Charon 4A Research Articles

Expression and dexamethasone regulation of the human corticotropin-releasing hormone gene in a mouse anterior pituitary cell line.

The factors controlling the expression of corticotropin-releasing hormone (CRH), a hypothalamic neuropeptide involved in the regulation of ACTH secretion, are poorly understood partly because a suitable in vitro model is lacking. To study the regulation of CRH gene expression, an 8-kilobase (kb) DNA fragment containing the entire human CRH gene as well as approximately 6 kb of 5' sequence and 0.8 kb of 3' sequence was isolated from a lambda Charon 4A human genomic library and introduced into a mouse anterior pituitary cell line, AtT-20, by CaPO4 transfection with a neomycin-selectable marker. Approximately 10% of the neomycin-resistant lines stably expressed the CRH gene and secreted radioimmunoassay-detectable CRH into culture media at levels greater than 100 pg/ml. By Southern blot analysis the 8-kb DNA fragment containing the CRH gene had been incorporated intact into the AtT-20 genome. In each CRH-producing strain, but not in the parent AtT-20 cell line, we detected by Northern blot analysis an RNA species that hybridized to two radioactive cRNA probes specific for either the 5' or 3' portion of CRH mRNA, and that co-migrated with placental CRH mRNA. Dexamethasone treatment for 24-96 h caused a specific decrease in CRH mRNA and peptide levels of 40-50% in the five CRH-producing cell lines with half-maximal suppression at approximately 10(-9) M dexamethasone, indicating that CRH gene expression is negatively regulated by glucocorticoids. Thus, we have established an in vitro model suitable for studying in detail those cis- and trans-acting factors which regulate CRH gene expression.

Molecular cloning and chromosomal localization of a gene coding for human cardiac myosin heavy-chain.

A human cardiac myosin heavy-chain (MHC) gene, cloned in a charon 4A phage, was isolated using two rat cardiac pCMHC DNA clones (pCMHC26: alpha-MHC type; and pCMHC5: beta-MHC type) as probes and shown to correspond to cardiac myosin heavy-chain of the alpha-type. The 4.3-KB cardiac genomic DNA clone was used as a probe in the Southern analysis of human genomic DNA from human-Chinese hamster or human-mouse somatic cell hybrids. The results show that the human cardiac MHC gene is assigned to chromosome 14 and the human cardiac and skeletal MHC genes do not cosegregate as do the mouse cardiac and skeletal MHC genes.

Myelin proteolipid protein gene structure and its regulation of expression in normal and jimpy mutant mice

The mouse proteolipid protein (PLP) gene was cloned into the λ bacteriophage Charon 4A. The organization and the nucleotide sequence of the exons of the mouse PLP gene were quite similar to those of their human counterparts, consisting of seven exons. The transcription of the PLP gene started from multiple sites. There was a unique sequence tandemly repeated four times, sharing homology with the herpes simplex virus DR2 sequence, upstream from the transcribed region. Expression of the myelin basic protein (MBP) is also restricted to the oligodendrocytes in the central nervous system as is the PLP expression. Homology search against the mouse MBP gene revealed that several boxes in the 5′-flanking region of PLP show a high degree of homology with the sequence present in the MBP 5′-flanking region, possibly of importance in the concomitant expression of both genes in the central nervous system. PLP-mRNA in jimpy mutant mice does not contain exon 5 and its content is greatly reduced. We analyzed the jimpy PLP-mRNA and showed that the transcription initiated from the same sites as those in normal mice. Cloning and sequencing of the 5′-flanking region of the jimpy PLP gene revealed that there were no mutations in the promoter region of the jimpy PLP gene. Therefore, it is likely that a mutation, presumably existing within the jimpy PLP gene, caused the skipping of exon 5 and directly affected the mRNA level.

Highly polymorphic locus D15S24 (CMW-1) maps to 15pter-q13. [HGM9 provisional no. D15S24

CMW-1, containing a 3.8 kb Eco RI fragment, was isolated from a flow sorted library cloned in Charon 21A from the Los Alamos National Laboratory (LA15NS02). The 3.8 kb fragment has also been inserted into the Eco RI site of pUC18. D15S24 maps to chromosome 15, region 15pter-q13, using a somatic cell hybrid regional mapping panel. Co-dominant segregation was shown for alleles detected with Eco RI and Taq I in two informative Caucasian families totaling 17 individuals. Coordinate variation using multiple enzymes suggests that CMW-1 detects a variable number of tandem repeats.

Efficient RecABC-dependent, homologous recombination between coliphage lambda and plasmids requires a phage ninR region gene.

A phage lambda gene that gives a 100-fold increase in recombinant frequencies for RecABC pathway-mediated, phage-plasmid homologous recombination (Shen and Huang 1986) maps to ninG (orf 204) of lambda. We call this gene rap, for recombination adept with plasmid. A similar determinant exists in Charon 4A and maps in phi 80-derived sequences, between nin5 and the Rz homology with lambda. The absence of the Rap+ phenotype from certain lambda vectors explains the inefficiency of screening the resulting phage libraries using phage-plasmid homologous recombination. The mapping of rap permits the construction of lambda vectors more suitable for this screening technique.

Structural organization of the mouse mitochondrial aspartate aminotransferase gene

Structural organization of the entire mouse mitochondrial aspartate aminotransferase (EC 2.6.1.1) gene was determined by analyzing the overlapping genomic clones obtained from a Charon 4A DNA library. The gene is 25 × 10 3 base-pairs long and contains ten exons interrupted by nine introns of various sizes. The 5′ and 3′-flanking regions, the exact sizes and boundaries of the exon blocks including the transcription-initiation sites were determined. The 5′ end of the gene lacks the prototypical 5′ transcriptional regulatory sequence elements, such as TATA and CAAT boxes, but contains G + C-rich sequences, two putative binding sites for a cellular transcription factor, Sp1, and multiple transcription-initiation sites. Moreover, the sequences around the transcription-initiation sites are compatible with the formation of a number of potentially stable stem-loop structures. The leader sequence, which is essential for the transport of the protein into the mitochondria, is coded by the first exon and is separated from the mature protein by the first intron. The pyridoxal 5′-phosphate-binding domain, consisting of seven alternating β-sheets and α-helical polypeptide strands, is separated by four introns present at the ends of α-helices. These genomic DNA structures suggest that the introns were not inserted into a previously uninterrupted coding sequence, but rather are products of evolution of the ancestral gene. However, a further correlation between the positions of introns relative to the well-defined structural domains of the mature protein was not obvious.

Rat glycine methyltransferase. Complete amino acid sequence deduced from a cDNA clone and characterization of the genomic DNA.

The amino terminus of glycine methyltransferase from rat liver is blocked. A hexapeptide containing the blocked amino-terminal residue was obtained from a tryptic digest of the purified enzyme and its amino acid sequence was determined to be Ac-Val-Asp-Ser-Val-Tyr-Arg by Edman degradation and fast-atom-bombardment mass spectrometry after fragmentation with Staphylococcus aureus protease V8. A full-length cDNA clone for the enzyme was isolated from a lambda gt11 rat liver cDNA library using the previously obtained pGMT A56 cDNA [Ogawa, H., Gomi, T., Horii, T., Ogawa, H. & Fujioka, M. (1984) Biochem. Biophys. Res. Commun. 124, 44-50] as a probe. The amino acid sequence deduced from the nucleotide sequence contained both amino- and carboxyl-terminal sequences. The predicted amino acid composition and molecular mass were also in agreement with the published data obtained with the purified protein. Five clones for the glycine methyltransferase gene were isolated from a Charon 4A library containing EcoRI digest of rat liver DNA by in situ plaque hybridization. All clones had inserts of 6500 base pairs, consistent with the size of EcoRI genomic DNA fragment determined by Southern blot hybridization. Sequence analysis of a 5400-bp fragment of the insert DNA lacking a 1100-bp 5' region and comparison of the sequence with that of the cDNA showed that the insert DNA entirely encoded glycine methyltransferase and the gene consisted of six exons and five introns. S1 nuclease protection mapping and primer extension analysis allowed us to propose that the A residue located 19 bp upstream from the translation initiation codon is the site of transcription initiation. TATA, CAAT and GC sequences, and the complementary sequence to the enhancer core element, were located upstream of the transcription initiation site.

Molecular cloning of Bacillus subtilis genes involved in DNA metabolism.

Different clones carrying a chromosomal DNA fragment able to transform Bacillus subtilis mutants dnaA13, dnaB19, dnaG5, recG40 and polA42 to a wild-type phenotype were isolated from a library constructed in plasmid pJH101. A lambda recombinant clone carrying a chromosomal fragment able to transform dnaC mutants was obtained from a lambda Charon 4A library. A restriction map of the cloned DNA fragments was constructed. The 11.3 kb cloned DNA fragment of plasmid pMP60-13 containing the wild-type sequence of dnaG5 was shown to transform a recF33 mutant as well.

Characterization of a cDNA coding for sex steroid-binding protein of human plasma

A cDNA (912 nucleotides) coding for human plasma sex steroid-binding protein (SBP) was characterized from a phage clone previously isolated by screening a Charon 21A human liver cDNA library with rat androgen binding protein (ABP) cDNA. The deduced amino acid sequence from the cDNA indicated that the insert was a partial clone coding for 281 amino acids starting with residue 92 (glycine) encompassing the alternating leucyl residues and the carboxyl-end 373 (histidine) as previously reported [(1986) Biochemistry 25, 7584]. The potential polyadenylation signal sequence ATTAAA is present as part of the 3′-coding region and the stop codon TAA. Both are followed by a short 20 untranslated nucleotides and a poly(A) tract of 49 nucleotides. Significant homologous sequences (76%) at the DNA level exist between human SBP and rat ABP which might suggest the possibility that both evolved from a common primordial gene. Demonstration of the presence of an SBP cDNA in a human liver cDNA library provides the first evidence that liver is the site of SBP biosynthesis.

Structural organization and chromosomal assignment of the parvalbumin gene.

The structure of the rat parvalbumin gene has been elucidated from analysis of six overlapping clones isolated from a rat lambda Charon 4A genomic library. Two of the clones were mapped in detail, and all exons were localized by Southern hybridization using fragments of a full-length parvalbumin cDNA (Epstein, P., Means, A. R., and Berchtold, M. W. (1986) J. Biol. Chem. 261, 5886-5891). The rat parvalbumin transcription unit is 15.5 kilobase pairs in length and contains four introns. The first intron divides the 5'-nontranslated region, whereas the other three interrupt coding DNA. All intron/extron boundaries were sequenced as was 377 base pairs immediately 5' from the putative transcription initiation site. The promoter region contains eukaryotic regulatory homologies to the "TATA" box at -24 and "CAAT" box at -47 and -156. In addition, two doublets consisting of 11-base pair direct repeats exist in the promoter region. Parvalbumin binds two Ca2+, whereas many other members of the same superfamily bind four. Comparison of the genes that encode these proteins provides a strong confirmation of the hypothesis that parvalbumin evolved from an ancestral gene specifying a four-domain Ca2+-binding protein. The rat parvalbumin gene was also utilized to assign its human counterpart to chromosome 22 from data obtained by hybridization to DNA from a somatic cell hybrid panel. It was also used to isolate a 7.5-kilobase pair EcoRI fragment from a human chromosome 22 DNA library.

Isolation of the CD7 gene from the DNA of transfected L cells.

Using DNA from L cells which expressed high levels of the CD7 (Leu-9 or HuLy-m2) antigen obtained after two cycles of transfection, a genomic library was constructed in the lambda phage Charon 4A. Recombinant clones containing the gene coding for this antigen were identified by first screening the library with both the HSV-tk gene and a probe detecting the human repetitive (Alu) sequences. DNA from 10 tk+ and 12 Alu+ recombinant clones was used to transfect L cells which were analyzed for the cell-surface expression of CD7 either early (48-72 h posttransfection) or later when hypoxanthine aminopterin thymidine-resistant colonies were obtained. Transfection with either Alu+ or tk+ recombinant phages led to transient early expression of CD7, and stable CD7+ transfectants were also established. Thus the CD7 gene has been isolated in a number of clones in association with either the Alu repetitive sequence or with the HSV-tk gene; the insert size in one of the genomic clones was 13.5 kb.

Structure of the 3' region of the human elastin gene: great abundance of Alu repetitive sequences and few coding sequences.

Two overlapping clones encompassing 8.5 kb of the human elastin gene were isolated from two genomic libraries constructed by partial digestion with either HaeIII/AluI or Sau3A and contained in lambda Charon 4A or EMBL3, respectively. The 6 kb of DNA comprising the most 3' portion of the gene were sequenced demonstrating an extremely low coding ratio since only three exons containing a total of 134 translated nucleotides were identified. Two exons totaling 78 bp of translated sequences which were previously found in the bovine gene were absent in the human gene. The 3' most exon encoded the unusual amino acid sequence, GGACLGKACGRKRK. The human gene was terminated by 1.2 kb of untranslated sequence which contained two polyadenylation attachment signals. The remainder of the 6 kb was composed of intervening sequences which were abundantly rich in Alu family repetitive sequences found in both orientations. This first report of the characterization of the human elastin gene suggests that significant variation in the gene may exist between species and raises the possibility of consequential polymorphism, mediated by recombination between Alu sequences, in the human population.

19] Isolation and structural analysis of the chromosomal gene for chicken calmodulin

Publisher Summary This chapter discusses the general procedure for the isolation and characterization of chromosomal genes for calcium-binding proteins as a means of further understanding their physiological regulation and molecular evolution. To isolate the chromosomal gene for calmodulin, a cDNA insert from pCB12 is used as a hybridization probe to screen a chicken genomic library. This probe, generated by digestion of pCB 12 with RsaI, is 350 bp in length and contains only the structural sequences coding for the protein. Initial screening for the calmodulin gene was carried out on the chicken genomic library constructed in λ phage Charon 4A. This chapter discusses methods required for subcloning of cosmid fragments, sequence analysis of the 5' end of the CaM gene, and estimation of the potential transcription-initiation site by primer extension analysis. The structure of the CaM gene is strikingly similar to the genes that encode other Ca2+-binding proteins from sea urchins, chicken, rat, and quail. Primer extension was utilized in this study to determine the start site of transcription. The availability of a synthetic oligonucleotide made this technique extremely easy as it was not necessary to isolate a specific fragment. With the transcriptional unit of the CaM gene defined, it is now possible to elucidate the regulation of CaM by Ca2+ at the level of the gene. In addition, the role of CaM in regulation of the cell cycle and in maintenance of cytoskeletal organization can now be directly examined.

Partial characterization of the human beta-myosin heavy-chain gene which is expressed in heart and skeletal muscle.

A human myosin heavy-chain gene, cloned in gamma Charon 4A phage (and as a clone designated lambda gMHC-1), was shown to code for a cardiac myosin heavy chain of the beta-type. The 5' end of the 14,200-base-pair genomic DNA clone is located in the head region of the myosin chain. The 3' end was shown to extent to the COOH terminus and includes the 3'-nontranslated sequence of the corresponding mRNA. The identification of lambda gMHC-1 as coding for a cardiac beta-myosin heavy chain was achieved by heteroduplex mapping using genomic cardiac myosin heavy-chain DNA of rabbit as a probe and, furthermore, by DNA sequence analysis of three selected subregions of the clones DNA including the 3'-nontranslated sequence. It was demonstrated by the S1 nuclease protection technique that the beta-myosin heavy-chain gene is transcribed in human heart muscle. In addition, we have found by the same technique that it is also expressed in human skeletal muscle.

Construction of a gene bank and identification of the ribulose bisphosphate carboxylase/oxygenase genes from the nutritionally versatile cyanobacterium Chlorogloeopsis fritschii

A gene bank of the nutritionally versatile, nitrogen-fixing cyanobacterium Chlorogloeopsis fritschii was constructed in λ Charon 4A. 2,800 recombinants containing 10–20 kbp C. fritschii DNA fragments were screened by Southern hybridization using probes containing the genes for the large (LSU) and small (SSU) subunits of ribulose bisphosphate carboxylase/oxygenase (RuBisCO) from Anacystis nidulans. A single recombinant plaque (λCDG1) containing a 10.9 kbp EcoR1 fragment from C. fritschii hybridized to both the LSU and SSU probes, indicating a possible linkage of these RuBisCO genes in C. fritschii. RuBisCO activity and protein were detected in λCDG1 lysates of Escherichia coli. Hybridization was also obtained between C. fritschii DNA and the LSU probe from Chlamydomonas reinhardtii, although no homology was detected using the LSU probe from maize or the SSU probe from pea.

Human Chromosome–Specific DNA Libraries: Construction and Availability

The goal of the National Laboratory Gene Library Project at the Los Alamos and Lawrence Livermore National Laboratories is the production of chromosome–specific human gene libraries and their distribution to the scientific community for studies of the molecular biology of genes and chromosomes, and for the study and diagnosis of genetic disease. The specific aim of Phase I of the project is the production of complete digest (4 kb average insert size) libraries from each of the 24 human chromosomal types purified by flow sorting. The bacteriophage vector is Charon 21A, which has both Eco R1 and Hind III insertion sites accommodating human DNA fragments up to 9.1 kb in size. Each laboratory has undertaken production of a complete set of chromosome–specific libraries, Los Alamos with Eco R1 and Livermore with Hind III; most of this task has now been accomplished. Close to 1200 library aliquots have been sent to about 300 laboratories world–wide through February 1986, at which time repository and distribution functions were transferred to the American Type Culture Collection, Rockville, Md. Following Phase I, we will begin the construction of libraries with large inserts in a more ad vanced, recently developed bacteriophage vector (about 20 kb inserts) or in a cosmid vector (about 40 kb inserts), and with characteristics better suited to basic studies of gene structure and function.

Isolation of molecular probes associated with the chromosome 15 instability in the Prader-Willi syndrome.

Flow cytometry and recombinant DNA techniques have been used to obtain reagents for a molecular analysis of the Prader-Willi syndrome (PWS). HindIII total-digest libraries were prepared in lambda phage Charon 21A from flow-sorted inverted duplicated no. 15 human chromosomes and propagated on recombination-proficient (LE392) and recBC-, sbcB- (DB1257) bacteria. Twelve distinct chromosome 15-specific probes have been isolated. Eight localized to the region 15q11----13. Four of these eight sublocalized to band 15q11.2 and are shown to be deleted in DNA of one of two patients examined with the PWS. Heteroduplex analysis of two of these clones, which grew on DB1257 but not on LE392, revealed stem-loop structures in the inserts, indicative of inverted, repeated DNA elements. Such DNA repeats might account for some of the cloning instability of DNA segments from proximal 15q. Analysis of the genetic and physical instability associated with the repeated sequences we have isolated from band 15q11.2 may elucidate the molecular basis for the instability of this chromosomal region in patients with the PWS or other diseases associated with chromosomal abnormalities in the proximal long arm of human chromosome 15.

Essential structure in the cloned transforming DNA that induces gene amplification of the Bacillus subtilis amyE-tmrB region.

Bacillus subtilis B7, a mutant which acquired gene amplification of the amyE-tmrB region, showed, as a result, hyperproductivity (about a 5- to 10-fold increase) of alpha-amylase and tunicamycin resistance. The mutational character was transferred to recipient cells by competence transformation. A 14-kilobase (kb) EcoRI chromosomal DNA fragment of strain B7 was found to have the transforming activity. We cloned a 6.4-kb EcoRI fragment on a phage vector lambda Charon 4A through a spontaneous deletion of 7.6 kb from the 14-kb fragment and subcloned a 1.6-kb HindIII fragment on pGR71. The cloned 6.4-kb EcoRI and 1.6-kb HindIII fragments retained the transforming activity of inducing gene amplification of the amyE-tmrB region. At the junction point (J) of the repeating units (16 kb), the tmrB gene was linked to a DNA region (M) located 4 kb upstream of amyE. The essential structure of the cloned, transforming (gene amplification-inducing) DNA was deduced to be that around J. The subcloned 1.6-kb HindIII fragment that retained the transforming activity was shown to be almost solely composed of the tmrB-J-M region. In addition, the DNA sequence around J was determined.

Construction of a genomic library from germinating seedlings of mung bean ( [formula omitted]) evidence for the presence of a class of repetitive sequences and selection of β-tubulin specific recombinant phage

We have constructed a genomic library of Vigna radiata from its total DNA in the phage charon 4A. Recombinant phages were used to hybridize with a family of mung bean repetitive DNA. At least 30% of recombinant phages showed positive hybridization with a specific type of sequences. These phages were also used to screen for β-tubulin-specific recombinants and a recombinant phage with β-tubulin gene was identified.

Chromosomal assignment of seven human genomic DNA sequences associated with restriction fragment length polymorphisms.

Seven phage clones containing human sequences were picked at random from a human genomic library cloned in Charon 4A. The clones are devoid of repetitive sequences and can be used to recognize restriction fragment length polymorphisms (Feder et al. 1985). The chromosomal locations of the sequences defined by the seven clones have been determined by Southern blotting and DNA hybridization to DNA from human-mouse somatic cell hybrids. The chromosomal assignment of these sequences should increase their value as genetic markers in family studies.