
- K Yoda
- Bioscience Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-01, Japan
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22
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Laurent AM, Puechberty J, Prades C, Gimenez S, Roizès G. Site-specific retrotransposition of L1 elements within human alphoid satellite sequences. Genomics 1997; 46:127-32. [PMID: 9403067 DOI: 10.1006/geno.1997.4987] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In the course of a search for microsatellites as centromeric polymorphic markers at the 3' ends of Alu or L1 elements, we observed a much higher frequency of L1 than Alu elements embedded within alpha satellite DNA. By sequence analysis of the L1 elements at their alphoid locus of insertion, we found that the insertion site was specific, with the consensus being (Py)2-10/ (Pu)3-7. All potential sites within the consensus alphoid 171-bp repeat are occupied by such elements. This confirms the finding by Feng et al. (1996; Human retrotransposon encodes a conserved endonuclease required for retrotransposition, Cell 87:905-916) that the progenitor L1 elements encode a site-specific endonuclease and that they generate copies that are inserted at these specific sites. The analysis of retrotransposed L1 elements within the alphoid domains of the acrocentric chromosomes showed that a number of loci are shared among all five acrocentrics. This sheds light on the manner in which centromeric regions of these chromosomes are exchanging information during evolution.
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Affiliation(s)
- A M Laurent
- Centre National de la Recherche Scientifique, ERS 155, Montpellier, France
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23
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Nilsson M, Krejci K, Koch J, Kwiatkowski M, Gustavsson P, Landegren U. Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. Nat Genet 1997; 16:252-5. [PMID: 9207789 DOI: 10.1038/ng0797-252] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chromosome centromeres, composed of repeated DNA sequences, orchestrate the correct segregation of chromatids in cell division. We have examined the centromeres of human chromosomes 13 and 21 by studying the distribution, in situ, of two alpha satellite sequences that differ in a single nucleotide position. This was possible using padlock probes, oligo-nucleotides that can be ligated into circles upon target recognition. The segregation of individual 13 and 21 homologues in a family was followed by monitoring of the signals from two differentially labelled probes, specific for either sequence variant. A characteristic arrangement of the repeat motifs in three separate spots, oriented transverse to the length axis of the metaphase chromosomes and bilaterally symmetric, indicates that only parts of the detected regions are involved in the centromeric region, joining the sister chromatids before anaphase.
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Affiliation(s)
- M Nilsson
- Beijer Laboratory, Department of Medical Genetics, Uppsala, Sweden.
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24
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Young AC, Chavez M, Giambernardi TA, Mattern V, McGill JR, Harris JM, Sarosdy MF, Patel P, Sakaguchi AY. Organization and expression of human telomere repeat binding factor genes. SOMATIC CELL AND MOLECULAR GENETICS 1997; 23:275-86. [PMID: 9542529 DOI: 10.1007/bf02674418] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ends of mammalian chromosomes terminate in structures called telomeres. Recently a human telomere repeat binding factor (TRF1) that binds the vertebrate TTAGGG telomeric repeat in situ was isolated by Chong et al. (1). TRF1 regulates telomere length (2), which is often altered in cancer cells. To understand their genetic organization, TRF1 genes were localized to human chromosomes 13cen, 21cen, and Xq13 by analysis of human monochromosomal hybrids, and by fluorescent in situ hybridization. We also confirmed the recent localization of a human TRF1 gene to chromosome 8, and provide evidence that this locus is alternatively spliced. In contrast to the TRF1 genes on chromosomes 8 and X, the chromosomes 13 and 21 TRF1 genes contained a 60 bp deletion in the coding region. The results suggest that two distinct forms of TRF1 are expressed and that the TRF1 gene family includes at least three pseudogenes whose dispersal in the human genome may have occurred via cDNA intermediates.
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Affiliation(s)
- A C Young
- Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio 78284, USA
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25
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Haaf T. Analysis of replication timing of ribosomal RNA genes by fluorescence in situ hybridization. DNA Cell Biol 1997; 16:341-5. [PMID: 9115643 DOI: 10.1089/dna.1997.16.341] [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: 02/04/2023] Open
Abstract
Fluorescence in situ hybridization has been used to study the replication timing of various repeat DNA families in the short arms of human acrocentric chromosomes. In interphase nuclei, unreplicated DNA segments show singlet hybridization signals whereas replicated loci have doublet signals. The distribution of these two patterns in unsynchronized cell cultures revealed that the rRNA gene clusters replicate earlier than the closely juxtaposed alpha- and beta-satellite DNA sequences. Within the rDNA repeat unit, replication of the intergenic spacer appears to precede that of the transcribed rDNA.
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Affiliation(s)
- T Haaf
- Max-Planck-Institute of Molecular Genetics, Berlin, Germany
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26
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Yoda K, Nakamura T, Masumoto H, Suzuki N, Kitagawa K, Nakano M, Shinjo A, Okazaki T. Centromere protein B of African green monkey cells: gene structure, cellular expression, and centromeric localization. Mol Cell Biol 1996; 16:5169-77. [PMID: 8756674 PMCID: PMC231517 DOI: 10.1128/mcb.16.9.5169] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Centromere protein B (CENP-B) is a centromeric DNA-binding protein which recognizes a 17-bp sequence (CENP-B box) in human and mouse centromeric satellite DNA. The African green monkey (AGM) is phylogenetically closer to humans than mice and is known to contain large amounts of alpha-satellite DNA, but there has been no report of CENP-B boxes or CENP-B in the centromere domains of its chromosomes. To elucidate the AGM CENP-B-CENP-B box interaction, we have analyzed the gene structure, expression, biochemical properties, and centromeric localization of its CENP-B. The amino acid sequence deduced from the cloned AGM CENP-B gene was established to be highly homologous to that of human and mouse CENP-B. In particular, the DNA binding and homodimer formation domains demonstrated 100% identity to their human and mouse counterparts. Immunoblotting and DNA mobility shift analyses revealed CENP-B to be expressed in AGM cell lines. As predicted from the gene structure, the AGM CENP-B in the cell extracts exhibited the same DNA binding specificity and homodimer forming activity as human CENP-B. By indirect immunofluorescent staining of AGM mitotic cells with anti-CENP-B antibodies, a centromere-specific localization of AGM CENP-B could be demonstrated. We also isolated AGM alpha-satellite DNA with a CENP-B box-like sequence with CENP-B affinity. These results not only prove that CENP-B functionally persists in AGM cells but also suggest that the AGM genome contains the recognition sequences for CENP-B (CENP-B boxes with the core recognition sequence or CENP-B box variants) in centromeric satellite DNA.
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Affiliation(s)
- K Yoda
- Department of Molecular Biology, School of Science, Nagoya University, Japan
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27
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Prades C, Laurent AM, Puechberty J, Yurov Y, Roizés G. SINE and LINE within human centromeres. J Mol Evol 1996; 42:37-43. [PMID: 8576962 DOI: 10.1007/bf00163209] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A number of the Alu and L1 elements present within the centromeric regions of the human chromosomes have been analyzed by polymerase chain reaction amplification. The oligonucleotide primers were homologous to the 3' end consensus sequences of either Alu or L1 in conjunction with an oligonucleotide primer homologous to alphoid sequences specific to different chromosomes. This allowed one to detect an unusual number of Alu and L1 polymorphisms at different loci. It is proposed that this results from molecular rearrangements which occur within the alpha-satellite DNA in which they are embedded (Marçais et al. J. Mol. Evol. 33:42-48, 1991) and not because the centromeric regions are targets for new insertions of such elements. The same analyses were made on cosmids and YACs originating from the centromeric region of chromosome 21 as well as on a collection of somatic hybrids containing chromosome 21 centromere as unique common human genetic material. The results were consistent with the above hypothesis.
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Affiliation(s)
- C Prades
- UPR 9008 Cnrs, Institut de biologie, Montpellier, France
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28
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Gravholt CH, Friedrich U. Molecular cytogenetic study of supernumerary marker chromosomes in an unselected group of children. AMERICAN JOURNAL OF MEDICAL GENETICS 1995; 56:106-11. [PMID: 7747772 DOI: 10.1002/ajmg.1320560124] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report on an unselected group of 24 children with small supernumerary marker chromosomes, found in a large sample of 34,910 consecutive newborns karyotyped at birth. Sixteen of these were available for reexamination. With the use of in situ hybridization with alpha-satellite centromere probes and satellite III, ribosomal and beta-satellite DNA probes, we have characterized these markers. In 14 of the 16 cases we have been able to determine the chromosomal origin of the marker. Twelve of the markers are derived from the acrocentric chromosomes. Of these 12 markers, 4 are derived from chromosome 14, 4 from chromosome 22, 3 from chromosome 15 and one is from either chromosome 13 or 21. Ten of these markers were initially ascertained with the satellite III DNA probe, taking advantage of the fact that satellite III DNA is found in the centromeric region of the following chromosomes: 1, 5, 9, 13, 14, 15, 16, 20, 21, 22, and Y. Two markers were derived from chromosomes 4 and 8. The origin of the last 2 markers could not be determined with the techniques employed. Only one of these children is psychometrically retarded and has a peculiar appearance. Unfortunately we were not able to determine the origin of the marker in her case. All other children developed normally.
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Affiliation(s)
- C H Gravholt
- Department of Biological Psychiatry, Aarhus University Hospital, Risskov, Denmark
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29
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Yurov YB, Laurent AM, Marcais B, Vorsanova SG, Roizes G. Analysis of pericentromeric chromosome 21 specific YAC clones by FISH: identification of new markers for molecular-cytogenetic application. Hum Genet 1995; 95:287-92. [PMID: 7868120 DOI: 10.1007/bf00225195] [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: 01/27/2023]
Abstract
Fluorescence in situ hybridization (FISH) of chromosome 21 specific yeast artificial chromosome (YAC) clones after Alu-PCR (polymerase chain reaction) amplification has been used to find new region-specific DNA probes for the heterochromatic region of chromosome 21. Six overlapping YAC clones from a pericentromeric contig map (region 21cen-21q11) were analyzed. Four YAC clones were characterized as hybridizing to several chromosomal locations. They are, therefore, either chimeric or shared by different chromosomes. Two of them containing alphoid satellite DNA, are localized at the centromeric regions of chromosomes 13 and 21 (clone 243A11), and on 13cen, 21cen and 1q3 (clone 781G5); the two others are localized at both 21q11 and 13q2 (clone 759D3), and at 18p (clone 770B3). Two YACs were strongly specific for chromosome 21q11 only (clones 124A7 and 881D2). These YACs were used effectively as probes for identifications of chromosome 21 during metaphase and interphase analysis of 12 individuals, including three families with Down syndrome offspring, and 6 aminocyte samples. The location of YAC clones on 21q11 close to the centromeric region allows the application of these clones as molecular probes for the analysis of marker chromosomes with partial deletions of the long arm as well as for pre- and postnatal diagnosis of trisomy 21 when alphoid or more distal region-specific DNA probes are uninformative. Overlapping YAC clones covering human chromosome 21q may be systematically used to detect a set of band-specific DNA probes for molecular-cytogenetic application.
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Affiliation(s)
- Y B Yurov
- Institut de Biologie, INSERM U. 249-CNRS UPR 9008, Montpellier, France
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30
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Soeda E, Hou DX, Osoegawa K, Atsuchi Y, Yamagata T, Shimokawa T, Kishida H, Soeda E, Okano S, Chumakov I. Cosmid assembly and anchoring to human chromosome 21. Genomics 1995; 25:73-84. [PMID: 7774958 DOI: 10.1016/0888-7543(95)80111-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A human chromosome 21-specific cosmid library from the Lawrence Livermore National Laboratory has been analyzed by two complementary methods, fingerprinting and hybridization; 40% coverage of the entire chromosome 21 has been achieved. To prepare a contig pool, approximately 9300 cosmid clones randomly selected from the library were fingerprinted and automatically assembled into 467 overlapping sets by the fluorescence-tagged restriction fragment method. The average size of the overlapping sets was 9.5 cosmids with minimal tiling paths consisting of 5.4 cosmids with a 10-kb extension each. However, as many as 10% of overlaps within members were estimated to be false. For regional localization, we hybridized gridded arrays of cosmids with inter-Alu-PCR probes obtained from YAC clones and somatic cell hybrids and assigned 592 cosmids to 26 subregions of 21q. Of these, 371 clones were incorporated into 139 contigs, anchoring the total 1864 cosmids to the subregion. The remaining 221 clones were mapped as orphans. To correlate the cytogenetic, YAC, and cosmid maps on 21q, the translocation breakpoints of the chromosomes contained in the somatic cell hybrids were mapped with respect to the STS content of the YACs. From the gene cluster regions, 176 ribosomal and 25 alphoid clones were isolated by hybridization. Together, these sets of anchored contigs and cosmids will provide a valuable resource for construction of a high-resolution map and for isolation of genes of interest from chromosome 21.
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Affiliation(s)
- E Soeda
- RIKEN Gene Bank, Institute of Physical and Chemical Research, Tsukuba Science City, Japan
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31
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Pellestor F, Girardet A, Andréo B, Charlieu JP. A polymorphic alpha satellite sequence specific for human chromosome 13 detected by oligonucleotide primed in situ labelling (PRINS). Hum Genet 1994; 94:346-8. [PMID: 7927326 DOI: 10.1007/bf00201590] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The centromeric alpha satellite DNA subfamilies from chromosomes 13 and 21 are almost identical in sequence and cannot be easily distinguished by mean of probes for Southern blot or in situ hybridisation. We have used the oligonucleotide-primed in situ (PRINS) labelling technique with primers defined from the alpha satellite sequence of chromosome 13. One primer was found to label specifically the centromeric region of chromosomes 13 and allowed the detection of a polymorphism between two chromosome 13 homologues in one individual.
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32
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Laurent AM, Marçais B, Muleris M, Roizès G. A rapid and simple method to isolate and characterize highly polymorphic markers from the centromeric regions of the human chromosomes. Nucleic Acids Res 1994; 22:194-9. [PMID: 8121804 PMCID: PMC307771 DOI: 10.1093/nar/22.2.194] [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: 01/28/2023] Open
Abstract
Using oligonucleotide primers complementary to the 3' ends of either the Alu or the L1Hs consensus sequences in conjunction with a primer complementary to alpha satellite subsets specific to different human chromosomes, it was possible to detect and characterize polymorphisms originating from the microsatellites which are often present downstream these repetitive elements. The methodology does not require cloning, sequencing or synthesis of specific primers. Centromeric location was confirmed by linkage analysis, in situ hybridization and sequencing. The method is proposed for the generation of polymorphic markers from all centromeric regions.
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33
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Cullen P, Rodgers CS, Callen DF, Connolly VM, Eyre H, Fells P, Gordon H, Winter RM, Thakker RV. Association of familial Duane anomaly and urogenital abnormalities with a bisatellited marker derived from chromosome 22. AMERICAN JOURNAL OF MEDICAL GENETICS 1993; 47:925-30. [PMID: 8279492 DOI: 10.1002/ajmg.1320470623] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We report a spectrum of defects that were found in an 18-year-old girl who presented for investigation of primary amenorrhea. The patient was found to have Duane anomaly, left renal agenesis, absent uterus, bilateral sensorineural deafness, and bilateral preauricular skin tags and sinuses. Investigation of her family showed that her brother also had Duane anomaly, right renal agenesis, sensorineural deafness, and preauricular skin tags and that their father had preauricular skin tags. Cytogenetic analysis, including in situ hybridisation of peripheral blood lymphocytes, demonstrated a supernumerary bisatellited marker chromosome derived from the region of chromosome 22pter-q11 in the affected individuals. Our findings indicate that a gene or genes located in the region of chromosome 22pter-q11 may be associated with the Duane anomaly and the development of the urogenital tract.
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Affiliation(s)
- P Cullen
- Division of Molecular Medicine, MRC Clinical Research Centre, Harrow, Middlesex, United Kingdom
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34
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Greig GM, Warburton PE, Willard HF. Organization and evolution of an alpha satellite DNA subset shared by human chromosomes 13 and 21. J Mol Evol 1993; 37:464-75. [PMID: 8283478 DOI: 10.1007/bf00160427] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The structure of the alpha satellite DNA higher-order repeat (HOR) unit from a subset shared by human chromosomes 13 and 21 (D13Z1 and D21Z1) has been examined in detail. By using a panel of hybrids possessing either a chromosome 13 or a chromosome 21, different HOR unit genotypes on chromosomes 13 and 21 have been distinguished. We have also determined the basis for a variant HOR unit structure found on approximately 8% of chromosomes 13 but not at all on chromosomes 21. Genomic restriction maps of the HOR units found on the two chromosome 13 genotypes and on the chromosome 21 genotype are constructed and compared. The nucleotide sequence of a predominant 1.9-kilobasepair HOR unit from the D13Z1/D21Z1 subset has been determined. The DNA sequences of different alpha satellite monomers comprising the HOR are compared, and the data are used to develop a model, based on unequal crossing-over, for the evolution of the current HOR unit found at the centromeres of both these chromosomes.
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MESH Headings
- Animals
- Base Sequence
- Biological Evolution
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 21
- Cloning, Molecular
- DNA, Satellite/genetics
- Deoxyribonucleases, Type II Site-Specific
- Genotype
- Humans
- Hybrid Cells
- Mice
- Models, Genetic
- Molecular Sequence Data
- Polymorphism, Genetic
- Repetitive Sequences, Nucleic Acid
- Restriction Mapping
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- G M Greig
- Department of Genetics, Stanford University, California 94305
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35
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Marçais B, Laurent AM, Charlieu JP, Roizès G. Organization of the variant domains of alpha satellite DNA on human chromosome 21. J Mol Evol 1993; 37:171-8. [PMID: 8411206 DOI: 10.1007/bf02407353] [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: 01/30/2023]
Abstract
The de novo creation of long, homogeneous, satellite DNA domains was postulated previously to occur by saltatory amplification. In this paper, pulsed field gel electrophoresis analysis of the alpha satellite DNA block organization of the human chromosome 21 supports this hypothesis. Double-dimension electrophoresis indicated that the variant copies of the basic alpha satellite repeat of chromosome 21 are organized in a single 3,150 Kb-long domain. It was also established that the other satellite DNAs found in man (beta, II, and III) are organized independently of the alpha satellite DNA block of the same chromosome.
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MESH Headings
- Base Sequence
- Biological Evolution
- Chromosomes, Human, Pair 21
- DNA, Satellite/genetics
- DNA, Satellite/isolation & purification
- Electrophoresis, Gel, Pulsed-Field
- Female
- Gene Amplification
- Genetic Variation
- Genetics, Population
- Genome, Human
- Humans
- Male
- Molecular Sequence Data
- Pedigree
- Polymorphism, Genetic
- Repetitive Sequences, Nucleic Acid
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Affiliation(s)
- B Marçais
- Institut de Biologie, U. 249 INSERM, LP 8402 CNRS, Montpellier, France
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36
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Voullaire LE, Slater HR, Petrovic V, Choo KH. A functional marker centromere with no detectable alpha-satellite, satellite III, or CENP-B protein: activation of a latent centromere? Am J Hum Genet 1993; 52:1153-63. [PMID: 7684888 PMCID: PMC1682274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We report the investigation of an unusual human supernumerary marker chromosome 10 designated "mar del(10)." This marker is present together with two other marker chromosomes in the karyotype of a boy with mild developmental delay. It has a functional centromere at a primary constriction and is mitotically stable. Fluorescence in situ hybridization (FISH) using alpha-satellite and satellite III DNA as probes failed to detect any signal at the primary constriction site. CENP-B protein could not be demonstrated, although the presence of at least some centromeric proteins was confirmed using a CREST antiserum. Consideration of these and other cytogenetic and FISH results supports a mechanism of formation of the mar del(10) chromosome involving the activation of a latent intercalary centromere at 10q25.
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Affiliation(s)
- L E Voullaire
- Murdoch Institute for Research into Birth Defects, Royal Children's Hospital, Parkville, Victoria, Australia
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37
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Vissel B, Choo KH. Evolutionary relationships of multiple alpha satellite subfamilies in the centromeres of human chromosomes 13, 14, and 21. J Mol Evol 1992; 35:137-46. [PMID: 1501254 DOI: 10.1007/bf00183225] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Using Southern and in situ hybridization analyses, we have earlier defined four different subfamilies of alpha satellite DNA (designated pTRA-1, -2, -4, and -7), each of which has a unique higher order structure represented almost identically on human chromosomes 13, 14, and 21. Here we present the complete sequence of single isolates of these four subfamilies, representing approximately 12 kb of sequence information. Sequences of the individual 171-bp monomers that constitute these four subfamilies (and a fifth subfamily, Alpha-R1, that is known to be present on chromosomes 13 and 21) were compared both within and between the different clones. The results indicate that, at the level of their primary sequence, the five alpha subfamilies are characterized by structures that are as unrelated to each other as the different alpha subfamilies from other chromosomes. However, sequence comparisons between monomers of these clones indicate the possibility that pTRA-2, -4, and -1 may have arisen, at least in part, from a common ancestral alphoid sequence. We also provide evidence that exchange of pTRA-1 between nonhomologous centromeres and its homogenization throughout the population, perhaps by unequal exchange mechanisms, could have occurred after the divergence of humans and chimpanzees. The evolution of multiple alphoid subfamilies within a single centromere suggests that unequal exchange mechanisms may be restricted to specific domains. This may in turn contribute to some requirement for subregional pairing of sequences along the length of the centromeres of these chromosomes.
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Affiliation(s)
- B Vissel
- Murdoch Institute for Research into Birth Defects, Royal Children's Hospital, Parkville, Victoria, Australia
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38
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Callen DF, Eyre H, Yip MY, Freemantle J, Haan EA. Molecular cytogenetic and clinical studies of 42 patients with marker chromosomes. AMERICAN JOURNAL OF MEDICAL GENETICS 1992; 43:709-15. [PMID: 1377870 DOI: 10.1002/ajmg.1320430412] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The molecular cytogenetic characterization and clinical details of 20 patients with marker chromosomes are presented. These 20 patients, together with another 22 patients previously published, represent a cohort in which the chromosomal origin of the marker chromosomes was successfully determined in all but one case. Examination of the pooled data suggests that the satellited markers derived from chromosomes 14, 15 (when metacentric or submetacentric), those whose origin is either 13 or 21, and those small ring autosomal markers derived from both alphoid and satellite II or III pericentric heterochromatin of chromosomes 1, 9, 15, and 16 are all associated with a low risk of phenotypic abnormality. The markers identified as i(18p), ring chromosomes derived from various autosomes, and satellited markers derived from chromosome 22 are associated with a high risk of phenotypic abnormality. The phenotype of patients with acrocentric markers derived from chromosome 15 was equivocal, perhaps as a result of imprinting. Additional data are required to confirm these trends. The mild mental retardation and abnormal face of a patient with a small ring chromosome derived from chromosome 4 are described. Identification of patients with small rings originating from particular chromosomes may allow the recognition of new syndromes.
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Affiliation(s)
- D F Callen
- Department of Cytogenetics, Adelaide Children's Hospital, South Australia
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39
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Jørgensen AL, Laursen HB, Jones C, Bak AL. Evolutionarily different alphoid repeat DNA on homologous chromosomes in human and chimpanzee. Proc Natl Acad Sci U S A 1992; 89:3310-4. [PMID: 1565621 PMCID: PMC48856 DOI: 10.1073/pnas.89.8.3310] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Centromeric alphoid DNA in primates represents a class of evolving repeat DNA. In humans, chromosomes 13 and 21 share one subfamily of alphoid DNA while chromosomes 14 and 22 share another subfamily. We show that similar pairwise homogenizations occur in the chimpanzee (Pan troglodytes), where chromosomes 14 and 22, homologous to human chromosomes 13 and 21, share one partially homogenized alphoid DNA subfamily and chromosomes 15 and 23, homologous to human chromosomes 14 and 22, share another extensively homogenized subfamily. Such a pattern of homogenization presumably predates speciation 3-10 million years ago. However, the alphoid DNA on these human and chimpanzee chromosomes is not orthologous but originates from two evolutionarily different repeat families. It follows that dramatic sequence evolution has occurred in a concerted fashion among the chromosomes in one or both species during or after separation.
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MESH Headings
- Animals
- Base Sequence
- Biological Evolution
- Centromere/physiology
- Chromosome Mapping
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 22
- DNA/genetics
- Hominidae/genetics
- Humans
- Molecular Sequence Data
- Pan troglodytes/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- A L Jørgensen
- Institute of Medical Microbiology, University of Aarhus, Denmark
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40
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Earle E, Shaffer LG, Kalitsis P, McQuillan C, Dale S, Choo KH. Identification of DNA sequences flanking the breakpoint of human t(14q21q) Robertsonian translocations. Am J Hum Genet 1992; 50:717-24. [PMID: 1550117 PMCID: PMC1682650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have employed molecular probes and in situ hybridization to investigate the DNA sequences flanking the breakpoint of a group of t(14q21q) Robertsonian translocations. In all the families studied, the probands were patients with Down syndrome who carried a de novo t(14q21q) translocation. The DNA probes used were two alphoid sequences, alphaRI and alphaXT, which are specific for the centromeres of chromosomes 13 and 21 and of chromosomes 14 and 22, respectively; a satellite III sequence, pTRS-47, which is specific for the proximal p11 region of chromosomes 14 and 22; and a newly defined satellite III DNA, pTRS-63, which is specific for the distal p11 region of chromosome 14. The two alphoid probes detected approximately the same amount of autoradiographic signal on the translocated chromosomes as was expected for chromosomes 14 and 21 of the originating parent, suggesting that there has been no loss of these centromeric sequences during the translocation events. Results with the two satellite III probes indicated that the domain corresponding to pTRS-47 was retained in the translocated chromosomes, whereas the domain for pTRS-63 was lost. These results have allowed us to place the translocation breakpoint between the pTRS-47 and pTRS-63 domains within the p11 region of chromosome 14.
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Affiliation(s)
- E Earle
- Murdoch Institute for Research into Birth Defects, Royal Children's Hospital, Parkville, Australia
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41
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Antonarakis SE, Petersen MB, McInnis MG, Adelsberger PA, Schinzel AA, Binkert F, Pangalos C, Raoul O, Slaugenhaupt SA, Hafez M. The meiotic stage of nondisjunction in trisomy 21: determination by using DNA polymorphisms. Am J Hum Genet 1992; 50:544-50. [PMID: 1347192 PMCID: PMC1684265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023] Open
Abstract
We have studied DNA polymorphisms at loci in the pericentromeric region on the long arm of chromosome 21 in 200 families with trisomy 21, in order to determine the meiotic origin of nondisjunction. Maintenance of heterozygosity for parental markers in the individual with trisomy 21 was interpreted as resulting from a meiosis I error, while reduction to homozygosity was attributed to a meiosis II error. Nondisjunction was paternal in 9 cases and was maternal in 188 cases, as reported earlier. Among the 188 maternal cases, nondisjunction occurred in meiosis I in 128 cases and in meiosis II in 38 cases; in 22 cases the DNA markers used were uninformative. Therefore meiosis I was responsible for 77.1% and meiosis II for 22.9% of maternal nondisjunction. Among the 9 paternal nondisjunction cases the error occurred in meiosis I in 2 cases (22.2%) and in meiosis II in 7 (77.8%) cases. Since there was no significant difference in the distribution of maternal ages between maternal I error versus maternal II error, it is unlikely that an error at a particular of maternal ages between maternal I error versus maternal II error, it is unlikely that an error at a particular meiotic stage contributes significantly to the increasing incidence of Down syndrome with advancing maternal age. Although the DNA polymorphisms used were at loci which map close to the centromere, it is likely that rare errors in meiotic-origin assignments may have occurred because of a small number of crossovers between the markers and the centromere.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S E Antonarakis
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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42
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Petersen MB, Adelsberger PA, Schinzel AA, Binkert F, Hinkel GK, Antonarakis SE. Down syndrome due to de novo Robertsonian translocation t(14q;21q): DNA polymorphism analysis suggests that the origin of the extra 21q is maternal. Am J Hum Genet 1991; 49:529-36. [PMID: 1831959 PMCID: PMC1683126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Down syndrome is rarely due to a de novo Robertsonian translocation t(14q;21q). DNA polymorphisms in eight families with Down syndrome due to de novo t(14q;21q) demonstrated maternal origin of the extra chromosome 21q in all cases. In seven nonmosaic cases the DNA markers showed crossing-over between two maternal chromosomes 21, and in one mosaic case no crossing-over was observed (this case was probably due to an early postzygotic nondisjunction). In the majority of cases (five of six informative families) the proximal marker D21S120 was reduced to homozygosity in the offspring with trisomy 21. The data can be best explained by chromatid translocation in meiosis I and by normal crossover and segregation in meiosis I and meiosis II.
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Affiliation(s)
- M B Petersen
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
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43
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Marçais B, Charlieu JP, Allain B, Brun E, Bellis M, Roizès G. On the mode of evolution of alpha satellite DNA in human populations. J Mol Evol 1991; 33:42-8. [PMID: 1909375 DOI: 10.1007/bf02100194] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The hypothesis that highly reiterated satellite DNAs in present-day populations evolve by molecular mechanisms that create, by saltatory amplification steps, new long arrays of satellite DNA, and that such long arrays are used for homogenization purposes, has been tested both in mouse and in humans. In mouse, the data obtained are consistent with this hypothesis. This was tested in more detail on chromosomes 13 and 21 of the human genome. A Centre d'Etudes du Polymorphisme Humain family, which in some individuals exhibits strong supplementary DNA bands following TaqI restriction endonuclease digestion and conventional gel electrophoresis, was analyzed by pulse field gel electrophoresis following restriction by BamHI. The supplementary bands on chromosome 13 (18 times the basic alpha satellite DNA repeat) and on chromosome 21 (a 9.5-mer) segregated with centromeric alpha satellite DNA blocks of 5 and 5.3 megabases, respectively. These are by far the largest alpha satellite block lengths seen in all chromosome 13 and chromosome 21 centromeric sequences so far analyzed in this manner. The possibility that these supplementary alpha satellite sequences were created in single individuals by saltatory amplification steps is discussed in light of our own data and that published by others. It is proposed that deletion events and unequal cross-overs, which both occur in large satellite DNA arrays, contribute to the homogenization of size and sequence of the alpha satellite DNA on most chromosomes of humans.
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Affiliation(s)
- B Marçais
- UPR 8402 C.N.R.S., U.249 INSERM, Montpellier, France
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44
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Erickson RP, Glover TW, Hall BK, Witt M. Polymerase chain reactions with alphoid-repeat primers in combination with Alu or LINEs primers, generate chromosome-specific DNA fragments. Ann Hum Genet 1991; 55:199-211. [PMID: 1763884 DOI: 10.1111/j.1469-1809.1991.tb00414.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Y alphoid primers in combination with Alu and LINEs primers generated new DNA fragments in polymerase chain reactions (PCR) on DNA from a Y-only somatic cell hybrid but not from X-only, 3-only, or 21-only hybrids. X alphoid primers used in a similar manner generated new DNA fragments from the X-only hybrid, and 1 of the primers (X2) also generated new DNA fragments on 3-only and 21-only hybrids when used in conjunction with Alu or LINEs primers. In all but one case, consensus alphoid primers generated new chromosome-specific fragments in PCR reactions with the Alu or LINEs primers. A search for cryptic Alu- or alphoid-alone PCR products as the source for one Alu-alphoid band (chosen at random) was negative. Partial sequencing of products demonstrated that alphoid and Alu sequences were indeed contiguous in some newly synthesized DNA fragments. While Alu or LINEs primers generate smears of DNA fragments on total human DNA, the alphoid-non-alphoid repeat combinations generated electrophoretically distinguishable bands of DNA when the template was total DNA. While these were distinguishable with different chromosome-specific alphoid primers, the DNA fragments were not of the same sizes as those generated with the chromosome-only hybrids.
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Affiliation(s)
- R P Erickson
- Department of Pediatrics and Communicable Diseases, University of Michigan School of Medicine, Ann Arbor 48109-0178
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45
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Callen DF, Eyre HJ, Ringenbergs ML, Freemantle CJ, Woodroffe P, Haan EA. Chromosomal origin of small ring marker chromosomes in man: characterization by molecular genetics. Am J Hum Genet 1991; 48:769-82. [PMID: 2014800 PMCID: PMC1682952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Ten cases of small ring chromosomes which did not stain with distamycinA/DAPI and did not possess satellite regions associated with nucleolus-organizing regions are described. In situ hybridization with a battery of biotinylated pericentric repeat probes specific either for individual chromosomes or for groups of chromosomes allowed the identification of the chromosomal origin of these marker chromosomes. There was one example of a marker derived from each of chromosomes 1, 3, 6, 14, 16, 18, 20, 13 or 21, and the X, and there were two examples of markers derived from chromosome 12. One case possessed two markers, one derived from chromosome 6, and one derived from the X. The mechanism of generation of ring marker chromosomes is discussed. Five of seven cases who could be phenotypically assessed were abnormal. Three of these--the first with a ring chromosome derived from chromosome 1; the second with two markers, one derived from chromosome 6 and the other from the X chromosome; and the third with a ring chromosome derived from chromosome 20--each possessed distinctive facies. Additional cases with identified rings may allow the delineation of new chromosomal syndromes.
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Affiliation(s)
- D F Callen
- Department of Cytogenetics and Molecular Genetics, Adelaide Children's Hospital, Australia
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46
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Kølvraa S, Koch J, Gregersen N, Jensen PK, Jørgensen AL, Petersen KB, Rasmussen K, Bolund L. Application of fluorescence in situ hybridization techniques in clinical genetics: use of two alphoid repeat probes detecting the centromeres of chromosomes 13 and 21 or chromosomes 14 and 22, respectively. Clin Genet 1991; 39:278-86. [PMID: 1829987 DOI: 10.1111/j.1399-0004.1991.tb03026.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two cloned DNA fragments, one derived from an alpha satellite subfamily common to chromosomes 13 and 21, and the other derived from a similar subfamily common to chromosomes 14 and 22, have been used as biotinylated probes in in situ hybridization studies. Under high stringency conditions, chromosome specific centromeric labelling can be obtained. The applications of this technique in clinical situations are illustrated on metaphases from a fetus with trisomy 21, a fetus with trisomy 13, and a child with clinical features of cat-eye syndrome.
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MESH Headings
- Centromere/ultrastructure
- Chromosome Banding
- Chromosomes, Human, Pair 13
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 22
- Cloning, Molecular
- DNA/genetics
- DNA Probes
- Down Syndrome/diagnosis
- Down Syndrome/genetics
- Genetic Markers/genetics
- Humans
- Microscopy, Fluorescence
- Prenatal Diagnosis
- Repetitive Sequences, Nucleic Acid/genetics
- Trisomy
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Affiliation(s)
- S Kølvraa
- Institute of Human Genetics, University of Aarhus, Denmark
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47
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Choo KH, Vissel B, Nagy A, Earle E, Kalitsis P. A survey of the genomic distribution of alpha satellite DNA on all the human chromosomes, and derivation of a new consensus sequence. Nucleic Acids Res 1991; 19:1179-82. [PMID: 2030938 PMCID: PMC333840 DOI: 10.1093/nar/19.6.1179] [Citation(s) in RCA: 181] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- K H Choo
- Murdoch Institute for Research into Birth Defects, Royal Children's Hospital, Parkville, Victoria, Australia
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48
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Baldini A, Miller DA, Miller OJ, Ryder OA, Mitchell AR. A chimpanzee-derived chromosome-specific alpha satellite DNA sequence conserved between chimpanzee and human. Chromosoma 1991; 100:156-61. [PMID: 2040204 DOI: 10.1007/bf00337244] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We describe a cloned 2.7 kb alpha satellite sequence, Pan-3, from the pygmy chimpanzee (Pan paniscus) that specifically hybridizes in situ to chromosome 19 in the pygmy chimpanzee and to the homeologous human chromosome, no. 17. Using high stringency conditions of hybridization on Southern blots, this sequence hybridized to DNA from both species of chimpanzee (P. paniscus and P. troglodytes) and from human but not to DNA from gorilla (Gorilla gorilla) or orangutan (Pongo pygmaeus). Partial sequence analysis showed that Pan-3 and a previously described human chromosome 17-specific clone have up to 91% sequence identity. To our knowledge this is the highest sequence similarity reported between alphoid subsets from human and any other primate.
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Affiliation(s)
- A Baldini
- Department of Molecular Biology and Genetics, Wayne State University, Detroit, MI 48201
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49
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Vissel B, Choo KH. Four distinct alpha satellite subfamilies shared by human chromosomes 13, 14 and 21. Nucleic Acids Res 1991; 19:271-7. [PMID: 2014167 PMCID: PMC333590 DOI: 10.1093/nar/19.2.271] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We describe the characterisation of four alpha satellite sequences which are found on a subset of the human acrocentric chromosomes. Direct sequence study, and analysis of somatic cell hybrids carrying specific human chromosomes indicate a unique 'higher-order structure' for each of the four sequences, suggesting that they belong to different subfamilies of alpha DNA. Under very high stringency of Southern hybridisation conditions, all four subfamilies were detected on chromosomes 13, 14 and 21, with 13 and 21 showing a slightly greater sequence homology in comparison to chromosome 14. None of these subfamilies were detected on chromosomes 15 and 22. In addition, we report preliminary evidence for a new alphoid subfamily that is specific for human chromosome 14. These results, together with those of earlier published work, indicate that the centromeres of the five acrocentric chromosomes are characterised by a number of clearly defined alphoid subfamilies or microdomains (with at least 5, 7, 3, 5 and 2 different ones on chromosomes 13, 14, 15, 21 and 22, respectively). These microdomains must impose a relatively stringent subregional pairing of the centromeres of two homologous chromosomes. The different alphoid subfamilies reported should serve as useful markers to allow further 'dissection' of the structure of the human centromere as well as the investigation of how the different nonhomologous chromosomes may interact in the aetiology of aberrations involving these chromosomes.
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Affiliation(s)
- B Vissel
- Murdoch Institute for Research into Birth Defects, Royal Children's Hospital, Parkville, Victoria, Australia
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50
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Marçais B, Bellis M, Gérard A, Pagès M, Boublik Y, Roizès G. Structural organization and polymorphism of the alpha satellite DNA sequences of chromosomes 13 and 21 as revealed by pulse field gel electrophoresis. Hum Genet 1991; 86:311-6. [PMID: 1997388 DOI: 10.1007/bf00202418] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
More than 30 unrelated individuals were analysed by pulse field gel electrophoresis for the alphoid centromeric sequences of chromosomes 13 and 21. These individuals had DNA patterns all different from each other and were most probably heterozygous at both loci. When several nuclear families were analysed in this manner, segregation was shown to be Mendelian, and no recombination event was detected over the 150 meioses scored in this study. Alphoid DNA sequences, therefore, constitute highly polymorphic centromeric markers, which can be used in linkage analysis for loci close to the centromeres of chromosomes 13 and 21.
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Affiliation(s)
- B Marçais
- UPR 8402 CNRS-U.249 INSERM, Institut de Biologie, Montpellier, France
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