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PubMed1994

Structure and chromosomal localization of the human PD-1 gene (PDCD1).

A cDNA encoding mouse PD-1, a member of the immunoglobulin superfamily was previously isolated from apoptosis-induced cells by subtractive hybridization. To determine the structure and chromosomal location of the human PD-1 gene, we screened a human T cell cDNA library by mouse PD-1 probe and isolated a cDNA coding for the human PD-1 protein. The deduced amino acid sequence of human PD-1 was 60% identical to the mouse counterpart, and a putative tyrosine kinase-association motif was well conserved. The human PD-1 gene was mapped to 2q37.3 by chromosomal in situ hybridization.

Amino Acid Sequence↗

PubMed1998

The genomic structure and chromosomal location of the human TR2 orphan receptor, a member of the steroid receptor superfamily.

Human TR2 orphan receptor, isolated from the testis and prostate, is a member of the steroid/thyroid hormone receptor superfamily. With the screening of a human genomic library and the combination of primer walking and PCR sequencing, we found that the entire TR2 orphan receptor gene coding region and 5'-untranslated region feature 13 introns and 14 exons, and that the consensus splice sequences (GT-AG) are present in all intron-exon boundaries. Within the region that codes for the DNA binding domain, TR2 orphan receptor gene has a distinct intron-exon junction. Whereas all other known steroid receptors have one splice site that separates their first and second zinc fingers in the DNA binding domain, TR2 orphan receptor has a rare splice site located in the middle of its first zinc finger. The identification of specific junction sequences for potential alternative splicing sites helps to explain the existence of multiple forms of TR2 orphan receptor cDNA (TR2-5, 7, 9, 11). The S1 nuclease protection assay for TR2 message revealed that there are multiple transcription initiations, and that the major cap site surrounded by an initiator-like sequence is located at the 104th nucleotide upstream from the translation start codon. Sequence analysis of a 2.7-kb DNA fragment upstream of the TR2 orphan receptor translation start codon unveiled several potential cis-acting elements, such as AP-1, HNF-5, GATA1 binding sites, and GC boxes. Using fluorescence in situ hybridization combined with a high-resolution G-banding technique, we found that the TR2 orphan receptor gene was mapped to human chromosome 12 at band q22, whereas the structurally closely related TR4 orphan receptor gene was mapped to human chromosome 3 at band q24.3.

Amino Acid Sequence↗

PubMed1998

Genomic structure and chromosomal localization of the mouse LIM domain-binding protein 1 gene, Ldb1.

The LIM domain is a structural motif that is well conserved throughout evolution in a variety of factors known to play important roles in development and cell regulation. Ldb genes encode LIM domain-binding (Ldb) factors. Here we report on the structural organization and chromosomal localization of the mouse Ldb1 gene. It contains at least 10 exons and spans approximately 4 kb of genomic DNA. The transcription initiation site is located 462 bp upstream of the translation initiation codon ATG as determined by 5'-RACE. Sequencing analysis of the 5'-flanking region shows TATA and CCAAT motifs as well as potential binding sites for GATA, CF-1, PEA3, HRE, APRRE, RARE, Myc, and c-Jun. Ldb1 maps to the distal region of mouse chromosome 19 that is syntenic with human chromosome 10q.

Animals↗

PubMed2000

Unusual chromosome architecture and behaviour at an HSR.

Amplification of sequences within mammalian chromosomes is often accompanied by the formation of homogeneously staining regions (HSRs). The arrangement of DNA sequences within such amplicons has been investigated, but little is known about the chromosome structure or behaviour of these unusual regions. We have analysed the metaphase chromosome structure of the dihydrofolate reductase (DHFR) amplicon of CHOC400 cells. The chromatin in this region contains hyperacetylated nucleosomes yet, at the same time, appears to be densely packed like heterochromatin. The region does not bind heterochromatin proteins. We show that the dense packing of the region is restricted to DNA located close to the chromosome core/scaffold. In contrast, levels of the chromosome scaffold protein topoisomerase II at HSRs are the same as those found at other euchromatic locations. Metaphase chromosome condensation of the HSR is shown to be sensitive to topoisomerase II inhibitors, and sister chromatids often appear to remain attached within the HSRs at metaphase. We suggest that these features underlie anaphase bridging and the aberrant interphase structure of the HSR. The DHFR amplicon is widely used as a model system to study mammalian DNA replication. We conclude that the higher-order chromosome structure of this amplicon is unusual and suggest that caution needs to be exercised in extrapolating data from HSRs to normal chromosomal loci.

Anaphase↗

PubMed1993

Human 4-hydroxyphenylpyruvate dioxygenase. Primary structure and chromosomal localization of the gene.

We report the primary structure of 4-hydroxyphenylpyruvate dioxygenase [4-hydroxyphenyl-pyruvate:oxygen oxidoreductase (hydroxylating, decarboxylating)]. The work is based on the isolation of cDNA clones from human liver lambda gt11 libraries. Several overlapping clones covering the coding sequence were characterized. In parallel, peptides from four different digests of the purified protein were analysed for their amino-acid sequence. These peptide sequences covered 86% of the cDNA-derived amino-acid sequence. This gives the sequence for a polypeptide of 392 amino acids with a calculated molecular mass of 44.8 kDa. There is more than 80% identity between the human and the pig enzymes and also between these enzymes and the F antigen from rat and the two allelic forms of this antigen from mouse. The enzyme has 53% conserved amino acids and 27% identical amino acids in common with 4-hydroxyphenylpyruvate dioxygenase from Pseudomonas sp. P.J. 874 and 52% conserved and 28% identical residues, with a protein from Shewanella colwelliana. At the C-terminus there is 61% identity between the seven proteins. These results indicate that these proteins are all 4-hydroxyphenylpyruvate dioxygenases. The identity of the C-terminus makes this part of the molecule a candidate for a functional role in the catalytic process. At conserved positions in all seven enzymes, there are two tyrosine residues and three histidine residues, i.e. amino acids which have been implicated as ligands for iron in 2-oxoacid-dependent dioxygenases. The gene encoding the enzyme was localized to chromosome 12q14-->qter by Southern-blot analysis of human-rodent somatic-cell hybrids.

4-Hydroxyphenylpyruvate Dioxygenase↗

PubMed1987

The chromosomal gene structure for murine granulocyte colony-stimulating factor.

The chromosomal gene for murine granulocyte colony-stimulating factor (G-CSF) has been isolated from a mouse genomic library. The nucleotide sequence analysis of the gene and its flanking region has revealed that the murine G-CSF gene is composed of four introns and five exons, which is similar to the human G-CSF gene. The S1 mapping analysis of murine G-CSF mRNA has identified the major transcription initiation site for the murine G-CSF gene at 36 base pairs upstream of the ATG initiation codon. In the flanking region, there are sequences of about 300 base pairs which are highly conserved between human and murine G-CSF genes. The decanucleotide GAGRTTCCAC, which was found at the 5'-flanking region of genes for other hemopoietic growth factors, was also present within the corresponding regions of human and murine G-CSF gene. Unlike the human G-CSF gene, no alternative splicing was observed for the murine G-CSF gene.

Amino Acid Sequence↗

PubMed1982

Nondisjunction and chromosome breakage in mouse oocytes after various x-ray doses.

The effect of varying X-ray doses (0.05-0.80 Gy) on preovulatory mouse oocytes was studied by measuring nondisjunction during the first meiotic division, as well as structural chromosome anomalies in ovulated oocytes at metaphase stage II. The incidence of nondisjunction (0.1% hyperploid oocytes) found in oocytes from nonirradiated NMRI-Han female mice was in accordance with the results previously obtained with the same strain. Significantly (P less than 0.05) more hyperploid oocytes (0.9%) were ovulated following irradiation with 0.8 Gy. There was no statistically significant increase of nondisjunction after low doses. Structural chromosome anomalies occurred, however, even after an irradiation dose as low as 0.05 Gy. The dose response for structural chromosome anomalies is altogether different from that of radiation-induced hyperploidy. We consider that irradiation of mature oocytes might well be less hazardous with regard to its potency for increasing nondisjunction during the first meiotic division when compared with the effect of chemical mutagens.

Animals↗

PubMed1988

Global variation in G+C content along vertebrate genome DNA. Possible correlation with chromosome band structures.

The global, rather than local, variation in G+C content along the nuclear DNA sequences of various organisms was studied using GenBank sequence data. When long DNA sequences of the genomes of Escherichia coli and Saccharomyces cerevisiae were examined, the levels of their G+C content (G+C%) were found to be within a narrow range around that of the whole genome. The G+C% levels for sequences of vertebrate genomes, however, were found to cover a wide range, showing that their genome is a mosaic of sequences with different G+C% levels, in each of which the sequence is fairly homogeneous in its G+C% for a very long distance. Through surveying a human genetic map and GenBank DNA sequences, the global variations in G+C% along the human genome DNA were found to be correlated with chromosome band structures.

Animals↗

PubMed1996

Tissue distribution, genomic structure, and chromosome mapping of mouse and human eukaryotic initiation factor 4E-binding proteins 1 and 2.

Two related eukaryotic initiation factor-4E binding proteins (4E-BP1 and 4E-BP2) were recently characterized for their capacity to bind specifically to eIF4E and inhibit its function. Here, we determined the cDNA sequence, tissue distribution, genomic structure, and chromosome localization of murine and human 4E-BP1 and 4E-BP2. Mouse 4E-BP1 and 4E-BP2 consist of 117 and 120 amino acids and exhibit 91. 5 and 95.0% identity, respectively, to their human homologues. 4E-BP1 mRNA is expressed in most tissues, but is most abundant in adipose tissue, pancreas, and skeletal muscle, while 4E-BP2 mRNA is ubiquitously expressed. The structures of the mouse 4E-BP1 and 4E-BP2 were determined. The 4E-BP1 gene consists of three exons and spans approximately 16 kb. In addition, two 4E-BP1 pseudogenes exist in the mouse genome. The 4E-BP2 gene spans approximately 20 kb and exhibits an identical genomic organization to that of 4E-BP1, with the protein coding portion of the gene divided into three exons. There are no pseudogenes for 4E-BP2. The chromosomal locations of 4E-BP1 and 4E-BP2 were determined in both mice and humans by fluorescence in situ hybridization analysis. Mouse 4E-BP1 and 4E-BP2 map to chromosomes 8 (A4-B1) and 10 (B4-B5), respectively, and human 4E-BP1 and 4E-BP2 localize to chromosomes 8p12 and 10q21-q22, respectively.

Adaptor Proteins, Signal Transducing↗

PubMed1994

Swedish survey on extra structurally abnormal chromosomes in 39 105 consecutive prenatal diagnoses: prevalence and characterization by fluorescence in situ hybridization.

During 7 years (1985-1992), 39,105 consecutive prenatal diagnoses (34,908 amniocenteses and 4197 chorionic villus samples) were made at the five largest clinical genetic laboratories in Sweden. Thirty-one cases of extra structurally abnormal chromosomes (ESACs) were found, giving a total prevalence of 0.8 per 1000. Twelve ESACs were inherited, 14 were de novo and in five the parental origin was unknown. This gives an estimated prevalence of 0.3-0.4 per 1000 for familial and 0.4-0.5 per 1000 for de novo ESACs. Retrospectively, the ESACs were characterized by fluorescence in situ hybridization (FISH). In nine cases, no material was available for this analysis. In 21 of the remaining 22 cases, the chromosomal origin could be identified by FISH. Seventeen of these (81 per cent) were derived from the acrocentric chromosomes, of which 13 originated from chromosome 15 (62 per cent). The most common ESAC was the inv dup(15) (57 per cent). Two cases were derived from chromosome 22, one from chromosome 14, and one from either chromosome 13 or chromosome 21. The four remaining cases consisted to two i(18p)s and two small ring chromosomes derived from chromosomes 4 and 19, respectively.

Amniocentesis↗

PubMed1999

Comparisons of genomic structures and chromosomal locations of the mouse aldose reductase and aldose reductase-like genes.

Aldose reductase (AR), best known as the first enzyme in the polyol pathway of sugar metabolism, has been implicated in a wide variety of physiological functions and in the etiology of diabetic complications. We have determined the structures and chromosomal locations of the mouse AR gene (Aldor1) and of two genes highly homologous to Aldor1: the fibroblast growth factor regulated protein gene (Fgfrp) and the androgen regulated vas deferens protein gene (Avdp). The number of introns and their locations in the mouse Aldor1 gene are identical to those of rat and human AR genes and also to those of Fgfrp and Avdp. Mouse Aldor1 gene was found to be located near the Cald1 (Caldesmon) and Ptn (Pleiotropin) loci at the proximal end of chromosome 6. The closely related genes Fgfrp and Avdp were also mapped in this region of the chromosome, suggesting that these three genes may have arisen by a gene duplication event.

Aldehyde Reductase↗

PubMed1999

Dithiothreitol induces sperm nuclear decondensation and protects against chromosome damage during male pronuclear formation in hybrid zygotes between Chinese hamster spermatozoa and Syrian hamster oocytes.

The present study was undertaken to investigate whether a time lag in sperm nuclear decondensation and male pronuclear formation in the course of development of eggs is associated with any occurrence of structural chromosome aberrations in male genomes of hybrid zygotes between Chinese hamster spermatozoa and zona-free Syrian hamster oocytes. Shortly after insemination, hybrid zygotes were treated with dithiothreitol (DTT) at different concentrations (0.1-10.0 mM) for 30 min to reduce protamine disulphide (S-S) bonds and thereby accelerate sperm nuclear decondensation and male pronuclear formation. The incidence of sperm nuclear decondensation and male pronuclear formation increased with increasing DTT concentrations, indicating that a reduction in S-S bonds effectively induces these cytological events. Chromosomes of male genomes in hybrid zygotes generated by treatment with 1.0 mM, 2.5 mM and 10.0 mM DTT were analysed at the first cleavage metaphase. Incidence of structural chromosome aberrations in each treatment was 34.5%, 27.1% and 24.7%, respectively. There was a significant difference between the incidences with 1.0 mM and 10.0 mM DTT treatment. As the time lag in nuclear decondensation and male pronuclear formation was greatest in the 1.0 mM treatment condition, followed in order by 2.5 mM and 10.0 mM, it is suggested that the lag in sperm nuclear development behind egg development is responsible for structural chromosome aberrations in male genomes of hybrid zygotes.

Acridine Orange↗

PubMed1991

The relationship between colony-forming ability, chromosome aberrations and incidence of micronuclei in V79 Chinese hamster cells exposed to microwave radiation.

Cultured V79 Chinese hamster fibroblast cells were exposed to continuous radiation, frequency 7.7 GHz, power density 0.5 mW/cm2 for 15, 30 and 60 min. The effect of microwave radiation on cell survival and on the incidence and frequency of micronuclei and structural chromosome aberrations was investigated. The decrease in the number of irradiated V79 cell colonies was related to the power density applied and to the time of exposure. In comparison with the control samples there was a significantly higher frequency of specific chromosome aberrations such as dicentric and ring chromosomes in irradiated cells. The presence of micronuclei in irradiated cells confirmed the changes that had occurred in chromosome structure. These results suggest that microwave radiation can induce damage in the structure of chromosomal DNA.

Animals↗

PubMed2000

Structure and chromosomal localization of human and mouse genes for hematopoietic prostaglandin D synthase. Conservation of the ancestral genomic structure of sigma-class glutathione S-transferase.

Hematopoietic prostaglandin D synthase (H-PGDS) is the key enzyme for the production of the D and J series of prostanoids, and the first recognized vertebrate homolog of sigma-class glutathione S-transferase (GST). We isolated the genes and cDNAs for human and mouse H-PGDSs. The human and mouse cDNAs contained a coding region corresponding to 199 amino-acid residues with calculated molecular masses of 23 343 and 23 226, respectively. Both H-PGDS proteins recombinantly expressed in Escherichia coli showed bifunctional activities for PGDS and GST, and had almost the same catalytic properties as the rat enzyme. Northern analyses demonstrated that the H-PGDS genes were expressed in a highly species-specific manner. Whereas the human gene was widely distributed, in contrast, the mouse gene was detected only in samples from oviduct and skin. By fluorescence in situ hybridization, the chromosomal localization of the human and mouse H-PGDS genes were mapped to 4q21-22 and 3D-E, respectively. The human and mouse H-PGDS genes spanned approximately 41 and 28 kb, respectively, and consisted of six exons divided by five introns. The exon/intron boundaries of both genes were completely identical to those of the sigma-class GST subfamily, although the amino-acid sequences of the latter were only 17.0-21.5% identical to those of either H-PGDS. These findings suggest that the H-PGDS genes evolved from the same ancestral gene as the members of the sigma-class GST family.

Amino Acid Sequence↗

PubMed1996

Relative biological effectiveness (RBE) of 252Cf fission neutrons for the induction of chromosome damage in human spermatozoa.

Effects of 60Co gamma-rays and 252Cf neutrons on human sperm chromosomes were studied using our interspecific in vitro fertilization system to estimate relative biological effectiveness (RBE) of neutrons. Semen samples were exposed to 0.5, 1.0 and 2.0 Gy of 60Co gamma-rays at 1.7 cGy/ min and 0.25, 0.5 and 1.0 Gy of 252Cf radiation at 1.3-1.7 cGy/ min. In the 60Co experiment, 509 spermatozoa from controls and 902 spermatozoa from the irradiated groups were karyotyped, while in the 252Cf experiment 460 control and 804 irradiated spermatozoa were analysed. In both 60Co and 252Cf experiments, incidences of spermatozoa with radiation-induced structural chromosome aberrations increased linearly with increase of dosage. The RBE of 252Cf neutrons for the induction of chromosomally abnormal spermatozoa was estimated to be 1.6. The number of induced structural chromosome aberrations per spermatozoon also increased linearly. The RBE of neutrons for this index was 2.0. Among structural chromosome aberrations observed, chromosome-type breaks were predominant in both 60Co and 252Cf experiments, and they showed a significant linear dose-dependent increase. Other types of aberrations such as chromosome-type exchanges and chromatid-type breaks also increased linearly with increase in dose. The RBEs of 252Cf neutrons for the induction of these three types of aberrations were 1.6, 3.2 and 3.9, respectively. Thus, the RBEs of neutrons for the induction of chromosome aberrations were smaller in human spermatozoa than in human lymphocytes, and mouse spermatogonia and embryos. This result is discussed from the point of view of DNA-repairing capacity of oocytes.

Animals↗

PubMed2005

A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae).

We updated the genetic map of rainbow trout (Oncorhynchus mykiss) for 2 outcrossed mapping panels, and used this map to assess the putative chromosome structure and recombination rate differences among linkage groups. We then used the rainbow trout sex-specific maps to make comparisons with 2 other ancestrally polyploid species of salmonid fishes, Arctic charr (Salvelinus alpinus) and Atlantic salmon (Salmo salar) to identify homeologous chromosome affinities within each species and ascertain homologous chromosome relationships among the species. Salmonid fishes exhibit a wide range of sex-specific differences in recombination rate, with some species having the largest differences for any vertebrate species studied to date. Our current estimate of female:male recombination rates in rainbow trout is 4.31:1. Chromosome structure and (or) size is associated with recombination rate differences between the sexes in rainbow trout. Linkage groups derived from presumptive acrocentric type chromosomes were observed to have much lower sex-specific differences in recombination rate than metacentric type linkage groups. Arctic charr is karyotypically the least derived species (i.e., possessing a high number of acrocentric chromosomes) and Atlantic salmon is the most derived (i.e., possessing a number of whole-arm fusions). Atlantic salmon have the largest female:male recombination ratio difference (i.e., 16.81:1) compared with rainbow trout, and Arctic charr (1.69:1). Comparisons of recombination rates between homologous segments of linkage groups among species indicated that when significant experiment-wise differences were detected (7/24 tests), recombination rates were generally higher in the species with a less-derived chromosome structure (6/7 significant comparisons). Greater similarity in linkage group syntenies were observed between Atlantic salmon and rainbow trout, suggesting their closer phylogenetic affinities, and most interspecific linkage group comparisons support a model that suggests whole chromosome arm translocations have occurred in the evolution of this group. However, some possible exceptions were detected and these findings are discussed in relation to their influence on segregation distortion patterns. We also report unusual meiotic segregation patterns in a female parent involving the duplicated (homeologous) linkage group pair 12/16 and discuss several models that may account for these patterns.

Animals↗

PubMed1996

Analysis of chromosome constitution of human spermatozoa with normal and aberrant head morphologies after injection into mouse oocytes.

The chromosome constitution of human spermatozoa was determined after injecting individual spermatozoa into mouse oocytes. Of a total 279 eggs arrested at first cleavage metaphase, 200 (71.7%) were suitable for the analysis of sperm chromosomes. Incidences of spermatozoa with numerical and structural chromosome aberrations were 1.3 and 6.9% respectively in spermatozoa with normal head morphology, showing values comparable with those found in previous studies using the hamster oocyte-human sperm fusion system. The ratio of X- to Y-bearing spermatozoa did not differ significantly from the expected 1:1 ratio. The incidence of structural chromosome aberrations was about four times higher in spermatozoa with amorphous, round and elongated heads (26.1%) than in those with morphologically normal heads, whereas the incidence of aneuploidy was not significantly different between the two groups. No increase in chromosome aberrations was found in spermatozoa with large heads. The same was true for spermatozoa with small heads. Although the sample size used in this study is rather small, the results nevertheless indicate that some morphological abnormalities in the sperm heads are associated with their chromosome defects.

Animals↗

PubMed1990

A human hepatocellular carcinoma cell line with multiple copies of structurally normal chromosomes.

At Veterans General Hospital (VGH), a cell line, HA59T(HA59T/VGH), was established from a primary hepatocellular carcinoma of a 52-year-old Chinese male patient. G-banded metaphases were analyzed at passages 12 and 62. Of the 200 cells counted, 68% had 100-110 chromosomes/cell at passage 12, and 74% had 90-100 chromosomes/cell at passage 62. The presence of multiple copies of a structurally normal chromosome in a single cell was common for most of the chromosomes. Both X and Y sex chromosomes were normally present in the majority of the cells. This cell line is karyotypically different from those reported in other literature.

Carcinoma, Hepatocellular↗