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PubMed1981

Localization of chromosomal protein HMG-1 in polytene chromosomes of Chironomus thummi.

The distribution of accessible antigenic sites in the chromosomal protein high mobility group one (HMG-1) in Chironomus thummi polytene chromosomes is visualized by immunofluorescence. The results indicate that (a) HMG-1 is distributed in a distinct banding pattern along the entire length of the chromosomes; (b) the banding pattern obtained with fluorescent antibody does not strictly correspond to that observed by phase-contrast microscopy; and (c) the amount of HMG-1 increases, and the fluorescent banding pattern changes, during the development of the organism. Our findings suggest that the protein may be involved in the modulation of the structure of selected loci in the chromosome.

Animals↗
PubMed1989

Consistent breakage between consensus recombinase heptamers of chromosome 9 DNA in a recurrent chromosomal translocation of human T cell leukemia.

Chromosomal translocations in lymphoid tumors frequently result from recombination between a normally rearranging antigen receptor gene and a normally non-rearranging second locus. The possibility that the lymphocyte recombinase apparatus plays a role in determining the position of breakage at the second locus has been a matter of controversy because of the inconsistent presence of heptamer-like recognition sequences adjoining breakpoints at this site. To further investigate this issue, sites of DNA recombination were analyzed in both the der(9) and der(7) products of t(7;9)(q34;q32), a recurrent translocation of human acute lymphoblastic leukemias (T-ALL). In each of three separate cases, the translocation has divided the TCR-beta locus, juxtaposing chromosome 9 DNA 5' to a J-region in the der(9) product and 3' to a D-region in the der(7) product, with variably sized N-insertions and small deletions detectable at the junctions. All three cases contain breakpoints in chromosome 9 DNA tightly clustered between two closely spaced, and oppositely oriented heptamer sequences, CAC(A/T)GTG, which perfectly match the consensus heptamer sequence recognized by the lymphocyte recombinase apparatus in normal antigen receptor gene rearrangement. In no case was there evidence of directly duplicated sequences in the two reciprocal products, as is often associated with recombination involving random staggered breakage of DNA. Taken together, these results support a mechanism for this particular translocation proceeding by recombinase-mediated breakage of both participating chromosomes.

Base Sequence↗
PubMed1997

Yeast artificial chromosome clones of rice chromosome 2 ordered using DNA markers.

Yeast artificial chromosome (YAC) clones were ordered for the physical mapping of rice chromosome 2, the last of the 12 rice chromosomes to be assigned YACs by the Rice Genome Research Program. A total of 128 restriction fragment length polymorphism markers and 4 sequence-tagged site (STS) markers located on our high-density genetic map were used for YAC clone landing. By colony/Southern hybridization and polymerase chain reaction screening, a total of 239 individual YACs were selected from our YAC library of 6934 clones covering six genome equivalents. The YACs located on the corresponding marker positions in the linkage map formed 43 contigs and islands and were estimated to encompass about 50% of the length of rice chromosome 2.

Blotting, Southern↗
PubMed1986

Rearrangement of genes located on homologous chromosomal segments in mouse and man: the location of genes for alpha- and beta-interferon, alpha-1 acid glycoprotein-1 and -2, and aminolevulinate dehydratase on mouse chromosome 4.

Gene mapping studies to determine the order of alpha- and beta-interferon (Ifa, Ifb), aminolevulinate dehydratase (Lv), and alpha-1 acid glycoprotein-1 and -2 (Orm-1, Orm-2) relative to each other and to the reference genes brown (b), B-cell maturation factor responsiveness (Bmfr-1), and major urinary protein-1 (Mup-1) are reported. The most likely order was Mup-1--Lv--b--Orm-1, Orm-2--Ifa, Ifb--Bmfr-1. This order suggested that two chromosomal segments located on chromosome 4 in the mouse and chromosome 9 in man have been conserved since divergence of lineages leading to man and mouse; these segments are marked by soluble aconitase-1 (Aco-1) and galactose-1 phosphate uridyl transferase (Galt) and by Lv and Orm-1. This order also demonstrated that, although genes located on opposite arms of chromosome 9 in man remain syntenic in the mouse, gene order has not been conserved; Ifa and Ifb are not located in their expected locations near Aco-1 and Galt. The position of Ifa and Ifb between Orm-1 and Bmfr-1 could not be determined with certainty because of apparent heterogeneity in recombination frequencies between crosses involving conventional laboratory strains of mice and crosses involving interspecific matings between laboratory mice and Mus spretus. This result suggests that caution must be exercised when using M. spretus in linkage crosses.

Animals↗
PubMed1990

Chromosomal assignment of mutations by specific chromosome loss in the yeast Saccharomyces cerevisiae.

Yeast 2-microns plasmids were integrated near the centromere of a different chromosome in each of 16 cir0 mapping strains of Saccharomyces cerevisiae. The specific chromosomes containing the integrated 2-microns plasmid DNA were lost at a high frequency after crossing the cir0 strains to cir+ strains. A recessive mutation in a cir+ strain can then be easily assigned to its chromosome using this set of mapping strains, since the phenotype of the recessive mutation will be manifested only in diploids having the integrated 2-microns plasmid and the unmapped mutation on homologous chromosomes.

Centromere↗
PubMed2002

The Y chromosome of Drosophila melanogaster exhibits chromosome-wide imprinting.

Genomic imprinting is well known as a regulatory property of a few specific chromosomal regions and leads to differential behavior of maternally and paternally inherited alleles. We surveyed the activity of two reporter genes in 23 independent P-element insertions on the heterochromatic Y chromosome of Drosophila melanogaster and found that all but one location showed differential expression of one or both genes according to the parental source of the chromosome. In contrast, genes inserted in autosomal heterochromatin generally did not show imprint-regulated expression. The imprints were established on Y-linked transgenes inserted into many different sequences and locations. We conclude that genomic imprinting affecting gene expression is a general property of the Drosophila Y chromosome and distinguishes the Y from the autosomal complement.

Animals↗
PubMed1975

The influence of chromosome content on the size and shape of sperm heads in Drosophila melanogaster and the demonstration of chromosome loss during spermiogenesis.

The volumes of sperm heads were estimated from three-dimensional reconstructions of serially sectioned bundles of nearly mature spermatid nuclei. Cysts from males in which all sperm are expected to have comparable amounts of chromatin (X/Y and 1n(3LR)/+) show unimodal frequency distributions of nuclear volumes, whereas cysts from males in which meiotic segregation is expected to deliver unequal amounts of chromatin material to spermatid nuclei show two (XY/O and XY/Y) or more (T(2;3)/+ ANd C(2L);C(2R)) modes. The mean volumes of the subpopulations in these cases are related in the same proportions as the metaphase lengths of their chromosomal complements. Thus the volumes of sperm nuclei are proportional to their DNA content. Sperm head shape, on the other hand, does not appear to be very sensitive to chromosomal constitution, as heads of different size do not vary greatly in shape.----The numbers of sperm heads in the various size classes in a cyst depart from mendelian expectations; these departures are caused by the elimination, during individualization, of chromosomes contained within micronuclei that are formed in spermatids at the end of the second meiotic division. The effect of this chromosome loss is to increase the proportion of nullosomic gametes in the sperm pool.----The relative frequencies of XY-bearing and nullo-X, nullo-Y sperm in XY/O males were estimated from the volume measurements. Taking this estimate as a measure of the fertilizing population, it is possible to infer from the change in sex ratio over time following insemination, that XY-bearing sperm have an advantage of 1.5 over nullo-X, nullo-Y sperm in leaving the seminal receptacle of the female for fertilization of ova.

Animals↗
PubMed1999

Genetic mapping of the copper toxicosis locus in Bedlington terriers to dog chromosome 10, in a region syntenic to human chromosome region 2p13-p16.

Abnormal hepatic copper accumulation is recognized as an inherited disorder in man, mouse, rat and dog. The major cause of hepatic copper accumulation in man is a dysfunctional ATP7B gene, causing Wilson disease (WD). Mutations in the ATP7B genes have also been demonstrated in mouse and rat. The ATP7B gene has been excluded in the much rarer human copper overload disease non-Indian childhood cirrhosis, indicating genetic heterogeneity. By investigating the common autosomal recessive copper toxicosis (CT) in Bedlington terriers, we have identified a new locus involved in progressive liver disease. We examined whether the WD gene ATP7B was also causative for CT by investigating the chromosomal co-localization of ATP7B and C04107, using fluorescence in situ hybridization (FISH). C04107 is an anonymous microsatellite marker closely linked to CT. However, BAC clones containing ATP7B and C04107 mapped to the canine chromosome regions CFA22q11 and CFA10q26, respectively, demonstrating that WD cannot be homologous to CT. The copper transport genes CTR1 and CTR2 were also excluded as candidate genes for CT since they both mapped to canine chromosome region CFA11q22. 2-22.5. A transcribed sequence identified from the C04107-containing BAC was found to be homologous to a gene expressed from human chromosome 2p13-p16, a region devoid of any positional candidate genes.

Adenosine Triphosphatases↗
PubMed1986

Chromosome mediated gene transfer of six DNA markers linked to the cystic fibrosis locus on human chromosome seven.

The DNA probes met and pJ3.11 are derived from loci on chromosome seven that are closely linked to, and probably flanking, the gene mutation causing cystic fibrosis (CF). We have shown that mitotic chromosomes from the cell line MNNG-HOS, which contains an activated met oncogene, can induce morphological transformation of mouse NIH-3T3 cells. Southern analysis of isolated transfectant cell lines with cloned dispersed repetitive human DNA sequences as probes demonstrated that several lines of transformed NIH 3T3 cells had stabley incorporated large segments of chromosome seven DNA. Southern blot analysis also demonstrated the presence of met, pJ3.11 and several other single copy sequences that had been previously localised to chromosome 7 within the transgenomes. In this way a further four genetic markers were shown to be physically linked to met, and thus to CF. These probes may prove useful in confirming the order of loci around CF and in the prenatal diagnosis of this common autosomal recessive disease.

Animals↗
PubMed2003

The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism.

The African trypanosome, Trypanosoma brucei, causes sleeping sickness in humans in sub-Saharan Africa. Here we report the sequence and analysis of the 1.1 Mb chromosome I, which encodes approximately 400 predicted genes organised into directional clusters, of which more than 100 are located in the largest cluster of 250 kb. A 160-kb region consists primarily of three gene families of unknown function, one of which contains a hotspot for retroelement insertion. We also identify five novel gene families. Indeed, almost 20% of predicted genes are members of families. In some cases, tandemly arrayed genes are 99-100% identical, suggesting an active process of amplification and gene conversion. One end of the chromosome consists of a putative bloodstream-form variant surface glycoprotein (VSG) gene expression site that appears truncated and degenerate. The other chromosome end carries VSG and expression site-associated genes and pseudogenes over 50 kb of subtelomeric sequence where, unusually, the telomere-proximal VSG gene is oriented away from the telomere. Our analysis includes the cataloguing of minor genetic variations between the chromosome I homologues and an estimate of crossing-over frequency during genetic exchange. Genetic polymorphisms are exceptionally rare in sequences located within and around the strand-switches between several gene clusters.

Animals↗
PubMed1996

An ordered yeast artificial chromosome library covering over half of rice chromosome 6.

Yeast artificial chromosome (YAC) clones carrying DNA marker sequences located on the rice genetic map of chromosome 6 were ordered for physical mapping. A total of 122 restriction fragment length polymorphism markers, 16 sequence-tagged site markers, and five random amplified polymorphic DNA markers located, on average, at 0.9-cM intervals, were used for YAC clone screening by colony/Southern hybridization and PCR screening, respectively. A total of 216 individual YACs were selected from our YAC library of 7000 clones covering six genome equivalents. Each DNA marker could select, on average, 4.8 YAC clones, with 11 clones being the maximum. The YACs localized to the corresponding linkage map positions form 43 contigs and encompass about 60% of rice chromosome 6. This is the first step in constructing a physical map covering the whole rice genome by chromosome landing with YAC clones. These YACs and data will be used soon to isolate phenotypical trait genes by map-based cloning.

Blotting, Southern↗
PubMed1997

Genetic mapping of five human chromosome 4 orthologues to bovine chromosomes 6 and 17.

Five loci that map to human chromosome 4 (HSA4) were selected to expand the bovine comparative linkage map. Loci included b-casein (CSN2), basic fibroblast growth factor (FGF2), immunoglobulin J chain (IGJ), interleukin 2 (IL2) and microsomal triglyceride transfer protein (MTTP). Polymorphisms for each locus were identified by either polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) or single-strand conformational polymorphism (SSCP) analysis. The bovine genes for CSN2, IGJ and MTTP were mapped by linkage analysis to chromosome 6; FGF2 and IL2 mapped to chromosome 17. These data refine a position of chromosomal evolution to a small region between FGF2 and the previously mapped complement I factor (IF).

Animals↗
PubMed2005

A refined radiation hybrid map of the telomeric region of bovine chromosome 18q25-q26 compared with human chromosome 19q13.

Genome-wide scans have mapped economically important quantitative trait loci (QTL) for mastitis susceptibility in dairy cattle at the telomeric end of bovine chromosome 18 (BTA18). In order to increase the density of markers in this chromosomal region and to improve breakpoint resolution in the human-bovine comparative map, this study describes the chromosomal assignment of seven newly developed gene-associated markers and five microsatellites and eight previously mapped sequence tagged site markers near these QTL. The orientation of KCNJ14, BAX, CD37, NKG7, LIM2, PRKCG, TNNT1, MGC2705, RPL28, EPN1, ZNF582, ZIM2, STK13, ZNF132 and SLC27A5 on the 3000-rad radiation hybrid (RH) map of BTA18 is homologous to the organization found on the corresponding 10 Mbp of human chromosome 19q (HSA19q). The resulting bovine RH map with a length of 20.9 cR spans over about 11 cM on the bovine linkage map. The location of KCNJ14 and SLC27A5 flanking the RH map on BTA18q25-26 has been confirmed by fluorescence in situ hybridization. The data of this refined human-bovine comparative map should improve selection of candidate genes for mastitis susceptibility in dairy cattle.

Animals↗
PubMed1994

Philadelphia-negative chronic myeloid leukaemia: detection by FISH of BCR-ABL fusion gene localized either to chromosome 9 or chromosome 22.

Dual-colour FISH has been used to study two patients with chronic myeloid leukaemia (CML) associated with a normal karyotype. Co-localization of signals from BCR and ABL cosmids was observed in interphase nuclei from both patients. In one patient, analysis of metaphase spreads showed that the 3' region of the ABL gene was deleted from one chromosome 9 and inserted into chromosome 22. In a second patient 5' BCR sequences were missing from one copy of chromosome 22, and co-localized with 3' ABL sequences on chromosome 9. These results demonstrate the molecular heterogeneity of Ph-negative CML. In addition, they illustrate the potential usefulness of dual-colour FISH on interphase nuclei for monitoring the response to treatment of patients with Ph-negative CML.

Blotting, Southern↗
PubMed1995

A 40 kb chromosomal fragment encoding Salmonella typhimurium invasion genes is absent from the corresponding region of the Escherichia coli K-12 chromosome.

Many Salmonella typhimurium genes are required for bacterial entry into host cells. P22 transduction analysis has localized several invasion loci near minute 59 on the S. typhimurium chromosome. To further characterize the 59-60 min chromosomal region, we determined the physical and genetic map of 85 kb of S. typhimurium DNA between srl and cysC. It was previously shown that some of the invasion genes from this region are not present in Escherichia coli K-12. We examined whether other S. typhimurium genes on the 85 kb of DNA were similarly absent from E. coli. We found that a contiguous 40 kb fragment of the S. typhimurium chromosome which encodes invasion genes is absent from the corresponding region of the E. coli K-12 chromosome and may represent a 'pathogenicity island'. We speculate that acquisition of the 40 kb region must have significantly advanced the evolution of Salmonella as a pathogen.

Base Sequence↗
PubMed1991

Chromosomal localization of the glucose phosphate isomerase (GPI) gene in cattle, sheep and goat by in situ hybridization--chromosomal banding homology versus molecular conservation in Bovidae.

A porcine genomic glucose phosphate isomerase (GPI) DNA probe was used for in situ hybridization with metaphase chromosomes in cattle, sheep and goat. The probe gave distinct signals on the q22----proximal part of the q24 segment of chromosome 18, 14 and 18 in cattle, sheep and goat, respectively, indicating the location of GPI gene. The three species belong to the family Bovidae and have high resemblance in chromosome banding patterns. The localization of the GPI locus to the same site on chromosomes with almost similar banding patterns suggests high degree of homology at these sites in the three species. Correlation between banding homologies and possible similarities at the molecular level is discussed.

Animals↗
PubMed1994

Bovine synteny group U7, previously assigned to G-banded chromosome 25 in the ISCNDA nomenclature, assigns to R-banded chromosome 29.

Four microsatellite-containing bovine cosmids have been regionally localized by fluorescence in situ hybridization to bovine R-banded chromosome 29 (BTA29) and to the 1;29 translocated chromosomes. PCR-analyses of a somatic hybrid cell panel assigned the four microsatellites to synteny group U7. One of the cosmids (IDVGA7) has been previously mapped to G-banded BTA25 allowing to assign U7 to this chromosome. Hence, it is concluded that G-banded BTA25 corresponds to R-banded BTA29. The occurrence of other misleading nomenclatures for small bovine chromosomes is discussed.

Animals↗
PubMed2000

From sequence to chromosome: the tip of the X chromosome of D. melanogaster.

One of the rewards of having a Drosophila melanogaster whole-genome sequence will be the potential to understand the molecular bases for structural features of chromosomes that have been a long-standing puzzle. Analysis of 2.6 megabases of sequence from the tip of the X chromosome of Drosophila identifies 273 genes. Cloned DNAs from the characteristic bulbous structure at the tip of the X chromosome in the region of the broad complex display an unusual pattern of in situ hybridization. Sequence analysis revealed that this region comprises 154 kilobases of DNA flanked by 1.2-kilobases of inverted repeats, each composed of a 350-base pair satellite related element. Thus, some aspects of chromosome structure appear to be revealed directly within the DNA sequence itself.

Animals↗