Human Genomic DNA Fragment Research Articles

Expression of the human pro-opiomelanocortin gene introduced into a rat glial cell line

A fragment of human genomic DNA containing the entire pro-opiomelanocortin (POMC) gene was introduced by transfection into the rat glial cell line C6. Blot analysis using poly(A)-rich RNA from the transformed C6 cells showed several hybridization bands. One band was similar in size (1.2 kb) to the POMC mRNA of human pituitary, while two were larger (2.6 and 2.2 kb) and the fourth smaller (800 bp). S1 nuclease mapping revealed that the POMC transcripts in transformed C6 cells were similar to those in non-pituitary tissues. Immunoreactive ACTH (ir-ACTH) was measurable in both the culture medium and cells. Gel chromatography showed that ir-ACTH in the medium eluted at a position identical to that of so-called big ACTH (approximately 40 kDa) which is found in the plasma of patients with ectopic ACTH syndrome. The human POMC gene could thus be expressed in the non-pituitary rat glial cell line C6, although the transcripts and translation products in C6 cells differ from those in the human pituitary. These results suggest that the transformed C6 cell may be a useful tool for studying the regulation of human POMC gene expression in non-pituitary cells.

Frameshift and nonsense mutations in a human genomic sequence homologous to a murine UDP-Gal:beta-D-Gal(1,4)-D-GlcNAc alpha(1,3)-galactosyltransferase cDNA.

We have previously isolated a murine UDP-Gal:beta-D-Gal(1,4)-D-GlcNAc alpha(1,3)-galactosyltransferase (alpha(1,3)-GT) cDNA (Larsen, R. D., Rajan, V. P., Ruff, M. M., Kukowska-Latallo, J., Cummings, R. D., and Lowe, J. B. (1989) Proc. Natl. Acad. Sci. U. S. A. 86, 8227-8231). This enzyme constructs the terminal alpha(1,3)-galactosyl linkage within the epitope Gal alpha 1----3Gal. This epitope is expressed by New World monkeys and many nonprimate mammals but generally not by Old World primates, anthropoid apes, or man. To investigate the molecular basis for the apparent species-specific absence of this enzyme and its oligosaccharide product, we have sequenced a human genomic DNA fragment homologous to the murine alpha(1,3)-GT cDNA. This fragment contains a 703-nucleotide region that shares 82% identity with a region of the murine cDNA encoding part of the enzyme's catalytic domain. The human sequence, however, has suffered deletion of single nucleotides at two separate positions, relative to the murine sequence. These frameshift mutations disrupt the translational reading frame that would otherwise maintain a 76% amino acid sequence identity between the human sequence and the murine alpha(1,3)-GT. Moreover, nonsense mutations exist within this disrupted reading frame that would truncate the human polypeptide, relative to the murine enzyme. We therefore propose that this human sequence represents a pseudogene and cannot determine expression of Gal alpha 1----3Gal epitopes on human cells.

Cloning and nucleotide sequence analysis of the human β-microseminoprotein gene

β-microseminoprotein (MSP) is a small protein (94 amino acids) synthesized by the epithelial cells of the prostate gland and secreted into the seminal plasma. Restriction endonuclease mapping of human genomic DNA with a human MSP cDNA probe identified a 19 kilobase (Kb) hybridizing band in both EcoRI and BamHI digestions. Subsequently, the 19 Kb EcoRI fragment of human genomic DNA containing the MSP gene was isolated and cloned into an EMBL4 phage vector. Screening of the recombinant phages resulted in the isolation of one clone containing the MSP gene. Restriction endonuclease mapping and sequence analysis of this clone revealed the human MSP gene of approximately 15 Kb in length. The gene contains four exons and three large introns of approximately 6, 1, and 7 Kb.

Expression of human IFN-gamma genomic DNA in transgenic mice.

We have introduced an 8.6-kb fragment of human genomic DNA containing the full length IFN-gamma gene into the mouse germline. The transgenic animals had no biologic or developmental defects as human IFN-gamma does not bind to the mouse IFN R. Regulation of the transgene paralleled that of the endogenous murine IFN-gamma gene in that: 1) it is not expressed constitutively in any tissue examined thus far, 2) it can be induced in thymus and spleen cells by T cell mitogens, 3) it is not expressed in B cells stimulated by LPS, and 4) it produces normal mRNA and biologically active IFN protein. Whereas expression of the transgene is likely restricted to T cells, we had observed that both fibroblasts and B cell lines could express the same DNA when transfected in vitro; this indicates that in vivo, developmental factors restrict expression of the IFN-gamma gene to T cells. These findings also indicate that the 8.6-kb fragment contains the regulatory elements necessary for normal tissue specific expression in vivo. Moreover, they indicate that the regulatory elements for this gene are completely preserved over the phylogenetic distance separating mouse and man, even though substantial drift has occurred in the structural gene, and probably in the IFN-gamma R as well.

Chromosomal localization of ARSB, the gene for human N-acetylgalactosamine-4-sulphatase.

A deficiency of N-acetylgalactosamine-4-sulphatase (G4S, gene symbol ARSB), results in the accumulation of undegraded substrate and the lysosomal storage disorder, Maroteaux-Lamy syndrome (mucopolysaccharidosis type VI). In situ hybridization using an 3H-labelled human G4S genomic DNA fragment to human metaphase chromosomes localized ARSB to chromosome 5q13-5q14. This location is consistent with, an refines, previous chromosomal assignments based on the expression of human G4S in somatic cell hybrids.

Deregulated expression of human c-jun transforms primary rat embryo cells in cooperation with an activated c-Ha-ras gene and transforms rat-1a cells as a single gene.

While the ability of the retroviral oncogene V-jun to transform chicken cells led to its discovery, the oncogenic potential of its cellular homologue, c-jun, which encodes a transcription factor, is unknown. We isolated a 1070-base-pair cDNA clone containing the unmutated entire open reading frame of c-jun from a human small cell lung cancer line. This cDNA as well as a 5.6-kilobase normal human genomic DNA fragment containing the c-jun gene were placed under the control of retroviral long terminal repeats and introduced into primary rat embryo cells (RECs), with or without other oncogenes, and into an immortal rat fibroblast cell line, Rat-1a, as a single gene. In Rat-1a cells the expression of human c-jun mRNA was associated with the ability to clone in soft agarose and form tumors in nude mice. When the c-jun cDNA or genomic DNA constructs were introduced into RECs, no foci of transformed cells were seen with c-jun alone or c-jun cotransfected with deregulated c-myc or L-myc protooncogenes. However, cotransfection of the c-jun constructs with an activated human c-Ha-ras gene led to foci of transformed cells which gave rise to immortalized cell lines that cloned in soft agarose and formed tumors in nude mice. Furthermore, formation of foci of transformed RECs by the c-jun/ras combination was augmented 3-fold by the tumor promoter phorbol 12-tetradecanoate 13-acetate. We conclude that deregulated expression of human c-jun can participate in malignant transformation of normal mammalian cells.

Regional localization and molecular characterization of a DNA sequence on the long arm of chromosome 22.

A human genomic DNA fragment, p22hom13 (D22S16), was isolated from a chromosome 22-specific library. After elimination of repetitive sequences, a single copy BamHI-EcoRI fragment was subcloned into pTZ18. By using mouse/human somatic cell hybrids and in situ hybridization, the new DNA probe was mapped to chromosome 22q13-qter. Its application in the analysis of the distal part of chromosome 22 and its diagnostic use in translocations are discussed.

Hyperinsulinemia in transgenic mice carrying multiple copies of the human insulin gene.

We are investigating human insulin gene expression in transgenic mice. An 8.8 kilobase (kb) human genomic DNA fragment, including the insulin gene (1.4 kb) and 2 kb of 5' human flanking sequences, was introduced into mouse embryos by pronuclear microinjection. Two lines of transgenic mice have been established, both of which carry the intact human gene in multiple copies. Animals from both lines have significantly higher insulin levels than control mice, and the degree of hyperinsulinemia shows a positive correlation with human gene copy number in the two lines. Expression of the human gene is confirmed by the detection of human C-peptide in plasma. Tissue specificity of expression is maintained, with human insulin mRNA detectable only in the pancreas. The transgenics maintain normal fasting blood glucose in spite of their high insulin levels, but preliminary studies show them to be glucose intolerant when given a glucose load. These mice provide a model system for further studies on the regulation of insulin gene expression and on the effects of chronic hyperinsulinemia on glucose homeostasis.

Chromosomal localization of human Na +,K +-ATPase α- and β-subunit genes

Na +,K +-ATPase is a heterodimeric enzyme responsible for the active maintenance of sodium and potassium gradients across the plasma membrane. Recently, cDNAs for several tissue-specific isoforms of the larger catalytic α-subunit and the smaller β-subunit have been cloned. We have hybridized rat brain and human kidney cDNA probes, as well as human genomic isoform-specific DNA fragments, to Southern filters containing panels of rodent × human somatic cell hybrid lines. The results obtained have allowed us to assign the loci for the ubiquitously expressed α-chain ( ATP1A1) to human chromosome 1, region 1p21→cen, and for the α2 isoform that predominates in neural and muscle tissues ( ATP1A2) to chromosome 1, region cen→q32. A common PstI RFLP was detected with the ATP1A2 probe. The α3 gene, which is expressed primarily in neural tissues ( ATP1A3), was assigned to human chromosome 19. A fourth α gene of unknown function (αD) that was isolated by molecular cloning ( ATP1AL1) was mapped to chromosome 13. Although evidence to date had suggested a single gene for the β-subunit, we found hybridizing restriction fragments derived from two different human chromosomes. On the basis of knowledge of conserved linkage goups on human and murine chromosomes, we propose that the coding gene ATP1B is located on the long arm of human chromosome 1 and that the sequence on human chromosome 4 ( ATP1BL1) is either a related gene or a pseudogene.

NcoI RFLP at the creatine kinase-muscle type gene locus (CKMM, chromosome 19)

A 3.2 kbp human genomic DNA fragment (BamHI-Sau3A) of the 3{prime} untranslated and 3{prime} flanking region of the CKMM gene was isolated and subcloned into the BamHI site of vector pSP64. The CKMM 3{prime}-probe identifies a 2-allele polymorphism with bands at 2.3 and 1.0 kbp (allele A) and 3.3 kbp (allele B). In addition a weak constant 4.2 kbp band is observed. This probe also detects a 2-allele TaqI RFLP reported previously, as either a 4.3 kbp (A) or a 4.2 kbp (B) band. The CKMM locus previously has been assigned to 19q13.2-q13.3. By Southern blot analysis of human-rodent somatic cell hybrids containing unique subregional fragments of chromosome 19 of man the authors have assigned the gene to 19q13.2. Co-dominant segregation was observed in 8 families with 3 generations.

The gene located at chromosome 18 band q21 is rearranged in uncultured diffuse lymphomas as well as follicular lymphomas

The karyotypic abnormality t(14;18)(q32;q21) is reported to occur in 75% of follicular lymphomas. This translocation results in the rearrangement of a putative oncogene bcl-2, which resides at chromosome 18 band q21 (the 18q21 gene). Using two human genomic DNA fragments cloned from the chromosome 18 band q21 as probes, we analyzed 65 uncultured human lymphoma samples by the Southern blot technique. The 18q21 gene was rearranged in 18 of 26 (69%) follicular lymphomas, 3 of 5 (60%) follicular lymphomas transformed to large cell lymphomas, 8 of 20 (40%) diffuse large cell lymphomas (DLCLs), and 2 of 7 (29%) small noncleaved cell lymphomas (SNCs). Our analysis detected rearrangement of the 18q21 gene in 10 of 13 (77%) cases in which the t(14;18)(q32;q21) translocation was found by cytogenetic techniques. Our analysis also proved helpful in difficult karyotyping situations: (a) identifying the donor chromosome fragment as chromosome 18 band q21 in 4 of 9 (44%) cases that cytogenetically displayed a 14q+ chromosome of unknown origin, and (b) identifying a rearrangement of chromosome 18 band q21 in 12 of 18 (67%) cases that cytogenetically yielded no cells in metaphase. We also demonstrated three cases of submicroscopic rearrangement of the 18q21 gene. In our studies, patients with DLCLs and rearrangement of the 18q21 gene had a significantly higher incidence of extranodal involvement when compared with patients with DLCLs and no 18q21 gene rearrangement (P = 0.03).

The Gene Located at Chromosome 18 Band q21 Is Rearranged in Uncultured Diffuse Lymphomas as Well as Follicular Lymphomas

The karyotypic abnormality t(14;18)(q32;q21) is reported to occur in 75% of follicular lymphomas. This translocation results in the rearrangement of a putative oncogene bcl-2, which resides at chromosome 18 band q21 (the 18q21 gene). Using two human genomic DNA fragments cloned from the chromosome 18 band q21 as probes, we analyzed 65 uncultured human lymphoma samples by the Southern blot technique. The 18q21 gene was rearranged in 18 of 26 (69%) follicular lymphomas, 3 of 5 (60%) follicular lymphomas transformed to large cell lymphomas, 8 of 20 (40%) diffuse large cell lymphomas (DLCLs), and 2 of 7 (29%) small noncleaved cell lymphomas (SNCs). Our analysis detected rearrangement of the 18q21 gene in 10 of 13 (77%) cases in which the t(14;18)(q32;q21) translocation was found by cytogenetic techniques. Our analysis also proved helpful in difficult karyotyping situations: (a) identifying the donor chromosome fragment as chromosome 18 band q21 in 4 of 9 (44%) cases that cytogenetically displayed a 14q+ chromosome of unknown origin, and (b) identifying a rearrangement of chromosome 18 band q21 in 12 of 18 (67%) cases that cytogenetically yielded no cells in metaphase. We also demonstrated three cases of submicroscopic rearrangement of the 18q21 gene. In our studies, patients with DLCLs and rearrangement of the 18q21 gene had a significantly higher incidence of extranodal involvement when compared with patients with DLCLs and no 18q21 gene rearrangement (P = 0.03).

DNA sequence and regional assignment of the human follicle-stimulating hormone beta-subunit gene to the short arm of human chromosome 11.

A human genomic DNA fragment in phage lambda containing FSHB, the gene for the beta-subunit of human follicle-stimulating hormone (FSH-beta), was analyzed and the nucleotide sequence of the region of the clone encoding FSH-beta was determined. A subclone of the lambda phage containing 67% of FSH-beta coding sequence was used as hybridization probe to determine the human chromosomal location of FSHB. A panel of mouse-human somatic cell hybrids containing reduced numbers of human chromosomes was screened with the FSHB probe; complete cosegregation of FSHB with human chromosome 11 was observed in all 26 cell hybrids tested. Analysis of a set of cell hybrids containing translocated derivatives of chromosome 11 further localized FSHB to the human chromosome region 11p11.2----11pter. A Hind III restriction fragment length polymorphism (RFLP) detected by another subclone of the lambda phage containing FSHB now provides a genetic marker for this region of the human genome.

HYPERINSULINEMIA IN TRANSGENIC MICE CARRYING MULTIPLE COPIES OF THE HUMAN INSULIN GENE: EVIDENCE FOR A GENE DOSAGE EFFECT

We are investigating insulin gene expression in transgenic mice carrying multiple copies of the human preproinsulin gene. An 8.8 kb EcoRI-Hind III human genomic DNA fragment containing the insulin gene was introduced into 1-cell mouse embryos by pronuclear microinjection. This DNA fragment includes 2kb of 5′ and 5.5kb of 3′ human flanking sequences. Two lines of insulin transgenie mice have been established that differ in copy number of the human gene: one line has 4 copies integrated per cell, the other 16 copies per cell. Total serum insulin levels were determined by RIA (Cambridge Medical). Fasted insulin levels in transgenie mice (mean ± SEM = 0.48 ± 0.08 ng/ml, n=37) were significantly higher than in controls (0.10 ± 0.01 ng/ml, n=10; p < 0.001). Comparing the 2 transgenic lines, there was considerable variation in insulin levels but those animals with more copies of the human gene have higher insulin levels (0.74 ± 0.20 ng/ml, n=11) than those with fewer copies (0.37 ± 0.06 ng/ml, n=26). Both lines have significantly higher insulin levels than control (p < 0.01). This is in contrast with previously reported insulin transgenics (Bucchini et al, PNAS 83:2511) in which insulin was not overexpressed. In this model system, insulin gene expression correlates with gene copy number, suggesting a direct gene dosage effect.

Regional localization and characterization of a DNA segment on the long arm of chromosome 21.

A human genomic DNA fragment, pAM37 (HGM8; D21S22), was mapped to chromosome 21q2.1-q2.21 by in situ hybridization. This segment is therefore situated on the boundary of the "pathological region" of Down syndrome. A genomic restriction map encompassing 35 kb of chromosome 21 was derived and two restriction fragment length polymorphisms (RFLPs) were mapped and characterized. A homologous sequence was detected in the mouse genome but no homologous RNA was detected in a range of human tissues. This DNA segment will contribute to the linkage mapping of chromosome 21 and will facilitate delineation of the pathological region of Down syndrome.

Isolation of a cDNA for human acid alpha-glucosidase and detection of genetic heterogeneity for mRNA in three alpha-glucosidase-deficient patients.

Lysosomal acid alpha-glucosidase (EC 3.2.1.3) hydrolyzes 1,4-linked alpha-D-glucose polymers present in glycogen. Genetic deficiency of acid alpha-glucosidase results in glycogen-storage disease type II, encompassing a spectrum of disorders of varying severity. To study the molecular basis for this heterogeneity, we sought to clone the coding sequence for human acid alpha-glucosidase. We screened 10(6) recombinant phage from a human liver cDNA expression library with an affinity-purified polyclonal antibody to human acid alpha-glucosidase. When we retested positive phage for reactivity to monoclonal antibodies, we identified a single phage, containing a 2-kilobase (kb) cDNA insert, that reacted with both polyclonal and monoclonal antibodies. The 2-kb cDNA hybridized to a 20-kb EcoRI fragment of human genomic DNA. This 20-kb EcoRI fragment was present only in DNA from somatic cell hybrids that retained the human chromosome 17 segment q21-q23, which contains the gene for human acid alpha-glucosidase. The cDNA also hybridized to a 3.4-kb mRNA, consistent with the size (approximately 105 kDa) of the acid alpha-glucosidase protein. Finally, in one of two infantile-onset acid alpha-glucosidase-deficient cell lines tested, the 3.4-kb mRNA was not detectable, whereas in an adult-onset cell line, an mRNA of reduced size and amount was found. Examination of DNA digested with restriction enzymes did not reveal any major deletions in the genomic DNA of these patients.

The 724 family of DNA sequences is interspersed about the pericentromeric regions of human acrocentric chromosomes.

We describe the organization of the complex, interspersed 724 family of DNA sequences that is distributed in multiple copies about the pericentromeric region of human acrocentric chromosomes. 724 family members were isolated using an efficient recombination-based assay for nucleotide sequence homology to screen a human genomic library. Eight related but distinct 724 family members were isolated that hybridized to a total of 20 different human-genomic EcoRI DNA fragments spanning 100,000 base pairs. In contrast with tandemly clustered satellite and ribosomal DNA sequences also located on the short arms of human acrocentric chromosomes, 724 family members are interspersed. No evidence for local interspersion or homology between 724 family members and ribosomal or satellite DNA sequences was found. Juxtaposition of the complex 724 family to the nucleolus organizer region was a recent event in primate evolution. The unique organization of 724 family members on each of the five human acrocentric chromosomes indicates that the 724 family continues to evolve within the human karyotype.

Propagation of some human DNA sequences in bacteriophage lambda vectors requires mutant Escherichia coli hosts.

The growth of clones of human genomic DNA fragments in a bacteriophage lambda vector has been examined in a number of different Escherichia coli hosts. A large proportion (8.9%) of the phages carrying different fragments of the human genome fail to grow on standard rec+ hosts but will grow on hosts carrying mutations in the recB, recC, and sbcB genes. Heteroduplex analysis in the electron microscope of DNA from four of these phages revealed substantial secondary structure, including snap-back regions 200-500 base pairs in length. Such structures were not found in phages from the same DNA library that grow in rec+ hosts. These results are interpreted in the light of prior observations [Leach, D.R.F. & Stahl, F. (1983) Nature (London) 305, 448-451] showing that inverted repetitions cloned in phage lambda can be propagated in recB recC sbcB hosts but not in rec+ hosts.

Enhanced gene expression by the poly(dT-dG).poly(dC-dA) sequence.

The sequence poly(dT-dG).poly(dC-dA) (TG-element) is a ubiquitous component of eucaryotic genomes and has the potential to adopt a left-handed DNA conformation (Z-DNA). In this report, we have tested the hypothesis that the TG-element can modulate gene expression. Human genomic DNA fragments (1 to 1.5 kilobases) containing a (dT-dG)n.(dC-dA)n tract (30, 40, or 50 base pairs) or chemically synthesized (dT-dG)n.(dC-dA)n fragments (50 to 130 base pairs) were inserted in the pSV2-cat (simian virus 40 enhancer plus) or pA10-cat (enhancer minus) expression vector plasmid. These constructs were transfected into CV-1 cells or HeLa cells, and their transcription was monitored by assaying chloramphenicol acetyltransferase activity. The results showed that pSV2-cat with the TG-element and pA10-cat with the TG-element synthesized more chloramphenicol acetyltransferase activity (2 to 10 times, depending on the location of the TG-element) than did parental pSV2-cat and pA10-cat DNAs, respectively. Furthermore, the TG-element appeared to have characteristics similar to those of viral enhancers: (i) the TG-element enhanced transcription from a distance, (ii) its closer location to the promoter was more effective, and (iii) its orientation was not crucial. However, its enhancer-like activity was much weaker than that of the simian virus 40 enhancer, and, unlike many viral enhancers, it was equally active in monkey and in human cells. These results suggest that the TG-element may influence the expression of cellular genes.

Enhanced gene expression by the poly(dT-dG).poly(dC-dA) sequence.

The sequence poly(dT-dG).poly(dC-dA) (TG-element) is a ubiquitous component of eucaryotic genomes and has the potential to adopt a left-handed DNA conformation (Z-DNA). In this report, we have tested the hypothesis that the TG-element can modulate gene expression. Human genomic DNA fragments (1 to 1.5 kilobases) containing a (dT-dG)n.(dC-dA)n tract (30, 40, or 50 base pairs) or chemically synthesized (dT-dG)n.(dC-dA)n fragments (50 to 130 base pairs) were inserted in the pSV2-cat (simian virus 40 enhancer plus) or pA10-cat (enhancer minus) expression vector plasmid. These constructs were transfected into CV-1 cells or HeLa cells, and their transcription was monitored by assaying chloramphenicol acetyltransferase activity. The results showed that pSV2-cat with the TG-element and pA10-cat with the TG-element synthesized more chloramphenicol acetyltransferase activity (2 to 10 times, depending on the location of the TG-element) than did parental pSV2-cat and pA10-cat DNAs, respectively. Furthermore, the TG-element appeared to have characteristics similar to those of viral enhancers: (i) the TG-element enhanced transcription from a distance, (ii) its closer location to the promoter was more effective, and (iii) its orientation was not crucial. However, its enhancer-like activity was much weaker than that of the simian virus 40 enhancer, and, unlike many viral enhancers, it was equally active in monkey and in human cells. These results suggest that the TG-element may influence the expression of cellular genes.