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Abstract
This review is intended to provide an overview of techniques and a source of reagents for physical mapping of the mouse genome. It focuses on those applications, methods, or resources unique to the mouse and on the generation of comparative physical maps. The reference list is not comprehensive; rather, recent reviews on each topic and selected representative examples are given.
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Affiliation(s)
- G E Herman
- Department of Pediatrics, Ohio State University, Columbus, USA
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2
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Brockdorff N, Ashworth A, Kay GF, McCabe VM, Norris DP, Cooper PJ, Swift S, Rastan S. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 1992; 71:515-26. [PMID: 1423610 DOI: 10.1016/0092-8674(92)90519-i] [Citation(s) in RCA: 750] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Xist gene maps to the X inactivation center region in both mouse and human, and previous analysis of the 3' end of the gene has demonstrated inactive X-specific expression, suggesting a possible role in X inactivation. We have now analyzed the entire mouse Xist gene. The mature inactive X-specific transcript is 15 kb in length and contains no conserved ORF. The Xist sequence contains a number of regions comprised of tandem repeats. Comparison with the human XIST gene demonstrates significant conservation of sequence and gene structure. Xist RNA is not associated with the translational machinery of the cell and is located almost exclusively in the nucleus. Together with conservation of inactive X-specific expression, these findings support a role for Xist in X inactivation, possibly as a functional RNA or as a chromatin organizer region.
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Affiliation(s)
- N Brockdorff
- Section of Comparative Biology, Medical Research Council Clinical Research Centre, Harrow, England
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3
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Faust CJ, Levinson B, Gitschier J, Herman GE. Extension of the physical map in the region of the mouse X chromosome homologous to human Xq28 and identification of an exception to conserved linkage. Genomics 1992; 13:1289-95. [PMID: 1354645 DOI: 10.1016/0888-7543(92)90048-w] [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: 10/26/2022]
Abstract
We have extended our pulsed-field gel map of the region of the mouse X chromosome homologous to human Xq28 to include the loci Gdx (DXS254Eh), P3 (DXS253Eh), G6pd, Cf-8, and F8a. Gdx, P3, and G6pd are demonstrated to be physically linked to the X-linked visual pigment locus (Rsvp) within a maximal distance of 340 kb, while G6pd and Cf-8 are approximately 900 kb apart. These studies favor a gene order of cen-Rsvp-Gdx-P3-G6pd-(Cf-8)-tel and extend the physical map of this region to 5 million bp. In conjunction with previous physical mapping studies in both mouse and human, the results suggest conserved linkage for loci in this region of the mouse X chromosome and human Xq28. However, employing pulsed-field gel electrophoresis and genetic pedigree analysis of interspecific backcross progeny, we have found close linkage of a clone encoding a mouse homolog for human factor VIII-associated gene A (F8A) to DXPas8, thus revealing the first exception to conserved gene order between murine and human loci in the region.
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Affiliation(s)
- C J Faust
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030
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4
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Watson ML, D'Eustachio P, Mock BA, Steinberg AD, Morse HC, Oakey RJ, Howard TA, Rochelle JM, Seldin MF. A linkage map of mouse chromosome 1 using an interspecific cross segregating for the gld autoimmunity mutation. Mamm Genome 1992; 2:158-71. [PMID: 1543910 DOI: 10.1007/bf00302874] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An interspecific backcross was used to define a high resolution linkage map of mouse Chromosome (Chr) 1 and to analyze the segregation of the generalized lymphoproliferative disease (gld) mutation. Mice homozygous for gld have multiple features of autoimmune disease. Analysis of up to 428 progeny from the backcross [(C3H/HeJ-gld x Mus spretus)F1 x C3H/HeJ-gld] established a map that spans 77.6 cM and includes 56 markers distributed over 34 ordered genetic loci. The gld mutation was mapped to a less than 1 cM segment on distal mouse Chr 1 using 357 gld phenotype-positive backcross mice. A second backcross, between the laboratory strains C57BL/6J and SWR/J, was examined to compare recombination frequency between selected markers on mouse Chr 1. Significant differences in crossover frequency were demonstrated between the interspecific backcross and the inbred laboratory cross for the entire interval studied. Sex difference in meiotic crossover frequency was also significant in the laboratory mouse cross. Two linkage groups known to be conserved between segments of mouse Chr 1 and the long arm of human Chrs 1 and 2 where further defined and a new conserved linkage group was identified that includes markers of distal mouse Chr 1 and human Chr 1, bands q32 to q42.
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Affiliation(s)
- M L Watson
- Department of Medicine, Duke University, Durham, North Carolina 27710
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5
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Nadeau JH, Davisson MT, Doolittle DP, Grant P, Hillyard AL, Kosowsky MR, Roderick TH. Comparative map for mice and humans. Mamm Genome 1992; 3:480-536. [PMID: 1392257 DOI: 10.1007/bf00778825] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- J H Nadeau
- Jackson Laboratory, Bar Harbor, Maine 04609
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Affiliation(s)
- S D Brown
- Department of Biochemistry and Molecular Genetics, St. Mary's Hospital Medical School, London, UK
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Faust CJ, Herman GE. Physical mapping of the loci Gabra3, DXPas8, CamL1, and Rsvp in a region of the mouse X chromosome homologous to human Xq28. Genomics 1991; 11:154-64. [PMID: 1684949 DOI: 10.1016/0888-7543(91)90112-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Using pulsed-field gel electrophoresis, a 3 million-bp physical map containing the X-linked loci Gabra3, DXPas8, CamL1, and Rsvp has been constructed for a segment of the mouse X chromosome homologous to human Xq28. Detailed mapping was performed using single and double digestions with rare-cutter restriction enzymes. Gabra3 and DXPas8 have been shown to be physically linked within a maximal distance of 1600 kb, DXPas8 and CamL1 within 750 kb, and CamL1 and Rsvp within 450 kb. In addition, several CpG islands have been detected in the region encompassing CamL1 and Rsvp. These studies confirm a gene order of cen-Gabra3-DXPas8-CamL1-Rsvp-tel determined by genetic mapping in interspecific backcrosses (A.S. Ryder-Cook et al., 1988, EMBO J. 7: 3017-3021; G.E. Herman et al., 1991, Genomics 9: 670-677). Physical distances for the loci studied agree with the calculated genetic distances. Assuming that there is conserved linkage between man and mouse in the region, the physical mapping data presented here may help to clarify the uncertain gene order for some human Xq28 loci.
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Affiliation(s)
- C J Faust
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030
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Brockdorff N, Kay G, Smith S, Keer JT, Hamvas RM, Brown SD, Rastan S. High-density molecular map of the central span of the mouse X chromosome. Genomics 1991; 10:17-22. [PMID: 1675191 DOI: 10.1016/0888-7543(91)90478-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A total of 17 linking clones previously sublocalized to the central span of the mouse X chromosome have been ordered by detailed analysis through interspecific Mus spretus/Mus musculus domesticus backcross progeny. These probes have been positioned with respect to existing DNA markers utilizing a new interspecific backcross segregating for the Tabby (Ta) locus. The density of clones within this 11.5-cM interval is now, on average, one clone every 1000 kb. This high-density map provides probes in the vicinity of a number of important genetic loci in this region which include the X-inactivation center, the Ta locus, and the mottled (Mo) locus, and therefore provides a molecular framework for identification of the genes encoded at these loci.
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Affiliation(s)
- N Brockdorff
- Section of Comparative Biology, MRC Clinical Research Centre, Harrow Middlesex, United Kingdom
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9
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Herman GE, Faust CJ, Darlison MG, Barnard EA. Genetic mapping of the mouse X chromosome in the region homologous to human Xq27-Xq28. Genomics 1991; 9:670-7. [PMID: 1674728 DOI: 10.1016/0888-7543(91)90360-q] [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: 12/28/2022]
Abstract
The four loci Gabra3, DXPas8, CamL1, and Bpa, located near the murine X-linked visual pigment gene (Rsvp), have been ordered using 248 backcross progeny from an interspecific mating of (B6CBA-Aw-J/A-Bpa) and Mus spretus. One hundred twenty backcross progeny have been analyzed at seven anchor loci spanning the X chromosome and form a regional mapping panel. An additional 128 progeny have been screened for recombination events between Cf-9 and Dmd. Eighteen recombinants between these loci have been detected in the 248 animals; all of the recombinants were screened at the other anchor loci to identify any double crossovers. Pedigree analysis using these recombinants strongly favors a gene order of (Cf-9)-Gabra3-(DXPas8, Bpa)-CamL1-(Rsvp, P3, Cf-8)-Dmd for the loci studied. Synteny with human Xq27-Xq28 is retained, although the relative order of some loci may differ between the two species.
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Affiliation(s)
- G E Herman
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030
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Seldin MF, Saunders AM, Rochelle JM, Howard TA. A proximal mouse chromosome 9 linkage map that further defines linkage groups homologous with segments of human chromosomes 11, 15, and 19. Genomics 1991; 9:678-85. [PMID: 1674729 DOI: 10.1016/0888-7543(91)90361-h] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A 42-cM map of proximal mouse chromosome 9, including eight loci defined by restriction fragment length variants, has been generated. Linkage was established by haplotype analyses of 114 interspecific backcross mice and indicated the following gene order: (centromere) Pvs-5.3 cM-Icam-1/Ldlr-18.4 cM-Thy-1-1.8 cM-Ncam-0.9 cM-Hexa-7.9 cM-Gsta-7.9 cM-Trf. Three of these loci, Pvs, Icam-1, and Hexa, have not been mapped previously. Together with previous mapping studies the current results suggested that chromosomal segments of mouse chromosomes 7 and 9 and chromosomal segments of human chromosomes 11, 15, and 19 derive from a single putative primordial chromosome. The studies support the postulate that detailed analysis of chromosome organization will be useful in defining events in mammalian evolution.
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MESH Headings
- Animals
- Blotting, Southern
- Chromosome Mapping
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 15
- Chromosomes, Human, Pair 19
- Crosses, Genetic
- DNA Probes
- Female
- Haplotypes
- Humans
- Male
- Mice
- Mice, Inbred C3H
- Muridae
- Polymorphism, Restriction Fragment Length
- Species Specificity
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Affiliation(s)
- M F Seldin
- Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710
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11
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Nadeau JH, Davisson MT, Doolittle DP, Grant P, Hillyard AL, Kosowsky M, Roderick TH. Comparative map for mice and humans. Mamm Genome 1991; 1 Spec No:S461-515. [PMID: 1799811 DOI: 10.1007/bf00656504] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- J H Nadeau
- Jackson Laboratory, Bar Harbor, ME 04609
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12
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Chapman VM, Stephenson DA, Mullins LJ, Keitz BT, Disteche C, Orkin SH. Linkage of the erythroid transcription factor gene (Gf-1) to the proximal region of the X chromosome of mice. Genomics 1991; 9:309-13. [PMID: 2004781 DOI: 10.1016/0888-7543(91)90258-g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have used a cDNA probe for mouse Gf-1 gene that encodes the erythroid cell transcription factor to identify genetic variation in genomic DNA between Mus species. The segregation of Gf-1 DNA variation was analyzed in Mus species crosses that have been previously typed for the segregation of more than 30 genes spanning 80 cM of the mouse X chromosome from the centromere to the border of the X-Y pairing region. We identified a single X chromosome locus in the mouse, Gf-1, and an analysis of recombinants from 203 backcross progeny mapped Gf-1 to the proximal portion of the chromosome, coincident with the Cybb locus and proximal to Otc gene locus. A gene order of centromere, DXWas70, Cybb/Gf-1, Otc, Timp was established for the mouse X chromosome, which is in agreement with the map position observed on the human X chromosome.
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Affiliation(s)
- V M Chapman
- Molecular and Cellular Biology Department, Roswell Park Cancer Institute, Buffalo, New York 14263
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13
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Affiliation(s)
- S D Brown
- Department of Biochemistry and Molecular Genetics, St. Mary's Hospital Medical School, London, UK
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Ikemura T, Wada K, Aota S. Giant G+C% mosaic structures of the human genome found by arrangement of GenBank human DNA sequences according to genetic positions. Genomics 1990; 8:207-16. [PMID: 2249845 DOI: 10.1016/0888-7543(90)90273-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To determine the overall variation in the G+C% distribution over long ranges of the human genome, DNA sequences of human genes, which were closely linked genetically or physically, were surveyed from the GenBank Data Bank. A total of 72 sequences longer than 2 kb, which were mutually linked within 500 kb, were identified. The sequences belonged to 17 linkage groups and were ordered in each group according to their genetic positions. Analyses of the G+C% distribution along the ordered sequences showed that sequences within each group almost always had similar G+C% levels, but those belonging to different groups often had different levels. Similar analyses of more distantly linked sequences (e.g., greater than 10 Mb) showed mosaic structures of G+C% distribution. These findings are consistent with predictions made from the "isochore" structures found by CsCl equilibrium centrifugation, in that the structures having homogeneous base compositions stretched over at least several hundred kilobases. A possible boundary of the giant G+C% mosaic structures was identified between X-linked G6PD and F8C.
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Affiliation(s)
- T Ikemura
- DNA Research Center, National Institute of Genetics, Shizuoka-ken, Japan
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15
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Abstract
The phenomenon of X-chromosome inactivation in female mammals, whereby one of the two X chromosome present in each cell of the female embryo is inactivated early in development, was first described by Mary Lyon in 1961. Nearly 30 years later, the mechanism of X-chromosome inactivation remains unknown. Strong evidence has accumulated over the years, however, for the involvement of a major switch or inactivation centre on the mouse X chromosome. Identification of the inactivation centre at the molecular level would be an important step in understanding the mechanism of X-inactivation. In this paper we review the evidence for the existence and location of the X-inactivation centre on the mouse X-chromosome, present data on the molecular genetic mapping of this region, and describe ongoing strategies we are using to attempt to identify the inactivation centre at the molecular level.
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Affiliation(s)
- S Rastan
- Section of Comparative Biology, Clinical Research Centre, Harrow, Middlesex, UK
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Brockdorff N, Montague M, Smith S, Rastan S. Construction and analysis of linking libraries from the mouse X chromosome. Genomics 1990; 7:573-8. [PMID: 2167288 DOI: 10.1016/0888-7543(90)90201-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A hybrid cell line containing the mouse X chromosome on a human background has been used to construct linking libraries from the mouse X chromosome, and approximately 250 unique EagI and NotI clones have been identified. Seventy-three clones have been sublocalized onto the X chromosome using interspecific Mus spretus/Mus domesticus crosses and a panel of somatic cell hybrids carrying one-half of reciprocal X-autosome translocations. The average spacing of the linking clones mapped to date is about one every 2 Mb of DNA. Two clones from the central region of the chromosome have been physically linked by pulsed-field gel electrophoresis. A large number of clones contain conserved sequences, indicating the presence of CpG-rich island-associated genes. The clones isolated from these libraries provide a valuable resource for comparative mapping between man and mouse X chromosomes, isolation of X-linked disease loci of interest by reverse genetics, and analysis of the long-range structure and organization of the chromosome.
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Affiliation(s)
- N Brockdorff
- Section of Comparative Biology, MRC Clinical Research Centre, Harrow, Middlesex, United Kingdom
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Filippi M, Tribioli C, Toniolo D. Linkage and sequence conservation of the X-linked genes DXS253E (P3) and DXS254E (GdX) in mouse and man. Genomics 1990; 7:453-7. [PMID: 1973144 DOI: 10.1016/0888-7543(90)90184-v] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Lambda G28, a mouse genomic clone homologous to the human P3 gene and associated with a CpG island, also hybridizes to human probes for the neighboring GdX gene. The two genes, P3 and GdX (DXS253E and DXS254E), physically linked on the human X chromosome, lie within a similar physical distance on the mouse X chromosome. The CpG island corresponds to that at the 5' of the human GdX gene. The relative orientation of the two genes is the same. The DNA sequence in coding and noncoding regions is very conserved.
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Affiliation(s)
- M Filippi
- Istituto di Genetica Biochimica ed Evoluzionistica, CNR, Pavia, Italy
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Levinson B, Kenwrick S, Lakich D, Hammonds G, Gitschier J. A transcribed gene in an intron of the human factor VIII gene. Genomics 1990; 7:1-11. [PMID: 2110545 DOI: 10.1016/0888-7543(90)90512-s] [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: 12/30/2022]
Abstract
We have identified a CpG island contained within the largest factor VIII intron. This island is associated with a 1.8-kb transcript and, unlike factor VIII, is produced abundantly in a wide variety of cell types. The nested gene is oriented in a direction opposite to that of factor VIII and contains no intervening sequences. A cDNA of 1739 bases was isolated from a human liver library and found to have a GC-rich, long open reading frame. Two computer-assisted methods (Fickett TESTCODE and Staden-McLachlan codon usage) predict that the gene codes for a protein. Two other copies of this gene are located within 1.1 Mb of the factor VIII gene. Northern blot analysis of RNA isolated from hemophilia patients deleted for factor VIII sequences has shown that both the intron gene and at least one other copy of the gene are transcribed. A homologous, transcribed sequence is also present in mice.
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Affiliation(s)
- B Levinson
- Howard Hughes Medical Institute, University of California, San Francisco 94143
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Nasir J, Fisher EM, Brockdorff N, Disteche CM, Lyon MF, Brown SD. Unusual molecular characteristics of a repeat sequence island within a Giemsa-positive band on the mouse X chromosome. Proc Natl Acad Sci U S A 1990; 87:399-403. [PMID: 2296595 PMCID: PMC53271 DOI: 10.1073/pnas.87.1.399] [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: 12/31/2022] Open
Abstract
The mouse genome contains 50 copies of a long complex repeat unit localized as a repeat sequence island to the A3 Giemsa-positive (dark) band on the mouse X chromosome. The repeat units are not tandemly arranged but are juxtaposed and inserted by unrelated sequences of high repetition. The repeat sequence island possesses two notable features that have been suggested as diagnostic features of mammalian Giemsa-positive bands. First, the repeat sequence island encompasses a 1-megabase region devoid of CpG islands; second, it features a high concentration of L1 long interspersed repeat sequences.
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Affiliation(s)
- J Nasir
- Department of Biochemistry and Molecular Genetics, Saint Mary's Hospital Medical School, London, United Kingdom
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