Fine structure of the human hypoxanthine phosphoribosyltransferase gene

Molecular structure of the human asparagine synthetase gene

The human gene for asparagine synthetase has been isolated and the molecular organization has been determined by mapping and DNA sequencing of intron-exon boundaries. The gene spans 35 kb and contains 13 exons. The structure of the human gene has a high degree of similarity to that of the hamster asparagine synthetase gene, with identical positions for all but one of the intron regions. The 5' upstream region of this gene, like other housekeeping genes, lacks conventional TATA and CAAT boxes. Comparisons of the 5' upstream sequences of the human and hamster genes show limited similarity; however, both have a very high G + C content which may play a role in expression through DNA methylation.

A comparison of mutation induction at the tk and hprt loci in human lymphoblastoid cells; quantitative differences are due to an additional class of mutations at the autosomal tk locus

X-Rays, ethyl methanesulfonate and ICR-191 induced 2 classes of trifluorothymidine-resistant mutants at the autosomal tk locus in human lymphoblastoid cells. These classes were differentiated by their growth rates; some mutants grew with a normal doubling time of 14-18 h (tk-NG), while others grew much more slowly, with doubling times of 21-44 h (tk-SG). Only mutants with normal growth rates were observed at the X-linked hprt locus; the frequencies of mutations induced at hprt were equal to those induced for tk-NG mutants. Thus, more mutations overall (by up to a factor of 6) were induced at tk than at hprt. These results are discussed in relation to recent studies in rodent cells, in which much greater mutation frequencies were observed at autosomal loci.

Molecular analysis of spontaneous and ethyl methanesulphonate-induced mutations of the hprt gene in hamster cells

Independent spontaneous or ethyl methanesulphonate (EMS)-induced mutants lacking HPRT enzyme activity were analysed for changes in hprt gene structure. Of 21 spontaneous mutants, 6 had total gene deletions, 2 had partial gene deletions, and 13 were indistinguishable from wild-type by Southern analysis. In contrast a sample of 23 EMS-induced mutants, each of which showed potentially interesting characteristics (e.g. high reversion frequency, X-chromosome rearrangement), showed no detectable hprt gene changes. RNA isolated from 59 mutants with presumptive point mutations (13 spontaneous, 46 EMS-induced) was analysed on dot blots for changes in the amount of hprt mRNA. A wide range of mRNA levels was found, from mutants with undetectable amounts to those with more than wild-type amounts. However, Northern blots of all these mutant RNAs revealed only one (EMS-induced) mutation with a change in hprt mRNA size. Taken with our previously-published data on these mutants, it is argued that they represent a broad range of mutational types, and that the hprt gene mutation system provides a sensitive means of distinguishing mutational spectra of different DNA-damaging agents.

Deletion screening at the hypoxanthine-guanine phosphoribosyltransferase locus in Chinese hamster cells using the polymerase chain reaction

We have developed a rapid screening method using the polymerase chain reaction (PCR) for detecting deletion mutations at the hypoxanthine-guanine phosphoribosyltransferase (hprt) locus in Chinese hamster cells. DNA was extracted from spontaneous and ultraviolet (UV) light- and X-ray-induced hprt-deficient mutants. Two primer sets were used to amplify 276 bp and 344 bp fragments containing the entire exon 3 and exon 9 coding sequence, respectively. The PCR was performed using Taq DNA polymerase for 40 cycles, and the PCR product was directly analyzed for the presence of the respective amplified DNA using electrophoresis on agarose gels stained with ethidium bromide. With this assay, we have analyzed 39 independently derived hprt-deficient mutants. Four of ten spontaneous mutants were found to have deletions in exon 9. UV light produced mutants with predominantly wild-type amplification patterns (10/14). X-ray induced mostly deletion patterns (11/15); six of these occurred only in exon 9, and five occurred in both exons 3 and 9. These observations are consistent with the classical notion that UV light induces predominantly missense mutations and X-ray produces a high proportion of deletion mutations. Deletion mutations occurred most frequently at the 3' end of the hprt gene, suggesting the possible existence of hot spots for deletions in this region. The PCR assay for deletion detection has the advantage that it can be completed in less than 4 hr without using radioisotopes. This assay should be useful for routine deletion screening.

Enzymatic amplification and characterization of large DNA fragments from genomic DNA

Conditions for DNA amplification in vitro using modified T7 DNA polymerase have been devised to obtain 2000-bp DNA fragments of the HGPRT gene directly from human genomic DNA. The DNA obtained from a 1.2 x 10(5)-fold amplification has been used for direct sequencing.

Mapping large spontaneous deletion endpoints in the human HPRT gene

In an attempt to understand the nature, frequency, and molecular origin of spontaneous mutations in human cells, we have analyzed 85 independent, spontaneous HPRT- human B-lymphoblast clones with particular emphasis on the determination and characterization of large structural alterations (i.e., deletions, insertions, duplications, etc.). Southern blot analysis using a full-length HPRT cDNA probe revealed that 39% (33/85) of these spontaneous mutants contained alterations affecting different regions of the gene. 12% (10/85) were total gene deletions, 25% (21/85) involved alterations with one or both endpoints intragenic to HPRT, and 2% (2/85) showed wild-type banding patterns with an additional hybridizing band. To further address the positional behavior of these alterations, the endpoints of the large deletions were mapped to specific exon/intron regions by hybridization of Southern blots with a series of HPRT exon-specific probes. This analysis revealed a disproportionate number of endpoints within the 3' portion of the gene. These findings are discussed in relation to the positional specificity of large alterations in human cells and the use of such an analysis for assessing the molecular mechanism(s) responsible for their production.

Human hypoxanthine-guanine phosphoribosyltransferase: a single nucleotide substitution in cDNA clones isolated from a patient with Lesch-Nyhan syndrome (HPRTMidland)

We have determined the molecular basis for hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency in a patient, J.H., with Lesch-Nyhan syndrome. Radioimmunoassay of lysates of erythrocytes or cultured B-lymphoblasts showed that this patient had no detectable HPRT enzyme activity or HPRT protein. HPRT-specific mRNA levels were normal by Northern analysis. We created a cDNA library from mRNA isolated from cultured lymphoblasts derived from this patient. Nucleotide sequencing of full-length HPRT cDNA clones revealed a single nucleotide (nt) substitution: a T-to-A transversion at nt 389. We have designated this variant HPRTMidland. The predicted amino acid (aa) substitution in HPRTMidland is a valine to aspartic acid at aa 130. This substitution is within 2 aa of the amino acid substitution in a previously defined HPRT variant, HPRTAnn Arbor. Both mutations are within a highly conserved sequence in the putative 5-phosphoribosyl-1-pyrophosphate-binding domain. The amino acid substitution in HPRTMidland causes a significant perturbation in the predicted secondary structure of this region. The HPRTMidland mutation affects a different domain of HPRT than the HPRTFlint mutation located at 167 nt away.

Characterization, evolutionary relationships, and chromosome location of processed mouse HPRT pseudogene

Studies on a cell line with amplified copies of the mouse hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene and HPRT gene transfer experiments revealed the existence of a nonfunctional HPRT-related sequence in the mouse genome. This sequence was isolated and found to be a processed HPRT pseudogene. With the exception of a small internal deletion, the pseudogene is believed to comprise a complete reverse transcript of HPRT mRNA, although the 3' end of the pseudogene was lost in the cloning process. A probe from a region flanking the mouse pseudogene was used to investigate the evolutionary relationships of mammalian HPRT pseudogenes. The pseudogenes in mouse and Chinese hamster appear to have a common origin, but no homology to any of the four known human HPRT pseudogenes was detected. A pseudogene-linked restriction fragment length polymorphism was used to map the pseudogene to the distal end of mouse chromosome 17.

Comparative study of DNase I sensitivity at the X-linked human HPRT locus

To examine the association between chromatin structure and gene expression at the human hypoxanthine phosphoribosyltransferase (HPRT) locus, DNase I sensitivity of active and inactive genes was analyzed. In a set of human-hamster hybrid lines containing either an active or an inactive human X chromosome, or a derivative of the latter in which the HPRT gene was reactivated by 5-azacytidine treatment, only the promoter region of the gene was found to contain a hypersensitive domain, and its presence was strictly correlated with gene activity. An S1 nuclease-sensitive site was mapped upstream from the DNase I hypersensitive domain using supercoiled plasmids. The overall level of DNase I sensitivity in the interior of the HPRT gene was also assessed by comparing the degradation of polymorphic restriction fragments on active and inactive alleles in both polyclonal and monoclonal lines of female human cells. In these internally controlled experiments, the active X chromosome was found to be approximately twofold more susceptible to DNase I digestion than the inactive X chromosome.

Identification of a single nucleotide change in a mutant gene for hypoxanthine-guanine phosphoribosyltransferase (HPRT Ann Arbor)

HPRT Ann Arbor is a variant of hypoxanthine (guanine) phosphoribosyl-transferase (HPRT: EC 2.4.2.8), which was identified in wo brothers with hyperuricemia and nephrolithiasis. In previous studies, this mutant enzyme was characterized by an increased Km for both substrates, a normal Vmax, a decreased intracellular concentration of enzyme protein, a normal subunit molecular weight and an acidic isoelectric point under native isoelectric focusing conditions. We have cloned a full-length cDNA for HPRT Ann Arbor and determined its complete nucleotide sequence. A single nucleotide change (T----G) at nucleotide position 396 has been identified. This transversion predicts an amino acid substitution from isoleucine (ATT) to methionine (ATG) in codon 132, which is located within the putative 5'-phosphoribosyl-1-pyrophosphate (PRPP)-binding site of HPRT.

Yeast ARS function and nuclear matrix association coincide in a short sequence from the human HPRT locus

A sequence that supports extrachromosomal replication of plasmids in yeast has been identified within the first intron of the human hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene. This represents the first isolation of such an autonomously replicating sequence (ARS) from an exactly known position in the human genome. This ARS shares similarities of imparted yeast phenotype and DNA sequence with other heterologous ARSs. In addition, this sequence is found to be a matrix association region (MAR) on the basis of specific binding to nuclear matrices prepared from several mammalian cell types. It also exhibits anomalous electrophoretic behavior, characteristic of bent DNA, on polyacrylamide gels. The coincidence of these properties supports the possibility that this region may play a role in DNA replication within its normal chromosomal context.

Spontaneous reversion of novel Lesch-Nyhan mutation by HPRT gene rearrangement

Molecular analysis of an unusual patient with the Lesch-Nyhan syndrome has suggested that the mutation is due to a partial HPRT gene duplication. We now report the cloning and sequencing of the mutant HPRT cDNA which shows the precise duplication of exons 2 and 3. This mutation is the result of an internal duplication of 16-20 kilobases of the gene. The structure of the mutant gene suggests that the duplication was not generated by a single unequal crossing-over event between two normal HPRT alleles. Growth of Epstein-Barr virus-transformed lymphoblasts from this patient in selective medium has permitted isolation of spontaneous HPRT+ revertants of this mutation. The reversion event involves a second major HPRT gene rearrangement where most or all of the duplicated portion of the mutant gene is deleted. The original mutation therefore has the potential for spontaneous somatic reversion. This may explain the relatively mild symptoms of the Lesch-Nyhan syndrome exhibited by this patient.

Chromosomal distribution of the RTVL-H family of human endogenous retrovirus-like sequences

We have analyzed the chromosomal distribution of a large family of human endogenous retrovirus-like sequences termed RTVL-H. In situ hybridizations suggest that these sequences are found on all human chromosomes. These results also indicate that clusters or concentrations of RTVL-H elements may exist on chromosomes 1p and 7q. Southern blotting experiments using somatic cell hybrids containing either the human chromosome 3 or the X chromosome confirm the presence of multiple dispersed RTVL-H sequences on these two chromosomes. These experiments also demonstrate that distinct RTVL-H banding patterns can be detected for each chromosome. Thus, RTVL-H probes may be useful in genome mapping studies.

Nucleotide sequence of the Drosophila glucose-6-phosphate dehydrogenase gene and comparison with the homologous human gene

Glucose-6-phosphate dehydrogenase (G6PD) has a major role in NADPH production and is found in almost all cell types. The structural gene for G6PD is X-linked in Drosophila melanogaster, as it is in most eukaryotic organisms, and due to its ubiquitous expression, it can be considered a typical 'housekeeping' gene. Here we present the complete nucleotide (nt) sequence of G6PD cDNAs as well as the genomic copy of the G6PD gene. The G6PD gene has three introns so that the protein-coding region is divided into four segments. The 5'-end of mature G6PD mRNA is located 289 +/- 1 nt upstream from the start codon. The sequence upstream from the transcription start point is G + T-rich and contains no commonly found transcription regulatory elements, such as a TATA box or GGGCGG sequence. D. melanogaster G6PD is 65% homologous with the human G6PD protein but has no homology with the human sequence for the first 42 amino acid residues. The G6PD gene was shown to be active when transduced to autosomal positions. For each transformant, G6PD activity in both male and female adults was not significantly different, indicating that the transduced gene, unlike the resident G6PD, is not dosage-compensated in males.

Monoclonality and abnormal parathyroid hormone genes in parathyroid adenomas

Previous work based on the relative tissue content of glucose-6-phosphate dehydrogenase isoenzymes suggested that parathyroid adenomas, like primary hyperplasia, may be multicellular (not clonal) in origin. We have reexamined this issue by using two independent molecular genetic methods. We report tumor-cell-specific restriction-fragment-length alterations involving the parathyroid hormone gene from two human parathyroid adenomas. These abnormal restriction fragments indicate that in each case a clonal proliferation of cells was present and also suggest that DNA alterations involving the parathyroid hormone locus may be important in the tumorigenesis or clonal evolution of some parathyroid adenomas. In addition, we used a restriction-fragment-length polymorphism in an X-linked gene (hypoxanthine phosphoribosyltransferase) to examine the clonality of eight parathyroid adenomas in women. Of these eight adenomas, six had the DNA hybridization pattern of monoclonality, and two had an equivocal pattern. None of five hyperplastic parathyroid glands had a monoclonal pattern. We conclude that some (and perhaps many) single parathyroid adenomas are monoclonal neoplasms. Our observations suggest that there is a fundamental biologic difference between parathyroid adenomas and primary hyperplasia--a difference that could prove useful in distinguishing these entities clinically.

Molecular analysis of mutations induced by N-ethyl-N-nitrosourea at the HPRT locus in mouse lymphoma cells

The molecular basis of 29 N-ethyl-N-nitrosourea (ENU)-induced HPRT-deficient mutants of mouse lymphoma cells (GRSL 13-2) was investigated using nucleic acid blot hybridization techniques. DNA from all 29 mutants showed normal restriction patterns on Southern blots when probed with HPRT cDNA, but 10 mutants differed from wild-type cells in their cytoplasmic HPRT mRNA level. In 5 mutants we found 10-25% of the normal amount of HPRT mRNA, whereas in another 5 mutants no HPRT mRNA could be detected at all. These mutants do not seem to be induced by hypermethylation of regulatory sequences of the HPRT gene, since they could not be reverted to an HPRT-proficient phenotype by treatment of the cells with 5-azacytidine.

Primary structure of human pancreatic secretory trypsin inhibitor (PSTI) gene

The human pancreatic secretory trypsin inhibitor (PSTI) gene was isolated from a human gene library. Restriction endonuclease mapping and DNA sequencing analysis revealed that this gene is approximately 7.5 kb long and is separated into four exons by three introns. The gene has multiple transcription start points and examination with a single-laser cell-sorter showed that it is located on chromosome 5.

Molecular studies of marsupial X chromosomes reveal limited sequence homology of mammalian X-linked genes

To explore the extent to which the X chromosome has been conserved during mammalian evolution, we compared six loci that are X-linked in the human genome with the corresponding genes of the North American marsupial, the Virginia opossum (Didelphis virginiana). Our analysis shows that in the opossum genome there are sequences highly homologous to those of human cDNAs for housekeeping genes, glucose-6-phosphoribosyltransferase (HPRT), phosphoglycerate kinase A (PGK1), and alpha-galactosidase A (GLA). However, ornithine transcarbamylase and blood clotting Factor IX--tissue-specific genes that are X-linked in eutherians mammals--have no highly conserved homologs in the marsupial genome. By cloning opossum G6PD and HPRT, we found that these genes are X-linked in the opossum and that homologous sequences are limited to coding regions. As all genomic fragments hybridizing with the human GLA probe show dosage effects, it is likely that the opossum counterpart is X-linked. Finally, the pattern of hybridization suggests that the autosomal pseudogenes of HPRT and PGK1 in the opossum have remained highly homologous to the human X-linked genes.

Molecular analysis of mbcl-2: structure and expression of the murine gene homologous to the human gene involved in follicular lymphoma

We have cloned the mouse bcl-2 (mbcl-2) genomic locus and analyzed it in detail. The gene is comprised of two exons separated by more than 15 kb. Two species of mRNAs are produced, and DNA sequencing analysis shows that they code for two proteins differing at their C terminus: a 7.5 kb transcript codes for a polypeptide of 236 amino acids, mbcl-2 alpha, and a 2.4 kb transcript, which derives from the 5' exon only, codes for a protein of 199 amino acids, mbcl-2 beta. The gene is characterized by very long (5' about 1.4 kb, and 3' about 5.1 kb) untranslated regions surrounding the relatively short coding region. We have mapped the 5' end of the mbcl-2 mRNAs by S1 protection analysis, and we have analyzed the promoter region. The expression of the mbcl-2 gene was analyzed in different cell lines and in mouse tissues. Expression is tissue-specific in adult tissues: spleen and thymus express the highest level of mbcl-2 transcripts. The mbcl-2 gene maps to mouse chromosome 1.

Molecular and biochemical analyses of spontaneous and X-ray-induced mutants in human lymphoblastoid cells

We have isolated a series of 14 spontaneously arising and 28 X-ray-induced mutants at the hypoxanthine-guanine phosphoribosyltransferase (hgprt) locus in human lymphoblastoid cells. Among the spontaneous mutants, 5/14 (36%) had detectable alterations in their restriction fragment pattern after hybridization with a human cDNA probe for hgprt. Of the 10 remaining mutants, 4 had partial HGPRT enzyme activity, which suggested that they contained point mutations. Among the 28 mutants induced by 150 rad of X-rays, 15 (54%) had deletions of part or all of the hgprt gene. 5 of the remaining 13 (18% overall) had partial HGPRT enzyme activity, which suggested that they contained point mutations. These data imply that in this human cell system, X-rays induce both point mutants which have residual enzyme activity as well as mutations involving relatively large deletions of DNA.

Structural analysis of the 5' region of the chromosomal gene for hamster histidyl-tRNA synthetase

The chromosomal gene (HRS) coding for hamster histidyl-tRNA synthetase, like many other housekeeping genes, lacks many of the features associated with promoters of RNA-polymerase-II-transcribed genes. HRS transcripts have multiple start points. Using RNase protection analysis, we also identified a 300-bp exon located only 36 bp away from the 5'-most start point of the HRS transcript. This exon hybridizes to a 3.5-kb transcript which transcribes from a different strand of DNA in the 5' region of the HRS gene. This divergent 3.5-kb transcript also has multiple transcription start points. The identity and function of this 3.5-kb transcript is not known.

Cloning and expression of the mouse pgk-1 gene and the nucleotide sequence of its promoter

We report the cloning of the mouse pgk-1 gene encoding the somatic cell isoform of the enzyme phosphoglycerate kinase. The gene is contained within a 16-kb region of the X chromosome and is interrupted by at least ten introns. The promoter region of the pgk-1 gene is rich in G and C nucleotides and contains five copies of the hexadeoxynucleotide, GGGCGG, the potential binding site for the Sp 1 transcription factor, a CCAAT sequence, but no TATA box. This promoter functions following DNA-mediated transfection into mammalian cells. The promoter of the mouse pgk-1 gene is homologous to the human pgk-1 promoter. A number of conserved motifs in the promoter may indicate a significant role for these sequences in expression of the pgk-1 gene.

Dioxin-inducible enhancer region upstream from the mouse P(1)450 gene and interaction with a heterologous SV40 promoter

In mouse hepatoma Hepa-1 cells, polycyclic aromatic compounds such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) activate transcription of the mouse P(1)450 gene via trans-acting regulatory factors that include the TCDD X receptor complex. The positive control element in the P(1)450 5'-flanking region was examined in control and TCDD-treated Hepa-1 stable transformants that had been transfected with either of two expression vectors containing the chloramphenicol acetyltransferase (CAT) gene: pA10-cat, which has the simian virus 40 (SV40) early core promoter (without enhancers) immediately upstream from the CAT gene; and pSV0-cat, which has no promoter or enhancer. When the 1-kb DNA fragment from -1,647 to -611 upstream from the P(1)450 gene is inserted in either orientation--immediately upstream or almost 2 kb further upstream--from the SV40 promoter in pA10-cat, there is enhancement of CAT activity that can be further induced three- to fourfold by TCDD. When the same experiment is carried out with the -1,247 to -823 fragment or the -1,051 to -823 fragment, but not the -1,247 to -1,052 fragment, TCDD responsiveness is lost, or at least masked, because of a large increase in constitutive CAT activity. pSV0-cat mutants containing internal deletions in the upstream flanking sequences of P(1)450 were constructed. A region of 300 bases (-1,218 to -918) is shown to be required for TCDD responsiveness, and one TCDD-inducible element can be dissociated from an enhancer of constitutive gene expression, whereas one or more other TCDD-inducible elements cannot.(ABSTRACT TRUNCATED AT 250 WORDS)

The primary structure of the putative oncogene pim-1 shows extensive homology with protein kinases

We have shown previously that the putative oncogene pim-1 is frequently activated by provirus insertion in murine leukemia virus-induced T cell lymphomas. Here we describe the structure of the pim-1 gene as determined by sequencing genomic and cDNA clones. The gene has an open reading frame, encoding a protein of 313 amino acids, extending over six exons and preceded and followed by stop codons in all reading frames. Proviruses always integrate outside the protein-encoding domain, showing a high preference for a small region in the 3'-terminal exon; integration in the 3' exon results in relatively high levels of pim-1 mRNA. Computer search reveals homology between pim-1 and protein kinases: all the domains characteristic of protein kinases are conserved in the pim-1 amino acid sequence. The highest homologies were observed with the protein-serine kinases.

Scrapie and cellular PrP isoforms are encoded by the same chromosomal gene

PrP 27-30 is the major protein in purified preparations of scrapie agent. An almost complete PrP cDNA was used to select PrP-related genomic clones from normal hamster DNA. The gene contains a noncoding exon of 56 to 82 bp and a 2 kb coding exon, separated by a 10 kb intron. Transcription initiates at the same multiple sites in vivo and in vitro. The promoter lacks a TATA box and contains three repeats of the sequence GCCCCGCCC, which resembles the Sp1 binding site found in "housekeeping" genes. The PrP coding sequence encodes a presumptive amino-terminal signal peptide. The primary structure of PrP encoded by the gene of a healthy animal does not differ from that encoded by a cDNA from a scrapie-infected animal, suggesting that the different properties of PrP from normal and scrapie-infected brains are due to post-translational events.

Structure of human cholecystokinin gene and its chromosomal location

We have determined the entire structure of human cholecystokinin (CCK) gene, which is 7 kb in size and separated into three exons. S1 endonuclease analysis has shown two putative transcription initiation sites that are preceded by 'TATA' equivalent sequences located 39 bp and 35 bp upstream from these sites. The promoter region contains five 'G-C box'-like sequences, which are believed to be sp 1-binding sites. By chromosome sorting in combination with velocity sedimentation and Southern hybridization, the human cck gene was mapped on the short arm of human chromosome 3.