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V M Chapman

Publications and source records attributed to V M Chapman.

At least 37 records · Page 2Linked to original sources
PubMed1995

The use of restriction landmark genomic scanning to scan the mouse genome for endogenous loci with imprinted patterns of methylation.

Restriction landmark genomic scanning (RLGS) has been used to screen endogenous loci for imprinted patterns of methylation. The screening method is based upon the identification of genetic variation in RLGS profiles between different strains and determining whether specific variant landmarks are transmitted equally to the progeny of reciprocal F1 matings. The RLGS profiles of C57BL/6 (B6) and DBA/2 (D2) and their reciprocal hybrids were produced with two enzyme combinations that used NotI as the landmark enzyme and two combinations that used BssHII. An estimated 13% of the spots are either B5- or D2-specific in these tests, giving a total of nearly 1000 variant loci that were examined for imprinted methylation. Three candidate loci for imprinted regulation were identified in these analyses. We also used crosses of more genetically diverse parents to increase the number of variant loci screened. Interspecific crosses of B6 with the M. musculus strain PWK and intrasubspecific crosses between B6 and the M. molossinus strain MSM expanded the levels of variation between the parental strains in the cross to an estimated 31% and 26%, respectively. The RLGS patterns for one NotI combination and one BssHII profile were examined for each of these crosses, giving approximately 2000 additional loci that were screened for imprinted patterns of methylation. Eight loci with imprinted patterns of transmission were observed out of 3040 loci tested. The chromosomal locations for the three B6 and D2 specific loci, Irlgs 1-3, were identified using BXD recombinant inbred strain analysis. Irlgs 1 and 3 are B6- and D2-specific loci that had the same strain distribution pattern which mapped to the central region of chromosome 9.(ABSTRACT TRUNCATED AT 250 WORDS)

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PubMed1995

Genetic mapping of restriction landmark genomic scanning loci in the mouse.

Restriction landmark genomic scanning (RLGS) was originally proposed as a high-speed method for surveying a large number of restriction landmarks in genomic DNA. The effort to apply this method to genetic analysis has been made, resulting in developing the new approach for the rapid construction of the genetic map of complex mammalian genomes (RLGS spot mapping). Especially, the use of NotI as the restriction landmark for genetic studies suggests that there is a high probability that a significant number of these RLGS loci will be associated with CpG islands of functional genes. Moreover, it is possible to use the RLGS spot mapping to analyze genetic map-poor species very rapidly for linkage of recessive mutations or segregating traits, because it does not rely upon cloned probes or sequences. In this paper, we summarize the progress that has been made in the practical application of the RLGS method to genetic analysis using congenic strains, recombinant inbred (RI) strains, and in interspecific backcrosses of mice.

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PubMed1995

A single gel analysis of 575 dominant and codominant restriction landmark genomic scanning loci in mice interspecific backcross progeny.

We identified 575 new NotI landmarks of C57BL/6(B)- and M. spretus (S)-specific, dominant and codominant loci which were segregated in B x S interspecific backcrosses (BSS), using the restriction landmark genomic scanning (RLGS) spot mapping method. All of these loci were visualized on a single RLGS profile which was produced with NotI-PvuII-PstI. These landmarks include 250 newly identified S-specific spots in addition to the previously reported 325 B-specific spots. The S-specific spots were identified by reading full or half intensity, based on the property that the spot intensity of the autoradiographic signal reflected the copy number of an end-labeled restriction landmark. The cumulative map is 1341 cM and it is based upon 985 meiotic events in 72 backcross progeny. This map covers 90% of the total estimated length of the mouse genetic map. This map provides a good tool for the high-speed genome scanning assay in the mouse genome by a single RLGS gel analysis.

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PubMed1995

Application of fluorescence in situ hybridization in genome analysis of the mouse.

Fluorescence in situ hybridization (FISH) is an effective technique for localizing cloned DNA probes directly onto metaphase chromosomes. Human genome mapping using FISH has been significantly enhanced by the development of new techniques, especially high-resolution gene mapping with direct R-banding FISH and physical gene ordering with multi-color FISH. By contrast, FISH techniques have not been put to practical use for the analysis of the mouse genome compared with the human. We have developed and modified FISH techniques for use in mouse genome analysis. In this article we summarize and review our recent results with FISH analyses in the following studies: (i) high-resolution gene mapping with the direct R-banding FISH, (ii) analysis of chromosomal rearrangement with multi-color FISH, (iii) establishment of centromere mapping with the major satellite DNA probe, (iv) analysis of chromatin structure in meiotic cells, and (v) application of FISH in cytogenetic studies of genetic variation in the mouse, showing that these applications of FISH are very useful for mouse genome analysis.

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PubMed1995

Lethality of Rw/Rw mouse embryos during early postimplantation development.

Three mutations in the mouse, white spotting (W), rump white (Rw), and patch (Ph), are described as a "gene triplet" on the basis of their close genetic linkage and similar mutant phenotypes. The finding that the W phenotype results from mutations altering the c-kit protooncogene, and that Ph is associated with the deletion of Pdgfra, suggested specific molecular reagents which could be used for the analysis of the chromosomal structure of the third mutation, rump white. Such studies indicated that Rw is associated with a large chromosomal inversion. In this study, we showed that it is possible to generate molecular markers specific for the Rw chromosome, as recombination is suppressed between the inverted portion of the Rw chromosome and the wild-type homologue. Using one such marker, we were able to genotype the offspring of Rw/+ intercrosses. This enabled us to show that Rw homozygote embryos die around 9.5 days of gestation. Histological analysis revealed that the embryos undergo gastrulation, forming three germ layers, and in some cases, exhibit a defined axial midline with an apparent notochordal plate. However, mutant embryos are significantly smaller than the wild-type, with the size difference evident from Day 7.5 and becoming more disparate as development progresses. These morphological data further support the genetic evidence indicating that the developmental lethality of the Rw mutation is not caused by the disruption of a gene within the cluster of RTKs in the central portion of mouse chromosome 5. Furthermore, we present evidence that both Kit and Pdgfra are expressed from the Rw chromosome in several adult tissues. The results of these studies suggest that the identification of the sequence(s) disrupted by the Rw mutation will provide further insight into the regulation of early postimplantation development.

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PubMed1995

Stage-specific induction and regulation by genomic imprinting of the mouse U2afbp-rs gene during preimplantation development.

The mouse U2afbp-rs gene is imprinted and expressed exclusively from the paternal allele in the adult. To determine whether the U2afbp-rs gene is regulated by imprinting in the early embryo and to examine its normal temporal pattern of expression, we used a new quantitative RT-PCR approach to compare U2afbp-rs gene expression between androgenetic and gynogenetic embryos and to monitor U2afbp-rs expression during normal preimplantation embryogenesis. The U2afbp-rs gene is transcriptionally induced transiently at the 2-cell stage, making it one of the first genes ever identified with this pattern of regulation. At the 2-cell stage, androgenones express approximately twice as much U2afbp-rs mRNA as normal embryos, while gynogenones express much less. Thus, genomic imprinting regulates the U2afbp-rs gene from the time of its initial induction, distinguishing it from some other autosomal imprinted genes that have been analyzed (e.g., Igf2r and Igf2). Because the function of the U2afbp-rs protein has not been determined, the significance of transient induction of the U2afbp-rs gene at the 2-cell stage is not clear. Our data indicate that abundant expression of the U2afbp-rs gene is not essential for early development since gynogenones form blastocysts at a high frequency.

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PubMed1995

A genomic clone containing a telomere array maps near the centromere of mouse chromosome 6.

A lambda clone of mouse DNA containing a short array of telomere hexamers has been localized by FISH to a region close to the centromere of Chromosome (Chr) 6. Amplification of DNA with primers flanking an SSR showed that most inbred strains carry one of two alleles, although five other alleles were found among the inbred strains and 11 other alleles were found in wild-derived mice. Analysis of the DNA from four Robertsonian translocations suggests that the amplified sequence is still present in these chromosomes. The finding of two fragments associated with the Sig mutant suggests that the clone lies within a congenic region created when the mutant, obtained in a (C3H x 101)F1, was backcrossed to C57BL/6J. This region might include all or part of the centromere. Comparison of the segregation of the amplification product with the segregation of centromeric heterochromatin in an interspecies backcross, (C57BL/6 x M. spretus)F1 x M. spretus, (BSS) shows 1/72 recombinants with the centromeric heterochromatin, while 1/62 recombinants occurred in a BSB backcross. Analysis of other loci at the proximal end of Chr 6 gives the combined map Hc6-0.73-D6Mit86-0.73-D6Rp2-2.2-D6Mitl-2.2-Wn t2-3.0-Cpa. Data from a third cross show that Cola2 lies between D6Mit82 and D6Rp2. The portion of the telomere array, Tel-rs3, that has been sequenced contains only 13/31 repeats of the consensus sequence. A variety of sequence changes from the consensus hexamer suggests that this array has been removed for a long time from evolutionary pressures to retain the TTAGGG sequence.

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PubMed1995

The X-linked methylated DNA binding protein, Mecp2, is subject to X inactivation in the mouse.

DNA methylation at the promoter region of X-linked genes is associated with the maintenance of X inactivation in mammals. One of the methylated DNA binding proteins, MECP2, that binds to methylated bases in DNA is encoded by a gene (Mecp2) located on the mouse X Chromosome (Chr). To determine whether this gene was expressed from the inactive X Chr, and X-autosome translocation (T(X;16)16H) system in which expression from the Mecp2 allele on the inactive X Chr could be assayed was used. Results from these experiments indicate that Mecp2 is subject to X inactivation in mouse.

Animals↗
PubMed1995

Physical mapping of the Tec and Gabrb1 loci reveals that the Wsh mutation on mouse chromosome 5 is associated with an inversion.

In the mouse, mutations in the c-Kit proto-oncogene, a member of the receptor tyrosine kinase (RTK) gene family, have pleiotropic effects on hematopoiesis, pigmentation and fertility (dominant spotting, W). However, in the Wsh allele the defect is confined to abnormal pigmentation caused by the disruption of 5' regulatory sequences of Kit leaving an intact structural gene. In this report, the previously published physical map around the Pdgfra-Kit-Flk1 RTK loci is extended by mapping the loci encoding the GABAA (gamma-aminobutyric acid) receptor subunit beta 1, Gabrb1 and a cytoplasmic kinase (Tec) 3 Mb proximal to Kit. PFGE analysis of the wild-type (C57BL/6J) chromosome demonstrates the following gene order: cen-Gabrb1-Tec-Pdgfra-Kit, whereas the analysis of Wsh/Wsh DNA is consistent with the order: cen-Gabrb1-Pdgfra-Tec-Kit. This altered physical map can be explained by an inversion on the Wsh chromosome located proximally to the Kit locus and spanning the 2.8 Mb Pdgfra-Tec chromosomal segment. This high resolution physical mapping study identifies large DNA fragments that span the two inversion breakpoints and potentially carry Kit upstream regulatory elements involved in the control of Kit expression during embryonic development.

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PubMed1995

mdxCv3 mouse is a model for electroretinography of Duchenne/Becker muscular dystrophy.

PURPOSE: To identify an animal model for the abnormal scotopic electroretinogram found in a majority of Duchenne and Becker muscular dystrophy patients. METHODS: Ganzfeld electroretinograms were recorded in dark-adapted normal C57BL/6 mice, and two strains of mice with different X-linked muscular dystrophy mutations (mdx and mdxCv3). Responses for the right eye were averaged and the amplitudes and implicit times of the a-wave and b-wave were measured. The electroretinogram was digitally filtered to extract the oscillatory potentials. Statistical analyses included one-way analysis of variance and the Scheffé S test. RESULTS: While the electroretinogram in mdx was normal, in mdxCv3 the scotopic b-wave was markedly reduced and the oscillatory potentials were delayed, similar to changes observed in Duchenne and Becker muscular dystrophy patients. Some of the mdxCv3 animals demonstrated negative configuration electroretinograms, with the b-wave amplitude reduced compared to that of the a-wave. CONCLUSIONS: Abnormalities found in the electroretinograms of Duchenne and Becker muscular dystrophy patients led to the identification of dystrophin in human retina and the discovery that dystrophin is required for normal retinal electrophysiology. These results indicate that mdxCv3 is a model for elucidating the role of dystrophin in retina and suggest that dystrophin isoforms, consisting of only the C-terminal domains of the full-length protein, may be important to the development of normal retinal electrical potentials.

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PubMed1994

Interspecific backcrosses provide an important new tool for centromere mapping of mouse chromosomes.

Centromere mapping of mouse chromosomes has been problematic due to a paucity of appropriate markers. As a result, the mapping of centromeres has most often relied on the use of Robertsonian chromosomes to mark chromosome ends. Many Robertsonian translocations have been shown to suppress recombination in pericentric regions; therefore, centromere mapping data generated by using Robertsonian chromosomes must be interpreted with caution. We have utilized a new tool for centromere mapping that is applicable to all mouse chromosomes (except the Y chromosome) and that potentially overcomes the inherent limitations of using Robertsonian translocations. Briefly, an interspecific backcross mapping panel was constructed from crosses of C57BL/6Ros and Mus spretus mice. The centromere of each chromosome was subsequently typed by in situ hybridization, using a major satellite probe that uniformly labels C57BL/6Ros centromeres but hybridizes only weakly to M. spretus centromeres. Genetic markers that were already known to map in the proximal region of each of the mouse chromosomes were then typed by segregation analyses of restriction fragment length polymorphisms. These studies have made it possible to align the interspecific genetic map of each of the mouse autosomes and the X chromosome with respect to the centromere. They also provide a basis for comparison with centromere mapping data generated previously by other means.

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PubMed1994

Generation of five high-complexity painting probe libraries from flow-sorted mouse chromosomes.

Mouse metaphase chromosomes were purified by flow sorting from the murine fibroblast cell line Mus spretus clone 5A. We sorted chromosomes that fell into five individual peaks based on the Hoechst 33258/chromomycin A3 DNA histogram: three peaks corresponding to the least amount of DNA and two peaks representing chromosomes with the most DNA content. This is the first example of the successful application of bivariate flow karyotyping to murine chromosome sorting. We then applied primer-directed in vitro DNA amplification using the polymerase chain reaction (PCR) to generate and label larger amounts of chromosome-specific DNA. In situ hybridization showed specific binding of the PCR products to mouse chromosomes Y, 19, 18, 3, and X as well as chromosomes 1 and 2. The combination of chromosome sorting from the M. spretus cell line and PCR proved to be highly valuable for generation of pools of DNA fragments that exhibit specific binding to mouse chromosomes and can be used to identify and delineate mouse metaphase chromosomes.

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PubMed1994

Mouse rump-white mutation associated with an inversion of chromosome 5.

The rump-white (Rw) mutation in the mouse was previously mapped as part of a cluster of spotting genes on Chromosome (Chr) 5 that includes the dominant spotting (W) and patch (Ph) loci. Recent studies have shown that the W locus encodes the KIT tyrosine kinase cell surface receptor and that Ph is a deletional mutation encompassing the platelet-derived growth factor receptor alpha subunit (Pdgfra) gene. However, the molecular basis of the Rw mutation remains to be established. We have analyzed an interspecific Mus spretus backcross segregating Rw and several loci proximal and distal to the W/Ph/Rw region to study the basis of this mutation. These studies indicated that loci within the En2 to Kit region of the chromosome do not recombine with one another even though they have been separated in other mapping studies presented here and elsewhere. We conducted a series of fluorescent in situ hybridization (FISH) studies with genomic probes to En2, Msx1, D5Buc1, and Kit to compare the physical order of these loci on the Rw and wild-type chromosomes. The Kit locus mapped to approximately the same region on both chromosomes of the Rw heterozygotes, while the positions of En2, Msx1, and D5Buc1 were reversed on the two chromosomes. Taken together, both the genetic and physical mapping data establish that the Rw mutation is associated with an inversion involving loci in the proximal region of Chromosome 5.

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PubMed1994

Linkage of phosphoribosylpyrophosphate synthetases 1 and 2, Prps1 and Prps2, on the mouse X chromosome.

The X Chromosome (Chr) genes for phosphoribosylpyrophosphate synthetases 1 and 2, Prps1 and Prps2, were mapped on the mouse X Chr with interspecific backcrosses between C57BL/6 (B6) and M. spretus (S). Southern analysis showed that Prps1 mapped between Plp and DXWas31, a mouse X Chr region that is homologous to Xq21-24 on the human X Chr while Prps2 mapped between DXWas31 and Amg, a region that is homologous to the map position of PRPS2 on Xp22 of the human X Chr. Additionally, other restriction fragments highlighted by PRS II showed autosomal segregation. In situ hybridization and FISH analysis of metaphase chromosome spreads prepared from lymphocytes of B6 or S male mice confirmed that there were in fact two different locations on the X Chr, X F1-2 and X F2-3 for Prps1 and 2 respectively, as well as two autosomal sites for Prps-like genes.

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PubMed1994

The murine Xe169 gene escapes X-inactivation like its human homologue.

Among a number of genes that escape X-chromosome inactivation in humans, three have been evaluated in mice and unexpectedly all three are subject to X-inactivation. We report here the cloning and expression studies of a novel mouse gene, Xe169, and show that it escapes X-inactivation like its human homologue. Xe169 was assigned to band F2/F3 on the mouse X chromosome by fluorescent in situ hybridization and Southern analysis indicates that the gene is located outside the pseudoautosomal region. Homologous, but divergent, sequences exist on the Y chromosome. In vitro and in vivo studies show that Xe169 is expressed from both the active and the inactive X chromosomes. Xe169 is the first cloned non-pseudoautosomal gene that escapes X-inactivation in mice.

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PubMed1994

Direct determination of NotI cleavage sites in the genomic DNA of adult mouse kidney and human trophoblast using whole-range restriction landmark genomic scanning.

Restriction landmark genomic scanning (RLGS) is a method for visualizing restriction landmarks, employing direct labeling of restriction sites of genomic DNA and high-resolution two-dimensional electrophoresis. We determined the conditions for both the first and second dimensions of RLGS that define all of the restriction fragments which carry the NotI landmark. Using this system, we determined the number of cleavable NotI sites of genomic DNA from the mouse kidney (C57BL/6) and from the human placenta. The mouse and human genomes were cleaved at 2,380 +/- 80 sites (4,760 +/- 160 spots) and 3,240 +/- 110 sites (6,480 +/- 220 spots), respectively with NotI.

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PubMed1994

CpG island promoter region methylation patterns of the inactive-X-chromosome hypoxanthine phosphoribosyltransferase (Hprt) gene.

Inactive-X-chromosome genes in mammalian females have methylated CpG islands. We have questioned whether there are variable levels of cytosine methylation at different CpG sites within the island that might indicate the presence of primary sites of methylation which may be critical for the maintenance of gene repression and candidate sites for the initiation of inactivation. To address these questions, we have analyzed the methylation patterns of 32 CpG sites of the X-linked hypoxanthine phosphoribosyltransferase (Hprt) gene on the active and inactive X chromosomes of mouse tissues and cell lines, using genomic sequencing of bisulfite-treated genomic DNA. Cytosine is deaminated by bisulfite, but methylcytosine is not affected. Cell lines that were heterozygous for the Hprt deletion mutation (Hprtb-m3) and a functional Hprt allele were selected with 6-thioguanine. The resulting cell populations uniformly carry the intact Hprt allele on the inactive X chromosome. The methylation of these CpG sites was determined either by the direct sequence analysis of bisulfite-treated and amplified DNA or by the sequence analysis of clones derived from the amplified DNA. No CpG methylation was detected on the active Hprt genes from either males or the active X chromosome of females. On average, 22 CpGs were methylated in the other 50% of female DNA, and the level of methylation at individual sites varied from 42 to 100%. Analysis of the inactive Hprt gene in two cell lines showed that averages of 14 and 18 CpGs were methylated and that the frequency of methylation at 32 individual sites ranged from 3 to 100%. The highest frequency of methylation in cell lines coincided with the sequences flanking transcription initiation sites. These results suggest that methylation patterns are heterogeneous within a tissue and even in clonal cell populations and that specific subsets of CpG sites sustain high methylation frequencies which may be critical for the maintenance of X-chromosome inactivation. The bisulfite method identified which CpG sites were methylated on the inactive X chromosome, and it provided a quantitative estimate of the frequency of methylation of these sites in genomic DNA.

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