Evolution, expression, and chromosomal location of a novel receptor tyrosine kinase gene, eph.

Partial sequence analysis of the genomic eph locus revealed that the splicing points of kinase domain-encoding exons were completely distinct from those of the other protein tyrosine kinase members reported, suggesting that this is the earliest evolutionary split within this family. In Northern (RNA) blot analysis, the eph gene was expressed in liver, lung, kidney, and testis of rat, and screening of 25 human cancers of various cell types showed preferential expression in cells of epithelial origin. Overexpression of eph mRNA was found in a hepatoma and a lung cancer without gene amplification. Comparison of cDNA sequences derived from a normal liver and a hepatoma that overproduces eph mRNA demonstrated that two of them were completely identical throughout the transmembrane to the carboxy-terminal portions. Southern blot analysis of DNAs from human-mouse hybrid clones with an eph probe showed that this gene was present on human chromosome 7.

Structure, expression, and chromosomal location of the human c-fgr gene.

The nucleotide sequence of seven exons of the human c-fgr gene, a cellular homolog of the oncogene of Gardner-Rasheed feline sarcoma virus, was determined. Twenty-six independent genomic clones were obtained from a human gene library with a DNA clone of Y73 avian sarcoma virus oncogene, v-yes, as a probe under relaxed hybridization conditions. Restriction mapping and partial sequence analyses revealed that two of these clones were derived from the c-fgr gene, distinct from the c-yes gene. Interestingly, the splicing points of the c-fgr gene were identical with those of the c-src gene throughout the seven exons, suggesting that the two proto-oncogenes were generated by gene duplication of an ancestral gene containing intervening sequences. On RNA blot hybridization the major transcript was found to be 2.6 kilobase long. Two additional transcripts of 3.5 and 4.7 kilobases were also detected. Furthermore, karyotype analysis of several human-mouse hybrid cells and Southern blot analyses of DNAs of the hybrids with a human c-fgr locus-specific probe showed that this gene is located on chromosome 1.

Specificity of the deletion of chromosome No. 15 in mouse plasmacytoma: brief communication.

Q-banding studies in two independent hyperdiploid mouse plasmacytomas, 63-1 and the NP-38-ABCD subline of MSPC-1, revealed that deletion of a No. 15 chromosome was common. The deletion of No. 15 appeared to result from a translocation between No. 12 and 15 in the NP-38-ABCD, as in most plasmacytomas. In 63-1, however, No. 10 was probably a recipient chromosome of the missing segment from the deleted No. 15, and both chromosomes No. 12 remained intact. These karyotypic features suggest that the deleted No. 15 is a tumor-specific marker chromosome in mouse plasmacytoma and that an abnormality of No. 12 is not essential for development of the tumor. The constitution of chromosomes in the two plasmacytomas remained remarkably stable in their homogeneous modal population.

Effect of mitochondrial DNA transmitted cytoplasmically from nontumorigenic to tumorigenic rat cells on the phenotypic expression of tumorigenicity.

The effect of mitochondrial DNA (mtDNA) on the phenotypic expression of tumorigenicity was examined by its cytoplasmic transmission from nontumorigenic cells to tumorigenic cells. Enucleated cells of the rat embryonic cell line 3Y1CAP, which are nontumorigenic and resistant to chloramphenicol, were fused with whole cells of the rat glioma C6BU-1 line, which are tumorigenic and resistant to 5-bromodeoxyuridine, and the cybrid colonies growing in selective medium with 5-bromodeoxyuridine (30 micrograms/ml) and chloramphenicol (50 micrograms/ml) were isolated clonally. Cytoplasmic transmission of 3Y1CAP mtDNA to C6BU-1 cells was confirmed by quantitative analysis of their mtDNA with restriction endonuclease. Subclones containing various amounts of mtDNA from 3Y1CAP cells were isolated from one cybrid clone, Y22, and their tumorigenicities were examined by inoculating 2 X 10(6) cells s.c. into nude mice. The tumorigenicities of these cybrid cubclones were almost identical to that of the nuclear donor C6BU-1 cells with respect to the tumor incidence (number of animals bearing tumors per number of animals inoculated), latent period, and growth rates of tumors. Moreover, analysis of chromosomes and mtDNAs of the cells recovered from the tumors obtained showed that the tumors were derived from the cells inoculated and that no selective overgrowth of segregants that had lost mtDNA from 3Y1CAP cells occurred in the nude mice. These observations suggest that expression of tumorigenicity of C6BU-1 cells was not suppressed by cytoplasmic transmission of nontumorigenic 3Y1CAP mtDNA.

Karyotypes of vasoformative sarcomas arising from BALB/3T3 cells attached to polycarbonate plates.

Four vasoformative sarcoma in vivo tumor lines arising from the s.c. implantation of 3 X 10(4) BALB/3T3 cells attached to a 1- X 5- X 10-mm polycarbonate platelet were shown to be quite similar in chromosome constitution to the parental 3T3 line. All tumors contained the same marker chromosomes that were present in the parent BALB/3T3 cells. The findings conclusively showed that the tumors had derived from BALB/3T3 cells and not from host cells or from the in vivo fusion of the inoculated 3T3 cells with host cells. Each tumor line had a unique karyotype that was markedly more homogeneous than that of the parental BALB/3T3 cells, strongly suggesting that each tumor represented a separate clone. An M1 marker chromosome was consistently present in each of the four tumor lines but was present in only about 50% of the parent BALB/3T3 cells; it therefore appeared to be a distinct and stable feature of the tumors.

Joining of the c-myc gene and a line 1 family member on chromosome 8 in a human primary giant cell carcinoma of the lung.

A rearranged c-myc gene found in a human primary giant cell carcinoma of the lung was analyzed. The rearrangement was found in the region about 6 kilobase pairs upstream of the c-myc gene. The breakpoint was joined to a sequence carrying a Line 1 (L1) family member located on chromosome 8. This in vivo rearrangement of the c-myc gene specific to tumor cells may represent one mechanism of activation of a protooncogene during tumorigenesis or tumor progression in human cancer.

Single nucleotide instability without microsatellite instability in rat mammary carcinomas.

Mutation frequencies (MnFs) of the lacI transgene and mutation rates (MRs) of the endogenous hprt gene were analyzed in two mammary carcinoma cell lines that we established from mammary carcinomas that had been induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in female lacI-transgenic rats. Using the lacI transgene, corrected MnF, which is the number of independent lacI mutations that occurred while 102 cells expanded into 10(7) cells and which reflect the dynamic increase of point mutations, was measured. The corrected MnFs in the two mammary carcinoma cell lines (59 x 10(-6) and 72 x 10(-6) mutations) were significantly higher than that in the primary culture of normal mammary epithelium (4.7 x 10(-6)). MRs of the hprt gene in the two mammary carcinoma cell lines (8.2 x 10(-7) and 11 x 10(-7) mutations/hprt/cell division) were also higher than the same control (1.4 x 10(-7)). A:T to C:G transversion was observed at significantly higher frequencies in the two cell lines (6 of 24 and 6 of 25 for lacI; 10 of 67 and 19 of 92 for hprt) than in the control (0 of 6 for lacI; 0 of 4 for hprt). Taking advantage of the lacI transgene, high frequencies of A:T to C:G transversion (6 of 38 and 8 of 33, respectively) was also confirmed in the primary carcinomas of the two cell lines, which indicated the presence of a common abnormality in the cell lines and in the primary carcinomas. Both the established cell lines and their primary carcinomas were negative for microsatellite instability, which is known to be caused mainly by mismatch repair insufficiency and to increase point mutations, and for p53 mutations. These findings showed that the two cell lines, and possibly their primary carcinomas, had increases in the MRs of point mutations attributable to a mechanism(s) different from mismatch repair insufficiency, and we would suggest that such a state be designated as single nucleotide instability (SNI).

Structure, promoter analysis and chromosomal assignment of the human APEX gene.

APEX nuclease is a mammalian DNA repair enzyme having apurinic/apyrimidinic endonuclease, 3'-5'-exonuclease, DNA 3' repair diesterase and DNA 3'-phosphatase activities. This report describes the organization of the gene (APEX gene) for human APEX nuclease. Human APEX gene was cloned using human APEX cDNA and a human leukocyte genomic library in bacteriophage vector EMBL-3. We proved that human APEX gene consists of 5 exons spanning 2.64 kilobases and suggested that the gene exists as a single copy in the haploid genome. The boundaries between exon and intron follow the GT/AG rule. The major transcription initiation site was assigned by primer extension analysis to C at 515 nucleotides upstream from the ATG initiation codon. The translation initiation and termination sites locate in the exon II and V, respectively. The 5' flanking region (0.89 kilobase) sequenced lacks typical TATA and CAAT boxes, but contains TATA- and CAAT-like sequences and putative cis-acting regulatory elements such as binding sites for Sp1, AP2 and ATF. A part of the 5' flanking region belongs to a CpG island, which extends to the intron II. The CpG island is thought to be a transcription regulatory region of APEX gene, a housekeeping gene. The promoter activity of the 5' upstream region was analyzed by introducing the region in HeLa cells in an expression construct containing luciferase gene as a reporter gene, and the region from position 130 bp upstream to position 205 bp downstream of the major transcription initiation site was shown to be enough for high promoter activity. Northern hybridization experiments suggested that the gene is expressed ubiquitously in human cells. The locus of APEX gene was mapped to human chromosome 14q11.2-q12 using the in situ hybridization technique.

Cloning and characterization of a mouse homologue (mNthl1) of Escherichia coli endonuclease III.

Endonuclease III (endoIII; nth gene product) of Escherichia coli is known to be a DNA repair enzyme having a relatively broad specificity for damaged pyrimidine bases of DNA. Here, we describe the cloning and characterization of the cDNA and the gene for a mouse homologue (mNthl1/mNth1) of endoIII. The cDNA was cloned from a mouse T-cell cDNA library with a probe prepared by PCR using the library and specific PCR primers synthesized based on the reported information of partial amino acid sequences of bovine NTHL1/NTH1 and of EST Data Bases. The cDNA is 1025 nucleotides long and encodes a protein consisting of 300 amino acids with a predicted molecular mass of 33.6 kDa. The amino acid sequence exhibits significant homologies to those of endoIII and its prokaryotic and eukaryotic homologues. The recombinant mNthl1 with a hexahistidine tag was overexpressed in a nth::cmr nei::Kmr double mutant of E. coli, and purified to apparent homogeneity. The enzyme showed thymine glycol DNA glycosylase, urea DNA glycosylase and AP lyase activities. Northern blot analysis indicated that mNthl1 mRNA is about 1 kb and is expressed ubiquitously. A 15 kb DNA fragment containing the mNthl1 gene was cloned from a mouse genomic library and sequenced. The gene consists of six exons and five introns spanning 6.09 kb. The sequenced 5' flanking region lacks a typical TATA box, but contains a CAAT box and putative binding sites for several transcription factors such as Ets, Sp1, AP-1 and AP-2. The mNthl1 gene was shown to lie immediately adjacent to the tuberous sclerosis 2 (Tsc2) gene in a 5'-to-5' orientation by sequence analysis and was assigned to chromosome 17A3 by in situ hybridization.

A simple, two-color fluorescence detection method for membrane blotting analysis using alkaline phosphatase and horseradish peroxidase.

We have developed a one-step, two-color fluorescence detection method using simultaneously two fluorogenic substrates for both Southern and Western blots on nylon membranes. For this enzyme-mediated reporter system, a mixture of (i) 3-hydroxy-N-2'-biphenyl-2-naphthalenecarboxamide phosphate ester (HNPP), a substrate for alkaline phosphatase and (ii) N-(4-amino-5-methoxy-2-methylphenyl)benzamide (AMMB), a fluorogenic substrate for horseradish peroxidase was used. The reaction with these substrates produces blue (HNPP) and yellow (AMMB) fluorescent signals under ultraviolet light (302 nm). Therefore, this simple method allows the simultaneous visualization of two different targets on a single nylon membrane, e.g. nucleic acids or proteins.

Genetic recombination in a chromosomal translocation t(2;8)(p11;q24) of a Burkitt's lymphoma cell line, KOBK101.

We analyzed a chromosomal translocation, t(2;8)(p11;q24), in a Burkitt's lymphoma cell line, KOBK101. The translocation reciprocally occurred between a site about 150 bp upstream from the J5 segment in the Ig kappa-encoding gene on chromosome 2 and the A-rich end of an Alu repetitive element located far downstream from the c-myc gene on chromosome 8. Short segments of both parental chromosomes were deleted at the rearrangement site. A sequence related to the heptamer recognition signal for the V-J recombination of Ig genes and a topoisomerase I-recognition sequence were detected at the breakpoints. The V-J recombination occurred on both chromosome 2 and the translocated chromosome 2p- at the J3 and J4 segments, respectively. The J region on the translocated chromosomes was mutated, as compared with that on the untranslocated chromosome, while the Alu element and its upstream sequence were conserved. These results suggest the following aspects to the chromosomal translocation of this cell line. A V-J recombination seems to have occurred at the proximal end of the J4 segment first, and then the translocation took place in the region between the J4 and J5 segments. The translocation may have been mediated by the functions of topoisomerase I and the Alu repetitive sequence located at the breakpoint, although the possibility cannot be ruled out that the recombination machinery for Ig gene rearrangements functioned irregularly.

Human M2-type pyruvate kinase: cDNA cloning, chromosomal assignment and expression in hepatoma.

Two overlapping clones, covering the entire coding sequence of human M2-type pyruvate kinase (PK) cDNA, were isolated and sequenced. Nucleotide sequencing results showed that they contained the 109-bp 5'-untranslated region, the 1593-bp coding region and the 585-bp 3'-untranslated region. Nucleotide sequence homology was 90% and 69% with rat M2-type and L-type PK cDNA, respectively. In situ hybridization using the human M2-type PK cDNA probe disclosed that the gene for M2-type PK is located at band q22 on chromosome 15. Northern blot analysis with RNA from human hepatoma demonstrated that M2-type PK was predominantly expressed in hepatoma cells, whereas L-type PK was preferentially expressed in the non-tumor portion of the liver.

Cloning and chromosome mapping of the human Mel-18 gene which encodes a DNA-binding protein with a new 'RING-finger' motif.

It has recently been reported that there exists a new 'RING-finger' protein family among the zinc-finger (Zf) proteins. Previously, we had isolated the mouse Mel-18 cDNA (mMel-18) encoding the nuclear RING-finger protein that exhibits an ability to bind to a nonspecific DNA column. Here, we have isolated and characterized the human Mel-18 cDNA (hMel-18) using the mMel-18 cDNA as a probe. The deduced hMel-18 protein contains 344 amino acids (38 kDa) with a RING-finger motif, a helix-loop-helix (HLH)-like structure and a Pro/Ser-rich region. The hMel-18 gene is conserved among vertebrates. Its mRNA is highly expressed in placenta, lung and kidney, but the level is low in liver, pancreas and skeletal muscle. Using in situ hybridization, we mapped hMel-18 to band q22 of chromosome 12. It is possible that the Mel-18/bmi-1 gene family represents a mammalian homologue of the Drosophila polycomb gene group.

Molecular cloning and chromosomal mapping of mouse intronless myc gene acting as a potent apoptosis inducer.

Our previous findings suggest that the activation of the rat intronless myc gene provides a selective advantage in tumor suppression through apoptosis induction. In the present study, to examine whether intronless myc gene acting as an apoptosis inducer is evolutionarily conserved in mammalian cells, we isolated the mouse intronless myc gene and characterized it. A sequence analysis demonstrated that mouse intronless myc gene, ms-myc, has a linearly opened translatable frame consisting of 1293bp with 90% homology with that of rat s-myc. The chromosomal locus of ms-myc was identified on chromosome 19B by a fluorescent in situ hybridization (FISH) analysis. Gene transfection experiments showed that the transient overexpression of ms-Myc with transactivation activity effectively induces cell death in a wild-type p53-independent manner. In addition, cells stably expressing transfected ms-myc became more susceptible to apoptosis induced by genotoxic stress such as UV-irradiation and hydrogen peroxide compared with untransfected control cells. These observations suggest that the rodents commonly contain an s-myc-type of intronless myc gene with apoptosis-inducing activity.

Human cardiac myosin heavy chain gene mapped within chromosome region 14q11.2----q13.

Our previous report demonstrated that two human cardiac alpha- and beta-myosin heavy-chains (MHCs) which correspond to MYH6 and MYH7 respectively, according to Human Gene Mapping nomenclature, were mapped to human chromosome 14 and that human cardiac and skeletal MHC genes do not cosegregate. For further analysis, the regional mapping method was used. DNA from 4 human deletion and 3 human duplication cell lines were prepared for southern blotting, hybridized with human cardiac alpha- and beta-MHC DNA probes, and the hybridization intensity relative to 46,XX or 46,XY DNA was estimated. The results showed that two human cardiac MHC genes segregated with the 14cen----q13 region of the long arm of human chromosome 14. In situ hybridization of 3H-labeled human cardiac alpha-MHC probe to normal human metaphase chromosome independently confirmed this result.

Human smooth muscle myosin heavy chain gene mapped to chromosomal region 16q12.

The partial nucleotide sequence encoding the rod portion of the entire amino acid sequence of human smooth muscle myosin heavy chain (MHC) which corresponds to MYH11, according to Human Gene Mapping nomenclature, has been determined by cloning a complementary DNA (cDNA) and sequencing the cDNA (UMYHSM). Northern blot analysis with the UMYHSM fragment (4.3 Kb) showed that the smooth muscle MHC of the human umbilical artery is expressed in the human umbilical artery, bladder, esophagus and trachea. Southern blot analysis of human genomic DNA from human-mouse or human-Chinese hamster somatic cell hybrids demonstrated that the human smooth muscle MHC was mapped to human chromosome 16. Regional mapping of UMYHSM was performed using human cell lines with partial deletion and trisomy of chromosome 16. As a result, the human smooth muscle MHC gene segregated with 16p11-q12. In situ hybridization of biotin-labeled human smooth muscle MHC probe (UMYHSM fragment) to normal human metaphase chromosome independently showed that the human smooth muscle MHC gene (MYH11) is assigned to chromosome region 16q12. Analysis of early metaphase chromosomes showed that hybridization signals were in 16q12.1. In the human, although skeletal, cardiac, smooth muscle, and nonmuscle MHC genes are mapped to chromosomes 17, 14, 16, and 22, respectively, structural similarities of these MHC genes strongly suggest the common origin of these genes.

Protein synthesis and tumorigenicity of the cytoplasmic hybrid between rat yolk sac tumor and mouse fibroblastic cell line.

Cytoplasmic hybrid (cybrid) cell lines were formed by fusing whole cells of rat yolk sac tumor cell line (EST-II) with cytoplasts of mouse fibroblastic cell line (B-82cap), a variant of mouse L cell line that is deficient in thymidine kinase (TK-) and resistant to chloramphenicol (capr). The cybrid cell line with the nucleus of EST-II and cytoplasma of B-82cap was successfully obtained using double selection with HAT and chloramphenicol-containing medium. The cybrid's ability to synthesize proteins such as albumin, alpha-fetoprotein, gamma-EST, and gamma-GTP was found to be approximately one-fourth that of the nuclear donor, EST-II, at a early time of growth in culture, but this was followed by a gradual increase during the period of observation. The nude mice undergoing subcutaneous transplantation of 1 X 10(6) cells of EST-II and cybrid were killed by the tumor growth, with the survival time being 56 +/- 11 and 105 +/- 25 days, respectively. The histologic findings of cybrid tumor closely resembled those of the nuclear donor, EST-II. These facts suggest that factors from both the nucleus and cytoplasma will be able to affect the gene expression of the cybrid cell line.

Karyotypic changes in serial transfers of leukemic cells of AKR mouse.

Four spontaneous AKR leukemias (T67, T68, T70, and T74) with a modal chromosome number of 40 were transplanted serially to syngeneic mice in order to assess the significance of trisomy 15 and other karyotypic changes in the development of leukemia. In T67 and T70, the chromosomally normal cell disappeared completely or decreased considerably in frequency at the first passage in vivo. The karyotype of the modal cells changed continuously in T67 during transplantation, conserving trisomy 17, while the pseudodiploid cells with trisomy 15 and monosomy X were stable from the first to the seventh transplant generations of T70. In contrast to these results, the primary cell population of T68 and T74 with modal cells having a normal karyotype remained essentially unchanged throughout 7 or 15 transplant generations, despite the occurrence of aneuploidy, which included trisomy 15 or trisomy 17 in low frequencies. It is thus evident that the diploid cell is compatible with being leukemic and that neither trisomy 15 nor trisomy 17 is necessary for the initiation and progression of AKR leukemia, although the former was detected in three of four primary leukemias used for this experiment and in all four during transplantation.

Chromosome and cell surface marker studies in 1-propyl-1-nitrosourea-induced thymic lymphomas of the rat.

Immunological cell surface markers were studied in seven transplantable 1-propyl-1-nitrosourea-induced thymic lymphoma lines in F344 rats by reactivity to anti-Thy-1.1, anti-rat Ig (anti-Ig), and anti-rat T-cell (anti-T) sera, and by the capacity to form rosettes with guinea pig red blood cells. All the tumor lines were estimated to be sensitive to anti-Thy-1.1 but insensitive to anti-Ig serum in the presence of complement. The differences in reactivity to anti-T serum and rosette-forming capacity (RFC) allowed classification of the lines into three types. In type I, three lines were highly sensitive to anti-T serum but low in RFC, indicating that these lymphomas probably originated from relatively mature intrathymic T cells. In type II, two lines were moderately sensitive to anti-T serum and relatively high in RFC, indicating that these lymphomas derived from intrathymic T cells. In type III lymphomas, the remaining two lines were not only insensitive to anti-T serum but also low in RFC, suggesting that these lymphomas might have arisen from immature precursors of T and/or B cells. The chromosome study revealed that type I lymphomas were diploid, with slight numerical and structural variations. Type II lymphomas were pseudodiploid or hypotetraploid, with considerable variation in the number and morphology of chromosomes. Type III lymphomas had a diploid or hyperdiploid constitution, with a moderate degree of karyotypic variation. Neither consistent nor common karyotypic alterations among the seven lines were found, although the karyotypic instability seemed to be related to the immunological types of the lymphoma lines, possibly reflecting the differentiation process of the target cells involved in the malignant transformation.

Genomic organization and chromosomal distribution of rat ID elements.

Identifier (ID) elements are members of a family of short interspersed nuclear elements (SINEs) in rodents. We investigated the genomic organization and chromosomal distribution of the ID elements in the rat, mouse and Chinese hamster. Southern blot hybridization analysis revealed that the ID elements are widespread in the rat genome, but concentrated in the mouse and Chinese hamster genomes, and that the copy of ID elements in the rat is about 5 times and 50 times that in the mouse and Chinese hamster, respectively. FISH analysis showed that the ID elements are predominantly distributed in the R-band regions of rat chromosomes. In mouse and Chinese hamster chromosomes, no specific distribution pattern of the ID elements was found. Furthermore, we found a distinct group of derivative ID elements in the rat, which contain partially repeated ID core domains, by PCR amplification using an ID core sequence. Such derivatives were not found in either the mouse or Chinese hamster. These findings suggest that explosive amplification of the ID elements in the rat has been accompanied by the occurrence of derivative ID elements and a predominant localization to the R-band regions. Similar associations found in the Alu family, one of the human SINEs, allow us to speculate that the rat ID elements and the human Alu family have analogous functions in chromosomal organization.