1
|
Brahe C, Tassone F, Millington-Ward A, Serra A, Gardiner K. Potential gene sequence isolation and regional mapping in human chromosome 21. AMERICAN JOURNAL OF MEDICAL GENETICS. SUPPLEMENT 2005; 7:120-4. [PMID: 2127361 DOI: 10.1002/ajmg.1320370724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The transcription start sites of many genes are associated with CpG-rich DNA regions (CpG islands) containing clusters of rare cutting, methylation-sensitive restriction enzyme sites [Bird, 1986]. To detect gene sequences from human chromosome 21, we have screened cloned DNA fragments from a chromosome 21-specific cosmid library for the presence of such restriction sites. Several DNA fragments containing rare cutter sites, including Sac II, were isolated and five of them partially characterized. The average insert size of the fragments was 38.4 kb. By using a panel of somatic cell hybrids, one insert was assigned to the distal part of region 21q21, three fragments to the region 21q22.1, and one sequence to the segment 21q22.2-22.3. Restriction mapping showed clusters of rare cutter sites in at least three of the cloned fragments, suggesting the presence of CpG islands. These fragments are thus good candidates for carriers of coding sequences.
Collapse
Affiliation(s)
- C Brahe
- Institute of Human Genetics, A. Gemelli School of Medicine, Rome, Italy
| | | | | | | | | |
Collapse
|
2
|
Petersen MB, Tranebjaerg L, McCormick MK, Michelsen N, Mikkelsen M, Antonarakis SE. Clinical, cytogenetic, and molecular genetic characterization of two unrelated patients with different duplications of 21q. AMERICAN JOURNAL OF MEDICAL GENETICS. SUPPLEMENT 2005; 7:104-9. [PMID: 2149934 DOI: 10.1002/ajmg.1320370721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We present 2 patients with dup(21q). Patient MP01 had mild mental retardation, facial findings characteristic of Down syndrome (DS), and a terminal duplication of chromosome 21. His karyotype was 46,XY,dup(21) (q22.1-qter). Patient MP03 had mild mental retardation, minor anomalies not characteristic of DS, and a duplication of the proximal long arm of chromosome 21, karyotype 46,XX,dup(21) (q11.2-q21.2). The patients were studied with single-copy DNA sequences from 20 loci on chromosome 21 to characterize the extent of the duplicated regions at the DNA level. DNA loci from D21S55 to COL6A1 were triplicated in patient MP01 while loci from D21S13 to D21S8 were triplicated in patient MP03. Our results support the hypothesis of a critical region of chromosome 21, which in triplicate is responsible for many of the facial changes associated with DS. Other genes outside this region may also contribute to other abnormalities observed in DS.
Collapse
Affiliation(s)
- M B Petersen
- Department of Medical Genetics, John F. Kennedy Institute, Glostrup, Denmark
| | | | | | | | | | | |
Collapse
|
3
|
Rahmani Z, Blouin JL, Créau-Goldberg N, Watkins PC, Mattei JF, Poissonnier M, Prieur M, Chettouh Z, Nicole A, Aurias A. Down syndrome critical region around D21S55 on proximal 21q22.3. AMERICAN JOURNAL OF MEDICAL GENETICS. SUPPLEMENT 2005; 7:98-103. [PMID: 2149984 DOI: 10.1002/ajmg.1320370720] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have analysed the DNA of 2 patients with many manifestations of Down syndrome and partial duplication of distinct regions of chromosome 21, respectively, q11.205----q22.300 and q22.300----qter (Rahmani et al.: Proceedings of the National Academy of Sciences of the United States of America 86:5958-5962, 1989). Assessment of the copy number of five chromosome 21 sequences (SOD1, D21S17, D21S55, ETS2, and D21S15) has shown that D21S55 was duplicated in both cases. The size of the common duplicated region can be estimated between 400 and 3,000 Kb, after the results of pulsed-field gel analysis and from the knowledge of regional mapping of the probes D21S17, D21S55, and ETS2. This region, located on the proximal part of 21q22.3, is postulated to contain genes the overexpression of which plays a major role in the pathogenesis of Down syndrome.
Collapse
Affiliation(s)
- Z Rahmani
- URA CNRS 1335, Laboratoire de Biochimie Génétique, Hôpital Necker-Enfants Malades, Paris, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Stinissen P, Van Roy B, Van Camp G, Backhovens H, Partoens P, Wehnert A, Verniers H, Dumon J, Vandenberghe A, Van Broeckhoven C. Study of the origin of nondisjunction in a family with two cases of Down syndrome using cytogenetic and molecular polymorphisms. AMERICAN JOURNAL OF MEDICAL GENETICS. SUPPLEMENT 2005; 7:133-6. [PMID: 1981473 DOI: 10.1002/ajmg.1320370727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We analyzed the possibility of inherited predisposition to nondisjunction in a family with two cases of Down syndrome using restriction fragment length polymorphisms and cytogenetic heteromorphisms. In both patients the extra chromosome 21 was the result of a nondisjunction event at first meiotic division in the mother. Since both patients are maternally related, genetic predisposition cannot be excluded in this family.
Collapse
Affiliation(s)
- P Stinissen
- Department of Biochemistry, University of Antwerp, Belgium
| | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Brahe C, Tassone F, Moscetti A, Millington-Ward A, Bova R, Serra A. Molecular study of parental origin of extra chromosome 21 in regular and de novo translocation trisomies. AMERICAN JOURNAL OF MEDICAL GENETICS. SUPPLEMENT 2005; 7:125-8. [PMID: 2149938 DOI: 10.1002/ajmg.1320370725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The parental origin of the extra chromosome 21 (or extra 21q) was determined in seven informative families with a Down syndrome (DS) child by using molecular polymorphisms. Five DS patients had regular trisomy, one a de novo 14/21 translocation and another a de novo 21/21 translocation or isochromosome 21q. In four families with regular trisomy, the extra chromosome was of maternal origin, and in one family it was paternally derived. In the two families with a de novo aberration, both the 14/21 translocation and 21/21 rearrangement originated during maternal meiosis. For a better evaluation of the stage of meiotic error and the occurrence of crossovers between nondisjoined chromosomes, the regional map position of four of the nine informative DNA markers, used in this study, was refined, leading to useful localizations in both centromeric and distal regions. Recombination events were found in two families with regular trisomy, one occurring between chromosomes 21 that failed to disjoin at maternal meiosis I, the other prior to a paternal meiosis II nondisjunction.
Collapse
Affiliation(s)
- C Brahe
- Institute of Human Genetics, A. Gemelli School of Medicine, Rome, Italy
| | | | | | | | | | | |
Collapse
|
6
|
Leonard JC, Toji LH, Bender PK, Beiswanger CM, Beck JC, Johnson RT. Panel description. Regional mapping panels for chromosomes 6, 9, and 16. Genomics 1999; 58:323-6. [PMID: 10373332 DOI: 10.1006/geno.1999.5835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- J C Leonard
- NIGMS Human Mutant Cell Repository, Coriell Cell Repositories, Coriell Institute for Medical Research, Camden, New Jersey 08103, USA
| | | | | | | | | | | |
Collapse
|
7
|
Leonard JC, Toji LH, Bender PK, Beiswanger CM, Beck JC. Regional mapping panels for chromosomes 8, 13, 21, and 22. Genomics 1998; 51:17-20. [PMID: 9693028 DOI: 10.1006/geno.1998.5375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- J C Leonard
- Coriell Cell Repositories, Coriell Institute for Medical Research, Camden, New Jersey, 08103, USA
| | | | | | | | | |
Collapse
|
8
|
Gabriele T, Tavaria M, Kola I, Anderson RL. Analysis of heat shock protein 70 in human chromosome 21 containing hybrids. Int J Biochem Cell Biol 1996; 28:905-10. [PMID: 8811838 DOI: 10.1016/1357-2725(96)00027-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
An Hsp70 gene, HspA3, has been given provisional assignment to chromosome 21 based on the heat induced expression of a 70 kDa protein in a Chinese hamster ovary-human hybrid cell line. This assignment has not been supported by hybridization data or by cloning of the gene. The aim of the current study is to clarify this localization. We have analysed a series of Chinese hamster ovary-human hybrid lines containing human chromosome 21 by two-dimensional gel electrophoresis and Western blot analysis with anti-Hsp70 antibodies. Only one of these, hybrid 72532-X6, was found to contain an additional Hsp70 protein. Three other hybrid cell lines spanning different parts of chromosome 21 did not contain any additional Hsp70 proteins. The Hsp70 protein in 72532-X6 is constitutively expressed and is not heat inducible. Southern blot analysis indicates that this protein is not the major human cognate protein, Hsp73 (Hsp70-8), but may be one of the other cognate Hsp70s. Our data indicate that hybrid cell lines containing human chromosome 21 do not express a human Hsp70, as has been reported previously. The recent report that the hybrid cell line used to make this claim also contains other human chromosome fragments leads us to conclude that an Hsp70 gene is not localized on human chromosome.
Collapse
Affiliation(s)
- T Gabriele
- Peter MacCallum Cancer Institute, East Melbourne, Victoria, Australia
| | | | | | | |
Collapse
|
9
|
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.
Collapse
Affiliation(s)
- C Prades
- UPR 9008 Cnrs, Institut de biologie, Montpellier, France
| | | | | | | | | |
Collapse
|
10
|
Hoyle J, Yulug IG, Johnstone K, Scambler PJ, Fisher EM. Characterisation of a short interspersed repeat (Mermaid) that has family members on human chromosome 21 and elsewhere in the human genome. Hum Genet 1996; 97:117-20. [PMID: 8557251 DOI: 10.1007/bf00218845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To understand the architecture of the human genome, we need a complete definition of all the repeat sequence families, as these make up the majority of human DNA. We have isolated a small DNA fragment from human chromosome 21 and have used sequence analysis of this fragment to uncover a new low copy repeat element of approximately 300 bp that we term the Mermaid repeat. This repeat is related to, but is different from, the MER12 repeat and is interspersed in the genome. Mermaid family members that we have studied are between 81%-87% identical to our preliminary consensus sequence. Therefore, we have added a new member to the large collection of human repetitive elements. In addition, we have mapped a Mermaid repeat to a telomeric position on the long arm of human chromosome 21, at 21q22.3.
Collapse
Affiliation(s)
- J Hoyle
- Department of Biochemistry and Molecular Genetics, St. Mary's Hospital Medical School, Imperial College, London, UK
| | | | | | | | | |
Collapse
|
11
|
Graw SL, Gardiner K, Hall-Johnson K, Hart I, Joetham A, Walton K, Donaldson D, Patterson D. Molecular analysis and breakpoint definition of a set of human chromosome 21 somatic cell hybrids. SOMATIC CELL AND MOLECULAR GENETICS 1995; 21:415-28. [PMID: 8600569 DOI: 10.1007/bf02310208] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Rodent-human somatic cell hybrids containing single human chromosomes or chromosome fragments are extremely valuable in physical mapping, marker analysis, and disease mapping. Chromosome 21 has been extensively studied in this fashion, and a single set of hybrids has been utilized in mapping the majority of chromosome 21 markers. The utility of a set of hybrids depends upon the definition of the human chromosome content. Recently, Chumakov and coworkers (1) utilized 198 chromosome 21 markers in the preliminary analysis of YACs spanning chromosome 21q. We have used these same markers to evaluate the STS content of a set of 27 chromosome 21 somatic cell hybrids, resulting in the description of the breakpoints at the molecular level, as well as the definition of 35 "bins. " The detailed molecular definition of chromosome 21 content of the hybrids, in combination with the further analysis of chromosome 21 YACs (2), has resulted in the most detailed picture of chromosome 21 to date.
Collapse
Affiliation(s)
- S L Graw
- Eleanor Roosevelt Institute, Denver, Colorado 80206, USA
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Wang D, Zhu Y, Smith CL. A set of inter-Alu PCR markers for chromosome 21 generated from pulsed-field gel-fractionated NotI restriction fragments. Genomics 1995; 26:318-26. [PMID: 7601458 DOI: 10.1016/0888-7543(95)80216-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genomic probes can be efficiently obtained for specific chromosomal regions by PCR amplification of gel slices containing fractionated restriction enzyme-cleaved DNA. Here, single-copy, human-specific DNA sequences were amplified using inter-Alu PCR on gel slices containing a NotI digest of DNA from hybrid cell line WAV17. Rodent cell line WAV17 contains human chromosome 21. About 75% of the 0.15- to 3-kb inter-Alu PCR products could be regionally assigned, en masse, by hybridization experiments using inter-Alu PCR probes generated from cell lines containing portions of chromosome 21. This work produced 10 new chromosome 21 markers that came from regions of 21q containing few useful markers. These markers were needed to finish a NotI restriction map for 21q (Wang and Smith (1994) Genomics 20: 441). This approach provides markers needed to close map gaps and for top-down mapping approaches.
Collapse
Affiliation(s)
- D Wang
- Center for Advanced Biotechnology, Boston University, Massachusetts 02215, USA
| | | | | |
Collapse
|
13
|
Raz R, Cheung K, Ling L, Levy DE. Three distinct loci on human chromosome 21 contribute to interferon-alpha/beta responsiveness. SOMATIC CELL AND MOLECULAR GENETICS 1995; 21:139-45. [PMID: 7570186 DOI: 10.1007/bf02255789] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The species specificity of interferons (IFNs) depends on restricted recognition of these ligands by multisubunit cell surface receptors. Expression of the human receptor subunit IFNAR in mouse cells conferred sensitivity only to one subtype of human IFN, IFN-alpha B. Other genes on human chromosome 21 were required for responses to other subtypes of type I IFN. In contrast, IFNAR expression in hamster cells did not confer sensitivity to any human IFN tested, including IFN-alpha B. Using human-hamster somatic cell hybrids, we mapped the Ifnabr gene, encoding a ligand-binding subunit of the IFN-alpha/beta (type I) receptor, to human chromosome 21. Ifnabr colocalized with Ifnar to the distal region of q22.1. The presence of a chromosomal fragment encoding IFNABR and IFNAR was also not sufficient to confer sensitivity to human IFN. In contrast, hybrids carrying in addition the region 21q22.2 showed a full response to human IFN-alpha B, suggesting that a gene located in this region encodes a third factor required for type I IFN receptor activity.
Collapse
Affiliation(s)
- R Raz
- Department of Pathology, New York University School of Medicine, New York 10016, USA
| | | | | | | |
Collapse
|
14
|
Ochman H, Buckholtz LA. Physical structure of human chromosome 21: an analysis of YACs spanning 21q. Mamm Genome 1995; 6:84-9. [PMID: 7767010 DOI: 10.1007/bf00303249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We have resolved the sizes of the yeast artificial chromosomes (YACs) from an ordered library spanning the entire long arm of Chromosome (Chr) 21 to examine the proximity of sequence-tagged sites (STS) originally used to position these clones. The average insert length was 540 kilobases, and some 18% of the 765 clones have either lost or generated multiple YACs during cultivation. Comparing the sizes of YACs that share common sites allowed the identification of an additional 8% of the clones with large scale additions or deletions. Maximum physical distances between chromosome markers, as established by the co-occurrence of STS on a single YAC, generally agreed with those estimated by other procedures, except for a large region in 21q21. In addition to providing insights into the structure, mapping and organization of this chromosome, knowledge of the sizes and contents of these clones will greatly facilitate the acquisition of any sequence present in this library.
Collapse
Affiliation(s)
- H Ochman
- Department of Biology, University of Rochester, New York 14627, USA
| | | |
Collapse
|
15
|
Bosch A, Wiemann S, Guimerà J, Ansorge W, Patterson D, Estivill X. Five new microsatellite polymorphisms at the q21 region of human chromosome 21. Hum Genet 1995; 95:119-22. [PMID: 7814016 DOI: 10.1007/bf00225090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Five clones, containing polymorphic CA-repeat sequences, have been isolated from a specific human chromosome 21 phage library and have been localised to band q21 of chromosome 21 using a somatic cell hybrid panel. These highly repetitive sequences (D21S1263, D21S1264, D21S1415, D21S1417 and D21S1420) have been characterised in the CEPH reference parents and have heterozygosities ranging from 0.30 to 0.81 and an average polymorphism information content (PIC) of 0.62. The relative order of these markers, based on the somatic cell hybrid panel, is cen-D21S1417, D21S1420-D21S1263, D21S1415-D21S1264-tel. The most polymorphic marker (D21S1264) has been included in the chromosome 21 genetic map. They have also been localised in the CEPH/Généthon YAC panel, providing a refined localisation of these polymorphic sequences. These five CA-repeat markers should provide a better characterisation of the q21 region of chromosome 21.
Collapse
Affiliation(s)
- A Bosch
- Molecular Genetics Department, Hospital Duran i Reynals, Barcelona, Catalunya, Spain
| | | | | | | | | | | |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- E Soeda
- RIKEN Gene Bank, Institute of Physical and Chemical Research, Tsukuba Science City, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
The translocation between chromosomes 8 and 21, t(8;21)(q22;q22), is the most frequent abnormality seen in approximately 46% of patients with acute myeloid leukemia with French-America-British (FAB)-M2 morphology and an aneuploid karyotype. The breakpoints in this translocation have been characterized at the molecular level, and the genes involved are AML1 on chromosome 21 and ETO (eight twenty one) on chromosome 8. AML1 has homology to the alpha subunit of the murine polyoma enhancer binding protein, pebp2, and to the segmentation gene, runt, of Drosophila melanogaster. ETO, also called MTG8 (myeloid translocation gene on 8) has no overall homology to known proteins, but it contains two DNA-binding zinc finger motifs and several regions that are proline- and serine-rich. Both AML1 and ETO are thought to be transcription factors because the motifs they contain are found in other transcription factors. Both genes are transcribed from telomere to centromere, and cytogenetic analysis of variant translocations has shown that the critical junction always conserved is on the derivative 8 chromosome. The rearrangement between the two chromosomes results in a fusion gene that contains the 5' region of AML1 including that homologous to runt fused to almost all of ETO. The fusion transcript from the der(8) chromosome is consistently detected in patients with the t(8;21). The translocation can be detected at the molecular level with selected genomic DNA probes from chromosome 21 and from chromosome 8 near the breakpoint in 80-100% of the t(8;21) patients at diagnosis and in relapse, and with reverse transcriptase-polymerase chain reaction (RT-PCR) in all of the patients at diagnosis and in long-term remission. These results indicate that leukemic clones are still circulating in patients who have been in remission for as long as 8 years.
Collapse
Affiliation(s)
- G Nucifora
- Department of Medicine, University of Chicago, Illinois
| | | |
Collapse
|
18
|
Bosch A, Wiemann S, Ansorge W, Patterson D, Estivill X. Three CA/GT repeat polymorphisms from loci D21S414 and D21S1234 on human chromosome 21. Hum Genet 1994; 93:359-60. [PMID: 8125493 DOI: 10.1007/bf00212043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report three new polymorphic CA repeat microsatellites (ABM-21, ABM-C37A, and ABM-C37B) in two different loci (D21S414 and D21S1234), located in bands q21 and q11.2 of human chromosome 21 (HC21) and that were isolated from a HC21 phage library (LA21NS01). Heterozygosities for ABM-21, ABM-C37A, and ABM-C37B were 0.74, 0.50, and 0.67 respectively. These three CA repeat markers should be useful in the construction of a high resolution genetic map of this region of HC21.
Collapse
Affiliation(s)
- A Bosch
- Molecular Genetics Department, Hospital Duran i Reynals, L'Hospitalet de Llobregat, Catalunya, Spain
| | | | | | | | | |
Collapse
|
19
|
Ozawa N, Kano T, Taga C, Hattori M, Sakaki Y, Suzuki H. An exon-trapping system with a newly constructed trapping vector pEXT2; its application to the proximal region of the human chromosome 21 long arm. FEBS Lett 1993; 325:303-8. [PMID: 7686513 DOI: 10.1016/0014-5793(93)81094-g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have developed an exon-trapping system with a newly constructed trapping vector containing multiple cloning sites (designated pEXT2). The system revealed high sensitivity for trapping a control exon from several hundred kbp of DNA. We have applied the system to the cosmid clones located on human chromosome 21p11-q21, and identified two fragments highly homologous to neurofibromatosis 1 (NF1) gene and a clearly transcribed fragment hybridized with approximately 1.6 kb RNA from human brain and human glioblastoma A172 cell.
Collapse
Affiliation(s)
- N Ozawa
- Shionogi Institute for Medical Science, Osaka, Japan
| | | | | | | | | | | |
Collapse
|
20
|
Crété N, Delabar JM, Rahmani Z, Yaspo ML, Kraus J, Marks A, Sinet PM, Créau-Goldberg N. Partial physical map of human chromosome 21 from fibroblast and lymphocyte DNA. Hum Genet 1993; 91:245-53. [PMID: 8478008 DOI: 10.1007/bf00218265] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A partial physical map of the human chromosome 21 including 26 genes and anonymous sequences was established by pulsed-field gel electrophoresis analysis of restriction fragments obtained from lymphocyte and fibroblast DNAs. The sizes of the restriction fragments obtained by total digestion with eight different enzymes were compared in these two tissues. Differences resulting from the variations in the methylation state of the restriction sites were frequently observed. These differences and partial digestions were used to estimate the order and the distances between genes and sequences. Six linkage groups were defined: D21S13-D21S16, D21S1-D21S11, D21S65-D21S17, (D21S55,ERG)-ETS2, BCEI-D21S19-D21S42-D21S113-CBS-CRYA1, and COL6A2-S100B. For six intergenic distances the resolution of previous maps was significantly increased.
Collapse
Affiliation(s)
- N Crété
- URA CNRS 1335, Hôpital Necker-Enfants Malades, Paris, France
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Cheng S, Lutfalla G, Uze G, Chumakov IM, Gardiner K. GART, SON, IFNAR, and CRF2-4 genes cluster on human chromosome 21 and mouse chromosome 16. Mamm Genome 1993; 4:338-42. [PMID: 8318737 DOI: 10.1007/bf00357094] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- S Cheng
- Eleanor Roosevelt Institute for Cancer Research, Denver, Colorado 80206
| | | | | | | | | |
Collapse
|
22
|
Chumakov I, Rigault P, Guillou S, Ougen P, Billaut A, Guasconi G, Gervy P, LeGall I, Soularue P, Grinas L. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature 1992; 359:380-7. [PMID: 1406950 DOI: 10.1038/359380a0] [Citation(s) in RCA: 297] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A continuous array of overlapping clones covering the entire human chromosome 21q was constructed from human yeast artificial chromosome libraries using sequence-tagged sites as landmarks specifically detected by polymerase chain reaction. The yeast artificial chromosome contiguous unit starts with pericentromeric and ends with subtelomeric loci of 21q. The resulting order of sequence-tagged sites is consistent with other physical and genetic mapping data. This set of overlapping clones will promote our knowledge of the structure of this chromosome and the function of its genes.
Collapse
Affiliation(s)
- I Chumakov
- Centre d'Etude du Polymorphisme Humain (CEPH), Paris, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Chang YJ, McCabe RT, Rennert H, Budarf ML, Sayegh R, Emanuel BS, Skolnick P, Strauss JF. The human "peripheral-type" benzodiazepine receptor: regional mapping of the gene and characterization of the receptor expressed from cDNA. DNA Cell Biol 1992; 11:471-80. [PMID: 1326278 DOI: 10.1089/dna.1992.11.471] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A cDNA for the human "peripheral-type" benzodiazepine receptor (PBR) was isolated from a liver cDNA library. The 851-nucleotide probe hybridized with a approximately 1 kb mRNA in Northern blots of RNA extracted from various human tissues and cell lines. The human PBR probe was hybridized to DNA from a somatic cell hybrid mapping panel to determine that the gene maps to chromosome 22. With a regional mapping panel for chromosome 22, we localized the gene within band 22q13.31. The ligand-binding properties of the receptor expressed from the cDNA were examined in transient expression experiments and compared to the endogenous human PBR. The PBR ligand [3H]PK 11195 had high affinity for the expressed receptor in COS-1 cells, but the affinities of a pair of isoquinoline propanamide enantiomers differed remarkably in expressed and endogenous human PBR. These findings reveal that the host cell and/or post-translational modification may have an important influence on PBR function.
Collapse
Affiliation(s)
- Y J Chang
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia 19104
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Lane MJ, Waterbury PG, Carroll WT, Smardon AM, Faldasz BD, Peshick SM, Mante S, Huckaby CS, Kouri RE, Hanlon DJ. Variation in genomic Alu repeat density as a basis for rapid construction of low resolution physical maps of human chromosomes. Chromosoma 1992; 101:349-57. [PMID: 1576885 DOI: 10.1007/bf00346014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human DNA restriction fragments containing high numbers of Alu repeat sequences can be preferentially detected in the presence of other human DNA restriction fragments in DNA from human: rodent somatic cell hybrids when the DNA is fragmented with enzymes that cleave mammalian DNA infrequently. This ability to lower the observed human DNA complexity allowed us to develop an approach to order rapidly somatic hybrid cell lines retaining overlapping human genomic domains. The ordering process also generates a relative physical map of the human fragments detected with Alu probe DNA. This process can generate physical mapping information for human genomic domains as large as an entire chromosome (100,000 kb). The strategy is demonstrated by ordering Alu-detected NotI fragments in a panel of mouse: human hybrid cells that span the entire long arm of human chromosome 17.
Collapse
Affiliation(s)
- M J Lane
- Department of Medicine, State University of New York, Syracuse 13210
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Ichikawa H, Shimizu K, Saito A, Wang DN, Oliva R, Kobayashi H, Kaneko Y, Miyoshi H, Smith CL, Cantor CR. Long-distance restriction mapping of the proximal long arm of human chromosome 21 with Not I linking clones. Proc Natl Acad Sci U S A 1992; 89:23-7. [PMID: 1346067 PMCID: PMC48167 DOI: 10.1073/pnas.89.1.23] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human chromosome 21 is the smallest of the 22 autosomes and 2 sex chromosomes. Hybridization of the human repetitive sequence Alu to pulsed-field gel-fractionated Not I-digested genomic DNA from a human-mouse hybrid cell line containing chromosome 21 as the sole human component identified chromosome 21 Not I restriction fragments. A Not I restriction map of regions of the chromosome was constructed, by identifying neighboring Alu bands with Not I linking clones. This approach simplifies the task of physical mapping and avoids ambiguities in Not I fragment assignments that arise from gel-to-gel mobility variations. A contiguous map was constructed with six Not I linking clones that covers at least the proximal one-third of the long arm of chromosome 21 and spans 20 megabases. A more detailed restriction map revealed 11 likely CpG islands in this region and localized 11 additional DNA markers.
Collapse
Affiliation(s)
- H Ichikawa
- Department of Immunology and Virology, Saitama Cancer Center Research Institute, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Gao J, Erickson P, Gardiner K, Le Beau MM, Diaz MO, Patterson D, Rowley JD, Drabkin HA. Isolation of a yeast artificial chromosome spanning the 8;21 translocation breakpoint t(8;21)(q22;q22.3) in acute myelogenous leukemia. Proc Natl Acad Sci U S A 1991; 88:4882-6. [PMID: 2052570 PMCID: PMC51771 DOI: 10.1073/pnas.88.11.4882] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The 8;21 translocation is one of the most common specific rearrangements in acute myelogenous leukemia. We have identified markers (D21S65 and a Not I boundary clone, Not-42, referred to as probe B) flanking the chromosome 21 translocation breakpoint (21q22.3) that demonstrate physical linkage in normal genomic DNA, by using at least three restriction endonucleases (Not I, Sac II, and BssHII), and that are located not more than 250-280 kilobases apart. Pulsed-field gel analysis of DNA from somatic cell hybrids containing the 8;21 translocation chromosomes demonstrates rearrangement of these markers. A 470-kilobase yeast artificial chromosome, YAC-Not-42, has been isolated that contains both probes. Mapping of lambda subclones constructed from YAC-Not-42 suggests that greater than 95% (25/26 probes tested) of the yeast artificial chromosome DNA is located on the proximal (D21S65) side of the breakpoint. In situ hybridization studies using metaphase chromosomes from five acute myelogenous leukemia patients with the 8;21 translocation confirmed these results and demonstrated the translocation of probe B to the derivative chromosome 8. A chromosome walk of approximately 39 kilobases from probe B has allowed identification of the breakpoint in DNA from a somatic cell hybrid containing the derivative chromosome 8. Since probe B contains conserved DNA sequences and is in close proximity to the translocation breakpoint, it may represent a portion of the involved gene on chromosome 21.
Collapse
MESH Headings
- Blotting, Southern
- Chromosomes, Fungal
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- DNA Probes
- DNA, Neoplasm/genetics
- Gene Library
- Humans
- Leukemia, Myeloid, Acute/genetics
- Nucleic Acid Hybridization
- Restriction Mapping
- Saccharomyces cerevisiae/genetics
- Translocation, Genetic
Collapse
Affiliation(s)
- J Gao
- Division of Medical Oncology, University of Colorado Health Sciences Center, Denver
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Gao JZ, Erickson P, Patterson D, Jones C, Drabkin H. Isolation and regional mapping of NotI and EagI clones from human chromosome 21. Genomics 1991; 10:166-72. [PMID: 2045100 DOI: 10.1016/0888-7543(91)90497-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
NotI and EagI boundary libraries were constructed for human chromosome 21. One hundred forty-seven clones were isolated from the somatic cell hybrid 72532X-6 and localized using a hybrid mapping panel. After identification of those clones, which were isolated more than once, as well as those probes derived from a previously unrecognized integrated non-chromosome-21 fragment, 58 individual boundary clones (plus 2 additional NotI-EcoRI clones isolated from a flow-sorted library) were localized to 11 separate regions. The distribution of these probes is highly nonrandom, with 50% of the clones located in the distal band 21q22.3. Two probes, Not50 and Eag101, map to regions in the very proximal long arm which may contain the gene responsible for familial Alzheimer's disease (AD1), and Not50 would appear to be more proximal than D21S16 (E9). Twenty-eight probes map to the region between superoxide dismutase (SOD1) and the ETS2 oncogene, which appears to contain genes responsible for many of the phenotypic features of Down syndrome. Twenty clones contain (GT)n repeats, as determined by hybridization to a CA polymer, and should provide additional highly polymorphic probes. Closure of gaps in the physical linkage map of chromosome 21 should be facilitated by the isolation of these probes, as they identify many of the unmethylated CpG-rich islands that have hindered pulsed-field gel analysis. They will also be useful in identifying a set of genes in proximity to NotI and EagI restriction sites, as well as conserved DNA sequences for comparative mapping studies.
Collapse
Affiliation(s)
- J Z Gao
- University of Colorado Health Sciences Center, Denver 80262
| | | | | | | | | |
Collapse
|
28
|
Bellis M, Gérard A, Charlieu JP, Marçais B, Brun ME, Viegas-Péquignot E, Carter DA, Roizès G. Construction and characterization of a partial library of yeast artificial chromosomes from human chromosome 21. DNA Cell Biol 1991; 10:301-10. [PMID: 2029338 DOI: 10.1089/dna.1991.10.301] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We report a protocol for cloning large DNA fragments in yeast artificial chromosomes (YAC). A partial library has been constructed from a somatic hybrid containing chromosome 21 as the single source of human DNA. About 4.0 Mb of human DNA was recovered in 17 YAC clones. Three clones were analyzed by in situ hybridization and mapped on chromosome 21. One clone hybridized with the chromosome 21 centromeric region and may provide new insight both on the molecular structure of centromere and on the localization of Alzheimer disease gene.
Collapse
Affiliation(s)
- M Bellis
- CNRS UPR 8402 & INSERM U. 249, Institut de Biologie, Montpellier, France
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Delattre O, Azambuja CJ, Aurias A, Zucman J, Peter M, Zhang F, Hors-Cayla MC, Rouleau G, Thomas G. Mapping of human chromosome 22 with a panel of somatic cell hybrids. Genomics 1991; 9:721-7. [PMID: 2037296 DOI: 10.1016/0888-7543(91)90366-m] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The adenylosuccinate lyase (ADSL) which is essential for generating adenylate, maps to the long arm of chromosome 22. By using a Chinese hamster ovary cell line deficient in ADSL activity, we have constructed a set of 17 somatic cell hybrids containing defined regions of human chromosome 22. This panel was extended with six additional hybrids, obtained in other laboratories using various methods of selection. Southern analysis of the hybrids with 38 chromosome 22 probes defined 14 different subregions which could be linearly organized on the long arm of chromosome 22. The order of the probes thus deduced is fully compatible with their previous localization and with the genetic map. The ADSL gene was further sublocalized between the MB and D22S22. This panel, which enables the rapid assignment of chromosome 22 single copy probes to small subregions, will be an important tool in the construction of a detailed physical map of this part of the genome.
Collapse
Affiliation(s)
- O Delattre
- Génétique des Tumeurs, Institut Curie, Paris, France
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Petersen MB, Slaugenhaupt SA, Lewis JG, Warren AC, Chakravarti A, Antonarakis SE. A genetic linkage map of 27 markers on human chromosome 21. Genomics 1991; 9:407-19. [PMID: 1674496 DOI: 10.1016/0888-7543(91)90406-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have constructed a genetic linkage map of the long arm of human chromosome 21 comprising 27 DNA markers. This map is an updated version of that reported earlier by group (1989, Genomics 4: 579-591), which contained 17 DNA markers. The current markers consist of 10 genes and 17 anonymous sequences. Traditional methods (restriction fragment length polymorphisms) were used to map 25 of these markers, whereas 2 markers were studied by polymerase chain reaction amplification of (GT)n dinucleotide repeats. Linkage analysis was performed on 40 CEPH families using the computer program packages LINKAGE, CRI-MAP, and MAPMAKER. Recombination rates were significantly different between the sexes, with the male map being 132 cM and the female map being 161 cM, assuming Kosambi interference and a variable ratio of sex difference in recombination. Approximately one-half of the crossovers in either sex occur distally, in terminal band 21q22.3, which also contains 16 of the markers studied. The average distance between adjacent markers was 6 cM.
Collapse
Affiliation(s)
- M B Petersen
- Center for Medical Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | | | | | | | | | | |
Collapse
|
31
|
Chromosome microdissection and cloning in human genome and genetic disease analysis. Proc Natl Acad Sci U S A 1991; 88:1844-8. [PMID: 2000391 PMCID: PMC51122 DOI: 10.1073/pnas.88.5.1844] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A procedure has been described for microdissection and microcloning of human chromosomal DNA sequences in which universal amplification of the dissected fragments by Mbo I linker adaptor and polymerase chain reaction is used. A very large library comprising 700,000 recombinant plasmid microclones from 30 dissected chromosomes of human chromosome 21 was constructed. Colony hybridization showed that 42% of the clones contained repetitive sequences and 58% contained single or low-copy sequences. The insert sizes generated by complete Mbo I cleavage ranged from 50 to 1100 base pairs with a mean of 416 base pairs. Southern blot analysis of microclones from the library confirmed their human origin and chromosome 21 specificity. Some of these clones have also been regionally mapped to specific sites of chromosome 21 by using a regional mapping panel of cell hybrids. This chromosome microtechnology can generate large numbers of microclones with unique sequences from defined chromosomal regions and can be used for processes such as (i) isolating corresponding yeast artificial chromosome clones with large inserts, (ii) screening various cDNA libraries for isolating expressed sequences, and (iii) constructing region-specific libraries of the entire human genome. The studies described here demonstrate the power of this technology for high-resolution genome analysis and explicate their use in an efficient search for disease-associated genes localized to specific chromosomal regions.
Collapse
|
32
|
Affiliation(s)
- D A Powers
- Hopkins Marine Station, Department of Biological Sciences, Stanford University, Pacific Grove, California 93950
| |
Collapse
|
33
|
Burmeister M, Kim S, Price ER, de Lange T, Tantravahi U, Myers RM, Cox DR. A map of the distal region of the long arm of human chromosome 21 constructed by radiation hybrid mapping and pulsed-field gel electrophoresis. Genomics 1991; 9:19-30. [PMID: 2004760 DOI: 10.1016/0888-7543(91)90216-2] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have used radiation hybrid (RH) mapping and pulsed-field gel electrophoresis (PFGE) to determine the order and positions of 28 DNA markers from the distal region of the long arm of human chromosome 21. The maps generated by these two methods are in good agreement. This study, combined with that of D. R. Cox et al. (1990, Science 250:245-250), results in an RH map that covers the long arm of chromosome 21 (21q). We have used a subtelomeric probe to show that our map includes the telomere and have identified single-copy genes and markers within 200 kbp of the telomere. Comparison of the physical and RH maps with genetic linkage maps shows "hot spots" of meiotic recombination in the distal region, one of which is close to the telomere, in agreement with previous cytogenetic observations of increased recombination frequency near telomeres.
Collapse
Affiliation(s)
- M Burmeister
- Department of Physiology, University of California, San Francisco 94143
| | | | | | | | | | | | | |
Collapse
|
34
|
Ferretti L, Leone P, Sgaramella V. Long range restriction analysis of the bovine casein genes. Nucleic Acids Res 1990; 18:6829-33. [PMID: 2263448 PMCID: PMC332738 DOI: 10.1093/nar/18.23.6829] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pulsed field gel electrophoresis (PFGE) was used to analyse the organization of the bovine alpha s1, alpha s2, beta and kappa casein genes. High molecular weight DNA was prepared from fibroblasts and lymphocytes embedded in agarose and was digested with the restriction endonucleases Clal, Sall, Smal, Xhol. The digestion products were separated by PFGE, transfered to nitrocellulose filters and hybridized to probes corresponding to the cDNAs of the four bovine casein genes. The casein genes were demonstrated to be physically linked within a region of 300 kb, represented by two adjacent Xhol fragments in fibroblasts and by a single fragment in lymphocytes. A restriction map of the casein locus was derived and the order of the genes was shown to be kappa, alpha s2, beta, alpha s1.
Collapse
|
35
|
Cox DR, Burmeister M, Price ER, Kim S, Myers RM. Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science 1990; 250:245-50. [PMID: 2218528 DOI: 10.1126/science.2218528] [Citation(s) in RCA: 462] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Radiation hybrid (RH) mapping, a somatic cell genetic technique, was developed as a general approach for constructing long-range maps of mammalian chromosomes. This statistical method depends on x-ray breakage of chromosomes to determine the distances between DNA markers, as well as their order on the chromosome. In addition, the method allows the relative likelihoods of alternative marker orders to be determined. The RH procedure was used to map 14 DNA probes from a region of human chromosome 21 spanning 20 megabase pairs. The map was confirmed by pulsed-field gel electrophoretic analysis. The results demonstrate the effectiveness of RH mapping for constructing high-resolution, contiguous maps of mammalian chromosomes.
Collapse
Affiliation(s)
- D R Cox
- Department of Psychiatry, University of California, San Francisco 94143
| | | | | | | | | |
Collapse
|
36
|
Langer JA, Rashidbaigi A, Lai LW, Patterson D, Jones C. Sublocalization on chromosome 21 of human interferon-alpha receptor gene and the gene for an interferon-gamma response protein. SOMATIC CELL AND MOLECULAR GENETICS 1990; 16:231-40. [PMID: 2141727 DOI: 10.1007/bf01233359] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The cellular responses to alpha and beta interferons (IFN-alpha and -beta) are mediated through the IFN-alpha/beta (type I) receptor, while the response to IFN-gamma is mediated through the IFN-gamma (type II) receptor. The receptors for IFN-alpha/beta and IFN-gamma are encoded by genes on human chromosomes 21 and 6q, respectively. The presence of chromosome 21q confers both ligand binding and responsiveness to human IFN-alpha/beta, whereas chromosome 6q confers binding of Hu-IFN-gamma, but not cellular responsiveness on somatic cell hybrids. Chromosome 6q (i.e., the Hu-IFN-gamma receptor gene) and chromosome 21q are both necessary for the cellular response of somatic cell hybrids (from fibroblasts) to Hu-IFN-gamma. It is conceivable that the factor mediating activity through the IFN-gamma receptor is, in fact, the IFN-alpha receptor, or that the two genes are distinct but part of an "interferon response" region. Here we more precisely localize on human chromosome 21 the genes for the IFN-alpha receptor and for the factor(s) mediating the action of IFN-gamma through the chromosome 6-encoded receptor. Hamster-human somatic cell hybrids containing various fragments of human chromosome 21 were used. The presence of the human IFN-alpha/beta receptor was determined by binding 32P-labeled human IFN-alpha to cells, covalently cross-linking the [32P]IFN-alpha-receptor complex, and analyzing it by SDS-polyacrylamide gel electrophoresis. The presence of the IFN-gamma receptor-related factor mediating cellular responsiveness was determined by HLA induction in hybrid cells containing the IFN-gamma receptor (chromosome 6q), a transfected copy of the human HLA-B7 gene, and various portions of chromosome 21. In all hybrids examined, the two genes cosegregate. Specifically, both genes are localized to the region of chromosome 21 containing the markers D21S58, D21S65, and GART and appear to be proximal to D21S58. The implications for IFN action are discussed.
Collapse
Affiliation(s)
- J A Langer
- Department of Molecular Genetics and Microbiology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway 08854-5635
| | | | | | | | | |
Collapse
|
37
|
Elson A, Levanon D, Brandeis M, Dafni N, Bernstein Y, Danciger E, Groner Y. The structure of the human liver-type phosphofructokinase gene. Genomics 1990; 7:47-56. [PMID: 2139864 DOI: 10.1016/0888-7543(90)90517-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have isolated the gene for the human liver-type phosphofructokinase, from upstream to the 5' mRNA terminus to beyond the polyadenylation site. The gene is at least 28 kb long and is divided into 22 exons; it contains conventional splice-junction sequences and one polyadenylation signal. Exons and introns are quite rich in G and C residues; some 60% of all nucleotides are either G or C. Five possible sites of polymorphism have been found. The gene structure reveals no signs of internal similarities despite protein sequence evidence which suggests that the PFK molecule is divided into two similar halves. The structure and organization of the human liver-type PFK gene are shown to be extremely similar to those of the rabbit muscle-type PFK.
Collapse
Affiliation(s)
- A Elson
- Department of Molecular Genetics and Virology, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | | | | | | |
Collapse
|
38
|
Higgins MJ, Turmel C, Noolandi J, Neumann PE, Lalande M. Construction of the physical map for three loci in chromosome band 13q14: comparison to the genetic map. Proc Natl Acad Sci U S A 1990; 87:3415-9. [PMID: 1970636 PMCID: PMC53911 DOI: 10.1073/pnas.87.9.3415] [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: 12/29/2022] Open
Abstract
Pulsed-field gel electrophoresis (PFGE) and deletion mapping are being used to construct a physical map of the long arm of human chromosome 13. The present study reports a 2700-kilobase (kb) Not I long-range restriction map encompassing the 13q14-specific loci D13S10, D13S21, and D13S22, which are detected by the cloned DNA markers p7D2, pG24E2.4, and pG14E1.9, respectively. Analysis of a panel of seven cell lines that showed differential methylation at a Not I site between D13S10 and D13S21 proved physical linkage of the two loci to the same 875-kb Not I fragment. D13S22 mapped to a different Not I fragment, precluding the possibility that D13S22 is located between D13S10 and D13S21. PFGE analysis of Not I partial digests placed the 1850-kb Not I fragment containing D13S22 immediately adjacent to the 875-kb fragment containing the other two loci. The proximal rearrangement breakpoint in a cell line carrying a del13(q14.1q21.2) was detected by D13S21 but not by D13S10, demonstrating that D13S21 lies proximal to D13S10. Quantitative analysis of hybridization signals of the three DNA probes to DNA from the same cell line indicated that only D13S10 was deleted, establishing the order of these loci to be cen-D13S22-D13S21-D13S10-tel. Surprisingly, this order was estimated to be 35,000 times less likely than that favored by genetic linkage analysis.
Collapse
Affiliation(s)
- M J Higgins
- National Research Council of Canada, Biotechnology Research Institute, Montreal, PQ
| | | | | | | | | |
Collapse
|
39
|
Affiliation(s)
- R S Larson
- Center for Blood Research, Harvard Medical School, Boston, MA 02115
| | | |
Collapse
|
40
|
Gardiner K, Horisberger M, Kraus J, Tantravahi U, Korenberg J, Rao V, Reddy S, Patterson D. Analysis of human chromosome 21: correlation of physical and cytogenetic maps; gene and CpG island distributions. EMBO J 1990; 9:25-34. [PMID: 2295313 PMCID: PMC551626 DOI: 10.1002/j.1460-2075.1990.tb08076.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human chromosome 21 has been analyzed by pulsed-field gel electrophoresis using somatic cell hybrids containing limited regions of the chromosome and greater than 60 unique sequence probes. Thirty-three independent NotI fragments have been identified, totalling 43 million bp. This must account for essentially the entire long arm, and therefore gaps remaining in the map must be small. The extent of the pulsed-field map has allowed the direct correlation of the physical map with the cytogenetic map: translocation breakpoints can be unambiguously positioned along the long arm and the distances between them measured in base pairs. Three breakpoints have been identified, providing physical confirmation of cytogenetic landmarks. Information on sequence organization has been obtained: (i) 60% of the unique sequence probes are located within 11 physical linkage groups which can be contained in only 20% of the long arm; (ii) 9/21 genes are clustered within 4%; (iii) translocation breakpoints appear to occur within CpG island regions, making their identification difficult by pulsed-field techniques. This analysis contributes to the human genome mapping effort, and provides information to guide the rapid investigation of the biology of chromosome 21.
Collapse
Affiliation(s)
- K Gardiner
- Eleanor Roosevelt Institute for Cancer Research, Denver, CO
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Rosen H, Law SK. The leukocyte cell surface receptor(s) for the iC3b product of complement. Curr Top Microbiol Immunol 1990; 153:99-122. [PMID: 2137074 DOI: 10.1007/978-3-642-74977-3_6] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
CR3 is probably the major adhesion molecule on monocytes and neutrophils. Its function as a phagocytic receptor for iC3b-coated particles has been well characterized. CR3 also has binding affinity for other ligands, including those that compete with iC3b such as fibrinogen, factor X, and beta-glucan, and those that do not such as bacterial LPS. CR3 binding to endothelial cells probably plays an important role in the extravascular migration of monocytes and neutrophils, but the ligand that it recognizes on endothelial cells has not been identified. Structurally CR3 belongs to the integrin family, and it shares a common subunit with p150,95 and LFA-1. The expression of these three membrane antigens appear to be limited to leukocytes, and they are sometimes referred to collectively as the leukocyte integrins. All three antigens have a common binding affinity for bacterial LPS. p150,95 also has affinity for iC3b, but p150,95/iC3b-dependent cellular responses has not been demonstrated. Its status as a complement receptor therefore awaits further experimental support.
Collapse
Affiliation(s)
- H Rosen
- Sir William Dunn School of Pathology, University of Oxford, UK
| | | |
Collapse
|
42
|
McCormick MK, Shero JH, Cheung MC, Kan YW, Hieter PA, Antonarakis SE. Construction of human chromosome 21-specific yeast artificial chromosomes. Proc Natl Acad Sci U S A 1989; 86:9991-5. [PMID: 2690083 PMCID: PMC298628 DOI: 10.1073/pnas.86.24.9991] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Chromosome 21-specific yeast artificial chromosomes (YACs) have been constructed by a method that performs all steps in agarose, allowing size selection by pulsed-field gel electrophoresis and the use of nanogram to microgram quantities of DNA. The DNA sources used were hybrid cell line WAV-17, containing chromosome 21 as the only human chromosome and flow-sorted chromosome 21. The transformation efficiency of ligation products was similar to that obtained in aqueous transformations and yielded YACs with sizes ranging from 100 kilobases (kb) to greater than 1 megabase when polyamines were included in the transformation procedure. Twenty-five YACs containing human DNA have been obtained from a mouse-human hybrid, ranging in size from 200 to greater than 1000 kb, with an average size of 410 kb. Ten of these YACs were localized to subregions of chromosome 21 by hybridization of RNA probes (corresponding to the YAC ends recovered in Escherichia coli) to a panel of somatic cell hybrid DNA. Twenty-one human YACs, ranging in size from 100 to 500 kb, with an average size of 150 kb, were obtained from approximately equal to 50 ng of flow-sorted chromosome 21 DNA. Three were localized to subregions of chromosome 21. YACs will aid the construction of a physical map of human chromosome 21 and the study of disorders associated with chromosome 21 such as Alzheimer disease and Down syndrome.
Collapse
Affiliation(s)
- M K McCormick
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | | | | | | | | |
Collapse
|
43
|
Bickmore WA, Porteous DJ, Christie S, Seawright A, Fletcher JM, Maule JC, Couillin P, Junien C, Hastie ND, van Heyningen V. CpG islands surround a DNA segment located between translocation breakpoints associated with genitourinary dysplasia and aniridia. Genomics 1989; 5:685-93. [PMID: 2556343 DOI: 10.1016/0888-7543(89)90109-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have isolated a DNA segment absent from all the constitutionally deleted chromosomes 11 of our patients with Wilms tumor. This marker separates two balanced translocations that break in band 11p13: the distal one associated with aniridia (AN2), and the proximal one with genitourinary dysplasia (GUD). The GUD breakpoint maps within the smallest region of overlap (SRO) for the Wilms tumor (WT) gene locus, thus strengthening the previous suggestion of an association between Wilms tumor and other abnormalities of the genitourinary system. The 11p13 translocation breakpoint associated with T-cell acute lymphatic leukemia (T-ALL) is centromeric to the SRO and separated from the WT locus by at least one known gene. This region of the human genome (11p13) is rich in CpG islands that potentially identify genes, some of which may be involved in the various phenotypes associated with the WAGR syndrome. This is consistent with the proposition that the majority of human genes are in G-negative bands.
Collapse
Affiliation(s)
- W A Bickmore
- MRC Human Genetics Unit, Western General Hospital, Edinburgh, United Kingdom
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Levine JD, Cech CL. Low Frequency Restriction Enzymes in Pulsed Field Electrophoresis. Nat Biotechnol 1989. [DOI: 10.1038/nbt1089-1033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
45
|
Gardiner K, Patterson D. Transverse alternating field electrophoresis and applications to mammalian genome mapping. Electrophoresis 1989; 10:296-302. [PMID: 2670545 DOI: 10.1002/elps.1150100505] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The transverse alternating field electrophoresis system is a pulsed field gel apparatus that has been used to separate DNA molecules that range in size from a few thousand to approximately 7 million base pairs. This apparatus uses a vertical gel and a simple electrode arrangement to produce electric fields that are uniform across all lanes of the gel. The velocity of identical molecules does not vary from lane to lane, and hence there is no distortion in the paths of the DNA. The performance of this system is illustrated here using the chromosomes from S. pombe and S. cerevisiae, and restriction enzyme digested mammalian DNA. The mobility of molecules up to 1100 kilobase pairs is linear with size and can be accomplished in overnight runs. Resolution of very large molecules requires electrophoresis for several days, but molecules from 200 to 7000 kilobase pairs can be separated on a single gel. This electrophoresis system has been used extensively in the construction of a physical map of human chromosome 21, and examples of this application are discussed.
Collapse
Affiliation(s)
- K Gardiner
- Eleanor Roosevelt Institute for Cancer Research, Denver, CO 80206
| | | |
Collapse
|
46
|
Affiliation(s)
- T K Kishimoto
- Center for Blood Research, Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115
| | | | | | | | | | | |
Collapse
|