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Dorritie K, Montagna C, Difilippantonio MJ, Ried T. Advanced molecular cytogenetics in human and mouse. Expert Rev Mol Diagn 2004; 4:663-76. [PMID: 15347260 PMCID: PMC4729310 DOI: 10.1586/14737159.4.5.663] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fluorescence in situ hybridization, spectral karyotyping, multiplex fluorescence in situ hybridization, comparative genomic hybridization, and more recently array comparative genomic hybridization, represent advancements in the field of molecular cytogenetics. The application of these techniques for the analysis of specimens from humans, or mouse models of human diseases, enables one to reliably identify and characterize complex chromosomal rearrangements resulting in alterations of the genome. As each of these techniques has advantages and limitations, a comprehensive analysis of cytogenetic aberrations can be accomplished through the utilization of a combination approach. As such, analyses of specific tumor types have proven invaluable in the identification of new tumor-specific chromosomal aberrations and imbalances (aneuploidy), as well as regions containing tumor-specific gene targets. Application of these techniques has already improved the classification of tumors into distinct categories, with the hope that this will lead to more tailored treatment strategies. These techniques, in particular the application of tumor-specific fluorescence in situ hybridization probes to interphase nuclei, are also powerful tools for the early identification of premalignant lesions.
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Affiliation(s)
| | - Cristina Montagna
- Genetics Branch, Center for CancerResearch, NCI/NIH, Bldg. 50, Rm. 1408, 50 South Drive, Bethesda, MD 20892–0913, USA, Tel: +1 301 435 3986, Fax: +1 301 402 1204
| | - Michael J. Difilippantonio
- Genetics Branch, Center for CancerResearch, NCI/NIH, Bldg. 50, Rm. 1408, 50 South Drive, Bethesda, MD 20892–8010, USA
| | - Thomas Ried
- Author for correspondence, Genetics Branch, Center for Cancer Research, NCI/NIH, Bldg. 50, Rm. 1408, 50 South Drive, Bethesda, MD, 20892–8010, USA, Tel.: +1 301 594 3118, Fax: +1 301 435 4428,
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2
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Kanai Y, Ushijima S, Tsuda H, Sakamoto M, Sugimura T, Hirohashi S. Aberrant DNA methylation on chromosome 16 is an early event in hepatocarcinogenesis. Jpn J Cancer Res 1996; 87:1210-7. [PMID: 9045955 PMCID: PMC5921026 DOI: 10.1111/j.1349-7006.1996.tb03135.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In order to clarify the significance of DNA methylation in both earlier and later stages of hepatocarcinogenesis, the DNA methylation state on chromosome 16, on which loss of heterozygosity (LOH) has frequently been detected in human hepatocellular carcinomas (HCCs), was examined. DNA from primary HCCs and tissues showing chronic hepatitis and liver cirrhosis, which are considered to be precancerous conditions, was analyzed by digestion with methylation-sensitive and non-sensitive restriction enzymes. DNA hypermethylation at the D16S32, tyrosine aminotransferase (TAT) and D16S7 loci and hypomethylation at the D16S4 locus were detected in 18%, 58%, 20% and 48% of examined HCCs, respectively. Aberrant DNA methylation occurred more frequently in advanced HCCs than in early HCCs. Moreover, DNA hypermethylation at the D16S32, TAT and D16S7 loci was frequently observed in chronic hepatitis and liver cirrhosis. The incidence of DNA hypermethylation was higher than that of LOH (42% at the TAT locus). These data suggest that DNA hypermethylation might predispose the locus to allelic loss. Aberrant DNA methylation is a significant change which may participate in the early developmental stages of HCCs.
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Affiliation(s)
- Y Kanai
- Pathology Division, National Cancer Center Research Institute, Tsukiji, Tokyo
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3
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Slagle BL, Zhou YZ, Birchmeier W, Scorsone KA. Deletion of the E-cadherin gene in hepatitis B virus-positive Chinese hepatocellular carcinomas. Hepatology 1993; 18:757-62. [PMID: 8104855 DOI: 10.1002/hep.1840180402] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Frequent allele loss from chromosome 16q was recently described for human tumors of the breast, prostate gland and liver, indicating the possible presence of a tumor-suppressor gene on that chromosome arm. In this study, the chromosome 16 allele status of 38 hepatocellular carcinomas in Chinese patients was determined with restriction-fragment-length polymorphism analysis. Tumor-specific allele loss was detected in 14 (74%) of 19 patients informative for 16p markers and in 22 (85%) of 26 patients informative for 16q markers. Quantitative densitometric analysis revealed reduction to hemizygosity of the E-cadherin cell adhesion gene (localized to 16q22.1) in 18 (64%) of the 28 patients for whom quantitative data were available. Reduced expression of E-cadherin has been associated with invasion and metastasis in several human cell lines and primary tumors, and our results suggest that one mechanism of reduced E-cadherin expression is the loss of one copy of the E-cadherin gene.
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Affiliation(s)
- B L Slagle
- Division of Molecular Virology, Baylor College of Medicine, Houston, Texas 77030
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4
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Miller AM, Savinelli EA, Couture SM, Hannigan GM, Han Z, Selden RF, Treco DA. Recombination walking: genetic selection of clones from pooled libraries of yeast artificial chromosomes by homologous recombination. Proc Natl Acad Sci U S A 1993; 90:8118-22. [PMID: 8367472 PMCID: PMC47299 DOI: 10.1073/pnas.90.17.8118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Recombination walking is based on the genetic selection of specific human clones from a yeast artificial chromosome (YAC) library by homologous recombination. The desired clone is selected from a pooled (unordered) YAC library, eliminating labor-intensive steps typically used in organizing and maintaining ordered YAC libraries. Recombination walking represents an efficient approach to library screening and is well suited for chromosome-walking approaches to the isolation of genes associated with common diseases.
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Affiliation(s)
- A M Miller
- Transkaryotic Therapies, Inc., Cambridge, MA 02139
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5
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Ya-gang X, Robinson WP, Spiegel R, Binkert F, Ruefenacht U, Schinzel AA. Parental origin of the supernumerary chromosome in trisomy 18. Clin Genet 1993; 44:57-61. [PMID: 8275560 DOI: 10.1111/j.1399-0004.1993.tb03847.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The parental origin of an extra chromosome in Edwards syndrome has been investigated in 23 families by the combination of the VNTR probe pERT25, two microsatellite polymorphisms for D18S34 and D18S40, and several two-allele polymorphisms. Of the 23 cases, 22 were informative, with 17 (77%) being maternal and 5 (23%) paternal in origin. These results support the previous investigations, suggesting that trisomy 18 is predominantly of maternal origin, although a higher rate of paternally derived cases was observed than previously reported. A significant increase in maternal age was found to be associated with meiotic nondisjunction. Parental age was increased in both the maternally and paternally derived cases, but the size of the latter class was small and did not reach statistical significance.
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Affiliation(s)
- X Ya-gang
- Institute of Medical Genetics, University of Zürich, Switzerland
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6
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Stallings RL, Doggett NA, Callen D, Apostolou S, Chen LZ, Nancarrow JK, Whitmore SA, Harris P, Michison H, Breuning M. Evaluation of a cosmid contig physical map of human chromosome 16. Genomics 1992; 13:1031-9. [PMID: 1505942 DOI: 10.1016/0888-7543(92)90016-l] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A cosmid contig physical map of human chromosome 16 has been developed by repetitive sequence finger-printing of approximately 4000 cosmid clones obtained from a chromosome 16-specific cosmid library. The arrangement of clones in contigs is determined by (1) estimating cosmid length and determining the likelihoods for all possible pairwise clone overlaps, using the fingerprint data, and (2) using an optimization technique to fit contig maps to these estimates. Two important questions concerning this contig map are how much of chromosome 16 is covered and how accurate are the assembled contigs. Both questions can be addressed by hybridization of single-copy sequence probes to gridded arrays of the cosmids. All of the fingerprinted clones have been arrayed on nylon membranes so that any region of interest can be identified by hybridization. The hybridization experiments indicate that approximately 84% of the euchromatic arms of chromosome 16 are covered by contigs and singleton cosmids. Both grid hybridization (26 contigs) and pulsed-field gel electrophoresis experiments (11 contigs) confirmed the assembled contigs, indicating that false positive overlaps occur infrequently in the present map. Furthermore, regional localization of 93 contigs and singleton cosmids to a somatic cell hybrid mapping panel indicates that there is no bias in the coverage of the euchromatic arms.
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Affiliation(s)
- R L Stallings
- Life Sciences Division, Los Alamos National Laboratory, New Mexico 87545
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7
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Ceccherini I, Romeo G, Lawrence S, Breuning MH, Harris PC, Himmelbauer H, Frischauf AM, Sutherland GR, Germino GG, Reeders ST. Construction of a map of chromosome 16 by using radiation hybrids. Proc Natl Acad Sci U S A 1992; 89:104-8. [PMID: 1729675 PMCID: PMC48184 DOI: 10.1073/pnas.89.1.104] [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: 12/28/2022] Open
Abstract
A human-hamster cell hybrid carrying a single copy of chromosome 16 as the only human genetic material was irradiated with a single dose of gamma-rays (7000 rads; 1 rad = 0.01 Gy) and then fused with a thymidine kinase-deficient hamster cell line (RJKM) to generate radiation hybrids retaining unselected fragments of this human chromosome. In two experiments, 223 hybrids were isolated in hypoxanthine/aminopterine/thymidine (HAT) medium and screened with 38 DNA probes, corresponding to anonymous DNA or gene sequences localized on chromosome 16. The most likely order and location of the 38 DNA sequences were established by multiple pairwise analysis and scaled to estimate physical distance in megabases. The order and the distances thus obtained are mostly consistent with available data on genetic and physical mapping of these markers, illustrating the usefulness of radiation hybrids for mapping.
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Affiliation(s)
- I Ceccherini
- Laboratorio di Genetica Molecolare, Istituto G. Gaslini, Genova, Italy
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8
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Shelley CS, Arnaout MA. The promoter of the CD11b gene directs myeloid-specific and developmentally regulated expression. Proc Natl Acad Sci U S A 1991; 88:10525-9. [PMID: 1683702 PMCID: PMC52961 DOI: 10.1073/pnas.88.23.10525] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human CD11b/CD18 (complement receptor type 3) is a member of the beta 2 integrin subfamily which also includes the heterodimers CD11a/CD18 and CD11c/CD18. The CD11 molecules and the common CD18 are the products of different genes that exhibit distinct though overlapping patterns of tissue- and developmental-specific expression. Whereas expression of CD11b and CD11c is almost exclusively restricted to cells of the myeloid lineage, that of CD11a and CD18 is panleukocytic. To begin to understand the mechanisms by which expression of these gene products is restricted to leukocytes and leukocyte subpopulations and to elucidate the mechanisms by which their expression is coordinated, we have cloned and characterized the promoter region of the CD11b gene. A single transcription initiation site has been identified and the region extending 242 base pairs upstream and 71 base pairs downstream of this site has been shown to be sufficient to direct tissue-, cell-, and development-specific expression in vitro, which mimics that of the CD11b gene in vivo. Within this region there are potential binding sites for transcription factors known to be involved in hematopoietic-specific and phorbol ester-inducible gene expression. Further analysis of this region of the CD11b gene and comparison with the promoters of the CD11a, CD11c, and CD18 genes should lead to significant insights into the molecular mechanisms by which these genes are regulated during hematopoietic development and upon activation.
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Affiliation(s)
- C S Shelley
- Leukocyte Biology and Inflammation Program, Harvard Medical School, Charlestown, MA
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9
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Chen LZ, Harris PC, Apostolou S, Baker E, Holman K, Lane SA, Nancarrow JK, Whitmore SA, Stallings RL, Hildebrand CE. A refined physical map of the long arm of human chromosome 16. Genomics 1991; 10:308-12. [PMID: 2071140 DOI: 10.1016/0888-7543(91)90313-4] [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: 12/30/2022]
Abstract
Mapping of 33 anonymous DNA probes and 12 genes to the long arm of chromosome 16 was achieved by the use of 14 mouse/human hybrid cell lines and the fragile site FRA16B. Two of the hybrid cell lines contained overlapping interstitial deletions in bands q21 and q22.1. The localization of the 12 genes has been refined. The breakpoints present in the hybrids, in conjunction with the fragile site, can potentially divide the long arm of chromosome 16 into 16 regions. However, this was reduced to 14 regions because in two instances there were no probes or genes that mapped between pairs of breakpoints.
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Affiliation(s)
- L Z Chen
- Department of Cytogenetics and Molecular Genetics, Adelaide Children's Hospital, South Australia
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10
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Kupke KG, Soreng AL, Müller U. Origin of the supernumerary X chromosome in a patient with fragile X and Klinefelter syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS 1991; 38:440-4. [PMID: 1673317 DOI: 10.1002/ajmg.1320380260] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report on a 10-year-old patient with the fragile X [fra(X)] syndrome and a 47,XXY karyotype. He had Martin-Bell syndrome, including typical craniofacial findings and mental retardation. The fra(X) was detected on both X chromosomes of the patient in 8% of the metaphases examined. DNA analysis using X-chromosome sequences from the pericentromeric region and from distal Xq suggests that the patient is homozygous at the fra(X) locus due to maternal nondisjunction during meiosis II.
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Affiliation(s)
- K G Kupke
- Division of Genetics, Children's Hospital, Boston, MA 02115
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11
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Abstract
Recent advances in understanding the molecular genetics of common adult tumors have indicated that multiple genetic alterations including the activation of oncogenes and the inactivation of tumor suppressor genes are important in the pathogenesis of these tumors. Loss of heterozygosity is a hallmark of tumor suppressor gene inactivation and has been used to identify chromosomal regions that contain these genes. We have examined allelic loss in the most common tumor in men, prostate cancer. Twenty-eight prostate cancer specimens have been examined for loss of heterozygosity at 11 different chromosomal arms including 3p, 7q, 9q, 10p, 10q, 11p, 13q, 16p, 16q, 17p, and 18q. Fifty-four percent (13/24) of clinically localized tumors and 4 of 4 metastatic tumors showed loss of heterozygosity on at least one chromosome. Chromosomes 16q and 10q exhibited the highest frequency of loss of heterozygosity with 30% of tumors showing loss at these chromosomes. These data demonstrate that allelic loss is a common event in prostate cancer and suggest that chromosomes 16q and 10q may contain the sites of tumor suppressor genes important in the pathogenesis of human prostate cancer.
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12
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Breuning MH, Snijdewint FG, Brunner H, Verwest A, Ijdo JW, Saris JJ, Dauwerse JG, Blonden L, Keith T, Callen DF. Map of 16 polymorphic loci on the short arm of chromosome 16 close to the polycystic kidney disease gene (PKD1). J Med Genet 1990; 27:603-13. [PMID: 1978860 PMCID: PMC1017238 DOI: 10.1136/jmg.27.10.603] [Citation(s) in RCA: 42] [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
To define the PKD1 locus further, the gene involved in the most frequent form of adult polycystic kidney disease, probes from 16 polymorphic loci were mapped on 16p13.1-pter with the combined use of cell lines containing rearranged chromosomes and family studies. Five breakpoints in the distal part of 16p arbitrarily subdivided the loci into five groups. By analysing 58 recombination events among 259 informative meioses in 12 large families with PKD, we were able to construct a linkage map for the distal part of 16p. The order of the markers obtained with chromosomal rearrangements was confirmed by the family studies. The D16S85 locus near alpha globin, D16S21, and D16S83 map distal, or telomeric, to PKD1. The polymorphic red cell enzyme phosphoglycolate phosphatase (PGP), D16S84, D16S259, and D16S246 showed no recombination with PKD1. The remaining nine RFLPs all map proximal to the PKD1 gene. By cosmid walking, additional RFLPs were detected at the D16S21 locus. A single intrahaplotype recombination observed defines the orientation of D16S21 relative to PKD1. The new polymorphisms are valuable for presymptomatic and prenatal diagnosis of PKD1. Furthermore, our map is both a good starting point for the physical map of 16p and a useful tool for the isolation of the PKD1 gene.
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Affiliation(s)
- M H Breuning
- Department of Human Genetics, State University Leiden, The Netherlands
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13
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Tsuda H, Zhang WD, Shimosato Y, Yokota J, Terada M, Sugimura T, Miyamura T, Hirohashi S. Allele loss on chromosome 16 associated with progression of human hepatocellular carcinoma. Proc Natl Acad Sci U S A 1990; 87:6791-4. [PMID: 2168560 PMCID: PMC54623 DOI: 10.1073/pnas.87.17.6791] [Citation(s) in RCA: 208] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Loss of heterozygosity on chromosome 16 is a common genetic alteration in human hepatocellular carcinoma (HCC). To clarify the pathogenetic significance of allele loss on chromosome 16, we performed restriction fragment length polymorphism analysis of 70 surgically resected tumors by using 15 polymorphic DNA markers for chromosome 16. Loss of heterozygosity on chromosome 16 was detected in 36 (52%) of 69 informative cases, and the common region of allele loss in these 36 tumors was located between the HP locus (16q22.1) and the CTRB locus (16q22.3-q23.2). These losses occurred more frequently in HCCs of poor differentiation, of larger size, and with metastasis, whereas they were not detected in HCC at the earliest stage. In addition, these losses were not associated with presence or absence of hepatitis B virus DNA integration or hepatitis C virus infection. These results show that loss of heterozygosity on chromosome 16 is a late event occurring after hepatocarcinogenesis and strongly suggest that this phenomenon is involved in enhancement of tumor aggressiveness during progression of HCC.
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Affiliation(s)
- H Tsuda
- Pathology Division, National Cancer Center Research Institute, Tokyo, Japan
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14
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Viguié F, Domenjoud L, Rousseau-Merck MF, Dadoune JP, Chevaillier P. Chromosomal localization of the human protamine genes, PRM1 and PRM2, to 16p13.3 by in situ hybridization. Hum Genet 1990; 85:171-4. [PMID: 2370044 DOI: 10.1007/bf00193191] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protamines are sperm-specific proteins that replace histones in the nuclear chromatin of mature spermatozoa. A chromosomal localization of the genes coding for human protamines has been achieved by in situ hybridization. Two cDNA probes of 423 bp and 397 bp containing the entire coding sequence for human protamine 1 (HP1) and human protamine 2 (HP2), respectively, have been used. The genes, called PRM1 and PRM2, have been found, tightly linked, on band 16p13.3. Arguments are given for the existence of these two genes as single copies, PRM1 coding for the unique HP1 protamine and PRM2 coding for a precursor of several proteins belonging to the HP2 family.
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Affiliation(s)
- F Viguié
- Groupe d'Etrude de la Formation et de la Maturation du Gamète Mâle, Université Paris V, France
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15
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Lux SE, Tse WT, Menninger JC, John KM, Harris P, Shalev O, Chilcote RR, Marchesi SL, Watkins PC, Bennett V. Hereditary spherocytosis associated with deletion of human erythrocyte ankyrin gene on chromosome 8. Nature 1990; 345:736-9. [PMID: 2141669 DOI: 10.1038/345736a0] [Citation(s) in RCA: 162] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hereditary spherocytosis (HS) is one of the most common hereditary haemolytic anaemias. HS red cells from both autosound dominant and recessive variants are spectrin-deficient, which correlates with the severity of the disease. Some patients with recessive HS have a mutation in the spectrin alpha-2 domain (S.L.M. et al., unpublished observations), and a few dominant HS patients have an unstable beta-spectrin that is easily oxidized, which damages the protein 4.1 binding site and weakens spectrin-actin interactions. In most patients, however, the cause of spectrin deficiency is unknown. The alpha- and beta-spectrin loci are on chromosomes 1 and 14 respectively. The only other genetic locus for HS is SPH2, on the short arm of chromosome 8 (8p11). This does not correspond to any of the known loci of genes for red cell membrane proteins including protein 4.1 (1p36.2-p34), the anion exchange protein (AE1, band 3; 17q21-qter), glycophorin C (2q14-q21), and beta-actin (7pter-q22). Human erythrocyte ankyrin, which links beta-spectrin to the anion exchange protein, has recently been cloned. We now show that the ankyrin gene maps to chromosome 8p11.2, and that one copy is missing from DNA of two unrelated children with severe HS and heterozygous deletions of chromosome 8 (del(8)(p11-p21.1)). Affected red cells are also ankyrin-deficient. The data suggest that defects or deficiency or ankyrin are responsible for HS at the SPH2 locus.
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Affiliation(s)
- S E Lux
- Division of Hematology/Oncology, Children's Hospital, Boston, Massachusetts
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16
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Harris PC, Barton NJ, Higgs DR, Reeders ST, Wilkie AO. A long-range restriction map between the alpha-globin complex and a marker closely linked to the polycystic kidney disease 1 (PKD1) locus. Genomics 1990; 7:195-206. [PMID: 2347584 DOI: 10.1016/0888-7543(90)90541-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Two polymorphic loci and two additional probes that map close to CMM65, which is tightly linked to the polycystic kidney disease 1 (PKD1) locus in chromosome band 16p13.3, are described. These new probes were isolated from a library that was enriched by preparative pulsed-field gel electrophoresis (PFGE) for sequences from a 320-kb NotI fragment that includes CMM65. Through the use of a panel of somatic cell hybrids and PFGE, the new polymorphic loci, PNL56S and NKISP1, were localized within 60 kb and approximately 250 kb distal to CMM65, respectively. A long-range restriction map linking these new probes and the distal markers EKMDA2, CMM103, and alpha-globin was constructed. These latter probes have been localized to regions approximately 900 kb, 1.2 Mb, and 1.9 Mb distal to CMM65, respectively. The entire region was found to be unusually rich in CpG dinucleotides. The new polymorphic probes and the long-range map will aid both the search for the PKD1 locus and the detailed characterization of this distal region of 16p.
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Affiliation(s)
- P C Harris
- Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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17
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Zhang WD, Hirohashi S, Tsuda H, Shimosato Y, Yokota J, Terada M, Sugimura T. Frequent loss of heterozygosity on chromosomes 16 and 4 in human hepatocellular carcinoma. Jpn J Cancer Res 1990; 81:108-11. [PMID: 1970554 PMCID: PMC5963891 DOI: 10.1111/j.1349-7006.1990.tb02534.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
By restriction fragment length polymorphism analysis, we examined loss of heterozygosity at 34 loci on 23 chromosomes in 35 surgically resected human hepatocellular carcinomas. Allele losses at the HP locus on chromosome 16q22 and at the MT2P1 locus on chromosome 4p11-q21 were detected in 57% (8/14) and 50% (8/16) of cases, respectively. Loss of heterozygosity on chromosomes 16q and 4 occurred simultaneously in 4 of 7 informative cases for both loci, and seemed to be important in the development of human hepatocellular carcinoma irrespective of the presence of hepatitis B virus infection. In contrast, the incidence of allele loss was low at the other loci, e.g., chromosome 1p, 3p, 11p, 13q or 17p, where one allele is frequently lost in other cancers.
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Affiliation(s)
- W D Zhang
- Pathology Division, National Cancer Center Research Institute, Tokyo
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18
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Abstract
A method is described that allows cloning of human telomeres in S. cerevisiae by joining human telomeric restriction fragments to yeast artificial chromosome halves. The resulting chimeric yeast-human chromosomes propagate as true linear chromosomes, demonstrating that the human telomere structure is capable of functioning in yeast and suggesting that telomere functions are evolutionarily conserved between yeast and human. One cloned human telomere, yHT1, contains 4 kb of human genomic DNA sequence next to the tandemly repeating TTAGGG hexanucleotide. Genomic hybridizations using both cloned DNA and TTAGGG repeats have revealed a common structural organization of human telomeres. This 4 kb of genomic DNA sequence is present in most, but not all, human telomeres, suggesting that the region is not involved in crucial chromosome-specific functions. However, the extent of common features among the human telomeres and possible similarities in organization with yeast telomeres suggest that this region may play a role in general chromosome behavior such as telomere-telomere interactions. Unlike the simple telomeric TTAGGG repeats, our cloned human genomic DNA sequence does not cross-hybridize with rodent DNA. Thus, this clone allows the identifications of the terminal restriction fragments of specific human chromosomes in human-rodent hybrid cells.
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Affiliation(s)
- J F Cheng
- Department of Genetics, College of Physicians and Surgeons, Columbia University, New York, NY 10032
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19
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Nicholls RD, Knoll JH, Glatt K, Hersh JH, Brewster TD, Graham JM, Wurster-Hill D, Wharton R, Latt SA. Restriction fragment length polymorphisms within proximal 15q and their use in molecular cytogenetics and the Prader-Willi syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS 1989; 33:66-77. [PMID: 2568752 DOI: 10.1002/ajmg.1320330109] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Restriction fragment length polymorphisms (RFLPs) are described in detail for 6 DNA probes (D15S9-13, D15S18) that localize to the proximal long arm of human chromosome 15 (15q11-15q13: this report and Tantravahi et al., Am. J. Med. Genet. 33:78-87. Multiple RFLPs are detected by the probe that identifies locus D15S13, and these RFLPs are shown by genomic mapping to result from a nearby insertion or deletion of 1.8 kilobases (kb) of DNA. This set of RFLPs detected by proximal 15q probes can be used for studies on the Prader-Willi syndrome (PWS) and on mentally retarded individuals with a supernumerary inv dup(15) chromosome. Five of the polymorphic loci (D15S9-13) map to the region implicated in the cause of the PWS (15q11.2-15q12). Each of 4 families tested with these probes, as well as an additional "PWS-like" patient, was informative by RFLP analysis. The two PWS deletions studied, which occurred de novo, were inherited from the chromosome 15 provided by the father. By contrast, the 2 inv dup(15) chromosomes analyzed were of maternal origin. The use of RFLPs can also simplify the molecular determination of copy number in chromosomal aneuploidy, as exemplified by analysis of individuals with the PWS and a deletion, patients with an inv dup(15), and one patient with a more complex rearrangement involving chromosome 15. Our studies demonstrate the application of DNA probes for both molecular cytogenetic studies on this chromosome region and the development of diagnostic molecular markers to aid early clinical diagnosis of the PWS.
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Affiliation(s)
- R D Nicholls
- Genetics Division, Children's Hospital, Boston, MA 02115
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20
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Callen DF, Hyland VJ, Baker EG, Fratini A, Gedeon AK, Mulley JC, Fernandez KE, Breuning MH, Sutherland GR. Mapping the short arm of human chromosome 16. Genomics 1989; 4:348-54. [PMID: 2714795 DOI: 10.1016/0888-7543(89)90341-8] [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: 01/02/2023]
Abstract
Physical mapping of 13 different breakpoints on the short arm of chromosome 16 using previously mapped probes and the subsequent mapping of additional probes enabled the division of this portion of the chromosome into six different intervals. D16S94 was mapped between HBA and D16S80 and is closer to PKD1 than either HBA or D16S80. A tight linkage group which includes FRA16A, D16S8, and D16S79 was identified. Seven breakpoints, including FRA16A, could not be separated by probe localizations. This study provides the basis for the development of detailed maps of the short arm of chromosome 16.
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Affiliation(s)
- D F Callen
- Cytogenetics Unit, Adelaide Children's Hospital, South Australia
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21
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Buckle VJ, Higgs DR, Wilkie AO, Super M, Weatherall DJ. Localisation of human alpha globin to 16p13.3----pter. J Med Genet 1988; 25:847-9. [PMID: 3236367 PMCID: PMC1051615 DOI: 10.1136/jmg.25.12.847] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A female child with alpha thalassaemia trait, moderate mental retardation, and dysmorphic features has inherited an abnormal chromosome 16 complement as a result of the unbalanced segregation of a maternal balanced translocation. Cytogenetic analysis indicates that the patient is monosomic for 16p13.3----pter and trisomic for 10q26.13----qter. DNA studies show that the patient has not inherited either maternal alpha globin allele. This accounts for the alpha thalassaemia trait in the child and places the human alpha globin complex in band 16p13.3----pter.
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Affiliation(s)
- V J Buckle
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford
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22
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Arnaout MA, Remold-O'Donnell E, Pierce MW, Harris P, Tenen DG. Molecular cloning of the alpha subunit of human and guinea pig leukocyte adhesion glycoprotein Mo1: chromosomal localization and homology to the alpha subunits of integrins. Proc Natl Acad Sci U S A 1988; 85:2776-80. [PMID: 2833753 PMCID: PMC280082 DOI: 10.1073/pnas.85.8.2776] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cell-surface glycoprotein Mo1 is a member of the family of leukocyte cell adhesion molecules (Leu-CAMs) that includes lymphocyte function-associated antigen 1 (LFA-1) and p150,95. Each Leu-CAM is a heterodimer with a distinct alpha subunit noncovalently associated with a common beta subunit. Leu-CAMs play crucial roles in cell-cell and cell-matrix interactions. We describe the isolation and analysis of two partial cDNA clones encoding the alpha subunit of the Leu-CAM Mo1 in humans and guinea pigs. A monoclonal antibody directed against an epitope in the carboxyl-terminal portion of the guinea pig alpha chain was used for immunoscreening a lambda gt11 expression library. The sequence of a 378-base-pair insert from one immunoreactive clone revealed a single continuous open reading frame encoding 126 amino acids including a 26-amino acid tryptic peptide isolated from the purified guinea pig alpha subunit. A cDNA clone of identical size was isolated from a human monocyte/lymphocyte cDNA library by using the guinea pig clone as a probe. The human clone also encoded a 126-amino acid peptide including the sequence of an additional tryptic peptide present in purified human Mo1 alpha chain. RNA gel blots revealed that mature Mo1 alpha chain mRNA is approximately 5 kilobases in guinea pigs and humans. Southern analysis of DNA from hamster-human hybrids localized the human Mo1 alpha chain to chromosome 16, which has been shown to contain the gene for the alpha chain of lymphocyte function-associated antigen 1. A comparison of the Mo1 alpha chain coding region revealed significant homologies with carboxyl-terminal portions of the alpha subunits of fibronectin, vitronectin, and platelet IIb/IIIa receptors. These data suggest that the alpha subunits of Leu-CAMs evolved by gene duplication from a common ancestral gene and strengthen the hypothesis that the alpha subunits of these heterodimeric cell adhesion molecules on myeloid and lymphoid cells, platelets, and fibroblasts are evolutionary related.
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Affiliation(s)
- M A Arnaout
- Renal Division, Children's Hospital, Boston, MA
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