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At least 685 records · Page 38Linked to original sources
PubMed1990

Nuclease mapping and DNA sequence analysis of transcripts from the dihydrofolate reductase-thymidylate synthase (R) region of Leishmania major.

Trypanosomatid protozoan parasites utilize a number of nonstandard mechanisms in expressing their genes. To probe these phenomena in a genetically accessible system, we have mapped termini of eight transcripts arising from the amplified R region including the DHFR-TS gene of methotrexate-resistant Leishmania major. Poly(A)+ RNAs transcribed from the DHFR-TS-coding strand exhibit features similar to those observed around other trypanosomatid protein-coding genes. These include close spacing, the presence of a transpliced miniexon on the 5' termini, heterogeneity at both 5' and 3' ends, and in some cases S1 nuclease protection of intertranscript regions. Other than the splice acceptor site, no consensus sequence elements associated with either 5' or 3' ends were detected, although polydinucleotide tracts tended to be near inter-transcript regions. Two poly(A)+ RNAs transcribed from the opposite strand of the upstream flanking regions lacked the miniexon. Sequencing of DNA encoding the overlapping 1.7 kb opposite strand transcripts (one bearing and one lacking the miniexon, both found on polysomes) revealed no reading frames likely to encode proteins, suggesting that at least some of these RNAs could be nonfunctional by-products of RNA processing.

Animals↗
PubMed1988

Minute virus of mice non-structural protein NS-1 is necessary and sufficient for trans-activation of the viral P39 promoter.

The genome of the autonomous parvovirus minute virus of mice (MVM) is organized in two overlapping transcription units: the genes coding for the two non-structural proteins (NS-1 ad NS-2) are transcribed from a promoter (P04) located at map unit 4, whereas the promoter controlling the capsid protein genes (P39) lies at map unit 39. We studied the effect of viral proteins on the activity of the P39 promoter in vivo. By site-directed mutagenesis we constructed clones encoding only one of the two NS proteins. The activity of the P39 promoter was measured in HeLa or EL-4 cells transfected with these clones, either by an RNase protection assay or by following the expression of a reporter gene, CAT (which codes for chloramphenicol acetyltransferase), placed under the control of this promoter. We found that the P39 promoter of strain MVMi is activated in trans by a viral gene product, and evidence to suggest that NS-1 is the only viral gene product responsible for this trans-activation. We also determined that the mechanism of trans-activation is very rapid, since all species of viral mRNAs appear together in non-synchronized infected EL-4 cells within a 2 h interval.

Amino Acid Sequence↗
PubMed1997

Mapping replication origins by nascent DNA strand length.

The mapping of replication origins by nascent DNA strand length determination is a very sensitive generally applicable method that identifies even single-copy origins in mammalian chromosomes. A major advantage of this procedure is that there is no need for synchronization of cells or treatment with metabolic agents, which allows the origin to be studied under physiological conditions. This technique is based upon the amplification of specific sequence markers on nascent DNA strands that initiated replication within the region of the putative origin. Therefore, this method requires detailed sequence information of the locus to be analyzed. As a first step, nascent DNA of proliferating cells is pulse-labeled with BrdU followed by size fractionation and purification with anti-BrdU antibodies. The position of putative origins can then be determined via identification of the shortest nascent strands that can be amplified by PCR and hybridized to probes homologous to the amplified segments. Here, we give a detailed description of the theory behind the method and a full recipe for its application. Advantages and limitations of the procedure are discussed.

Animals↗
PubMed1988

Structural diversity of the patatin gene family in potato cv. Desiree.

We have used a combined genetical and molecular approach to study the structural diversity of the patatin gene family in tetraploid Solanum tuberosum L. cv. Desiree (2n = 4x = 48). Nine dihaploid derivatives (2n = 2x = 24) of cv. Desiree were isolated by gynogenesis through prickle pollination with S. phureja Juz et Buk. Patatin DNA sequences in Desiree and in the dihaploids were examined by probing Southern blots of restriction endonucleases HindIII and XbaI digested DNA with patatin cDNA region-specific gene probes and by more detailed examination (restriction endonuclease mapping and partial DNA sequencing) of 10 patatin genomic clones in bacteriophage lambda replacement vector EMBL4. This provided positive identification for most individual patatin gene family members and some estimate of their organisation and diversity. Most of the 64-72 patatin DNA copies showed little allelic variation based on HindIII and XbaI restriction fragment length polymorphism (RFLP) mapping and did not appear to be very tightly clustered. Four of the 6-8 class I patatin genes (without a characteristic 22 bp insert in their untranslated leader DNA), showed apparent allelic homogeneity, whilst the remaining class I genes comigrated with a single class II patatin gene RFLP subclass. Of the isolated clones, 4 contained apparent pseudogenes lacking 5' control sequences and exon-1 DNA while another clone contained a patatin gene truncated at the 5' region due to the cloning event. The remaining 5 all contained class II genes (with the 22 bp insert) and these showed varying degrees of sequence homology for 400 bp of conserved 5' coding and non-coding DNA (from 77%-95%). In one case the extent of homology differed, with complete sequence divergence upstream of position -80 from the start of transcription. The structural diversity of the patatin gene family is discussed in relation to expression of individual patatin genes and the use of cv. Desiree as a host for potato transformation experiments.

Base Sequence↗
PubMed1990

RNA processing and ribonucleoprotein assembly studied in vivo by RNA transfection.

We present a method for studying RNA processing and ribonucleoprotein assembly in vivo, by using RNA synthesized in vitro. SP6-transcribed 32P-labeled U2 small nuclear RNA precursor molecules were introduced into cultured human 293 cells by calcium phosphate-mediated uptake, as in standard DNA transfection experiments. RNase protection mapping demonstrated that the introduced pre-U2 RNA underwent accurate 3' end processing. The introduced U2 RNA was assembled into ribonucleoprotein particles that reacted with an antibody specific for proteins known to be associated with the U2 small nuclear ribonucleoprotein particle. The 3' end-processed, ribonucleoprotein-assembled U2 RNA accumulated in the nuclear fraction. When pre-U2 RNA with a 7-methylguanosine group at the 5' end was introduced into cells, it underwent conversion to a 2,2,7-trimethylguanosine cap structure, a characteristic feature of the U-small nuclear RNAs. Pre-U2 RNA introduced with an adenosine cap (Ap-ppG) also underwent processing, small nuclear ribonucleoprotein assembly, and nuclear accumulation, establishing that a methylated guanosine cap structure is not required for these steps in U2 small nuclear ribonucleoprotein biosynthesis. Beyond its demonstrated usefulness in the study of small nuclear ribonucleoprotein biosynthesis, RNA transfection may be of general applicability to the investigation of eukaryotic RNA processing in vivo and may also offer opportunities for introducing therapeutically targeted RNAs (ribozymes or antisense RNA) into cells.

Base Sequence↗
PubMed1990

A contribution of the core-promoter and its surrounding regions to the preferential transcription of the fibroin gene in posterior silk gland extracts.

Complementation of a posterior silk gland (psg) extract to a HeLa cell extract specifically enhances the transcription of the Bombyx mori fibroin gene. To map the regions responsible for this enhancement, the fibroin promoter was dissected and the transcriptional function of each region was analyzed. Besides the upstream promoter element 5' to the TATA box, two downstream elements were found to be important for the preferential transcription of the fibroin gene in the complementation system as well as in the psg extract. The minimal fibroin promoter from -37 to +10 (core-promoter) was preferentially transcribed in the psg extract, while the transcription efficiencies of other promoters like one of the Bombyx chorion genes and the adenovirus 2 major late promoter (Ad2MLP) were considerably lower. The transcription from the core-promoter was further enhanced when combined with either the intronic element from +156 to +454 or the upstream element. Both the upstream and intronic elements also stimulated the transcription from the Ad2MLP in an orientation independent manner. These results demonstrate that the transcription of the fibroin gene is mediated through an integration of multiple regulatory elements.

Animals↗
PubMed1995

Use of a nitrocellulose film substrate in matrix-assisted laser desorption/ionization mass spectrometry for DNA mapping and screening.

A nitrocellulose film is used as a substrate in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) studies of DNA. PCR products and DNA fragment digests obtained from biochemical procedures can be analyzed with the use of a nitrocellulose substrate in MALDI MS whereas no signal is observed with the use of a stainless steel substrate. In this method, on-probe purification allows for effective elimination of the interfering effects of salts, buffers, and other contaminants that are usually present in DNA samples, which serve as important limiting factors in the DNA molecular ion yield in the MALDI process. The use of the nitrocellulose film substrate also appears to improve the shot-to-shot and sample-to-sample reproducibility of the ion yield due to the more homogeneous coverage of matrix/analyte over the sample surface. With the use of the nitrocellulose substrate, DNA fragments of up to 622 base pairs in complex mixtures provide mass spectra with minimal sample purification. Although only species corresponding to single-stranded DNA were detected, a mass calibration scheme was established allowing an accuracy of within one base pair for fragments of < 250 bp under the experimental conditions. Despite the low mass resolution of the spectra obtained, the method has been successfully used for rapid DNA screening for sample disease genes and PCR products.

Base Sequence↗
PubMed1988

On the specificity and effects on transcription of P-element insertions at the yellow locus of Drosophila melanogaster.

Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates that P-elements inserted into the transcribed region of y can terminate y transcription. While the great majority of the P-element insertions into the preferred target site abolish y activity, this loss of activity is not due to disruption of the insertion site since imprecise excision events which do not restore the wild type sequence at the insertion site can restore y function. We further demonstrate that a mutant caused by a 221bp P-element insertion into the 5' transcribed but non-translated region, which show partial y activity, produces a larger mutant transcript consistent with it being a product of transcriptional readthrough. We present results which suggest that imprecise excision events which restore (or partially restore) y activity can occur by deleting P-element internal sequences which normally act to terminate y transcription.

Animals↗
PubMed2006

Confirmation of association of the GABRA2 gene with alcohol dependence by subtype-specific analysis.

OBJECTIVES: Three recent studies revealed a haplotypic association of alcohol dependence with the gene encoding the alpha2 subunit of the gamma-aminobutyric acid type A (GABAA) receptor (GABRA2). The present study examined whether variation of the GABRA2 gene confers susceptibility to different subtypes of alcohol dependence in the German population. METHODS: A total of 257 German alcohol-dependent patients and 88 healthy population controls were genotyped for six single-nucleotide polymorphisms covering the middle part and the 3' end of GABRA2. Allelic, genotypic and haplotypic comparisons were done for subgroups of alcohol-dependent patients with a presumed high genetic load. RESULTS: The overall alcohol-dependent patients vs. control group comparison confirmed positive allelic association for five of six single-nucleotide polymorphisms mapping from intron 3 to the 3' end of GABRA2 (P=0.01-0.02). Haplotype analysis revealed two common haplotypes accounting for approximately 90% of the chromosomes within the patients and controls. The less frequent haplotype was significantly more prevalent among the alcohol-dependent patients (45%) than among the controls [29%; odds ratio (OR)=1.97, 95% confidence interval (CI): 1.30-2.96]. The strength of association increased, if the subsets of alcohol-dependent patients with a positive family history (OR=2.60, 95% CI: 1.63-4.13), withdrawal seizures (OR=2.22, 95% CI: 1.30-3.79) or an early onset (OR=2.19, 95% CI: 1.24-3.88) were analyzed. CONCLUSIONS: Although our study was limited by the number of cases being larger than the number of controls, the results confirm GABRA2 as a susceptibility gene for alcohol dependence in the German population. We found a consistent increase of the susceptibility effect in alcohol-dependent patients with a presumed strong genetic predisposition.

Adult↗
PubMed1989

Molecular genetic analysis of a hybrid gene encoding Sta glycophorin of the human erythrocyte membrane.

Sta is an antigen of the human MNSs blood group system carried by a variant glycophorin residing in the erythrocyte membrane. We examined the structure, organization, and inheritance of Sta gene identified in genomic DNA from an Oriental family. Southern blotting detected a useful genetic marker tightly linked to the Sta gene. Differential hybridization and secondary restriction analyses showed that Sta gene is a fusion hybrid of delta and alpha glycophorin genes. Genomic mapping by extensive use of synthetic oligonucleotides, with overlapping sequence specificity, allowed us to define the delta-alpha junction site and disclose the organization of the variant gene. The junction point of Sta hybrid gene is encompassed by an unexpressed exonlike sequence of the delta gene at the 5' site, and an expressed sequence of the alpha gene spanning codons 59 through 71, at the 3' site. Dosage quantification demonstrated the occurrence of Sta gene as a single copy in the genome. Blood group inheritance, evaluated by DNA typing, established the tight linkage of Sta to the alpha M and delta S genes. The data support a single unequal crossing-over event between misaligned delta and alpha genes on the homologous chromosomes as the mechanism for the origin of Sta gene. The Sta gene is similar in overall structure to another delta-alpha hybrid gene, Dantu, but differs from it in junction structure, copy number, gene linkage, and antigen specificity.

Amino Acid Sequence↗
PubMed1999

Unique expression patterns of myosin heavy chain genes in the ductus arteriosus and uterus of rabbits.

In smooth muscle tissue, two smooth muscle myosin heavy chain (MHC) isoforms (SM1, SM2) and two non-muscle MHC isoforms (NMA, NMB) have been identified. The purpose of our study was to clarify whether smooth muscle MHC mRNA expression reflects the physiological and functional state of the muscle. We studied the expression pattern of MHC mRNAs, using the S1-nuclease mapping procedure, in functionally and morphologically changeable organs; the ductus arteriosus (DA) during development (25 and 29 days of gestation, and from 3-day-old neonates) and uteri from virgin, day-10 pregnant (P10) and day-29 pregnant (P29) rabbits. The results demonstrated that SM2 expression was greater in the fetal DA than in the fetal aortic and pulmonary arteries, but that it decreased significantly following closure of DA. In the gravid uterus, SM1 expression was significantly (P<0.05) strong compared to other MHC mRNAs from virgin to P10 rabbits. During pregnancy, NMB expression showed a tendency to increase until P10, and after P10, SM2 expression increased dramatically and NMB expression decreased to give almost a mirror image of the SM2 expression. Smooth muscle type (SM1, SM2) was significantly (P<0.05) strong compared to non-muscle type expression (NMA, NMB) at P29. These data suggest that smooth muscle MHC mRNA, especially SM2 expression reflects the physiological and functional state of the smooth muscle.

Animals↗
PubMed1989

Pathways of evolution of influenza A (H1N1) viruses from 1977 to 1986 as determined by oligonucleotide mapping and sequencing studies.

The evolutionary relationships of epidemic influenza A (H1N1) viruses isolated between 1982 and 1986 have been examined by oligonucleotide mapping and partial DNA sequencing. The T1 mapping studies confirmed our previous report that the evolution of the influenza virus genome generally results in an average of four to six oligonucleotide changes per year. Between 1982 and 1986, however, two apparent exceptions to this finding occurred. H1N1 antigenic variants (including the A/Chile/83 and A/Victoria/83 reference strains) that caused influenza outbreaks and epidemics from 1983 to 1984 differed by 20 to 30 oligonucleotides from viruses isolated during the previous influenza season. T1 mapping of individual RNA segments and sequencing revealed that all six internal genes of a representative 1983 A/Chile-like virus were more closely related to genes of non-reassortant H1N1 viruses that circulated from 1977 to 1982 than to genes of H3N2 viruses. Therefore, the 1983 variant viruses were not H1N1-H3N2 reassortants. The A/Taiwan/86-like H1N1 antigenic variants that emerged in south-east Asia in the spring of 1986 and caused epidemic activity the following winter also exhibited changes of 20 to 30 oligonucleotides from the A/Chile/83-like or A/Victoria/83-like H1N1 viruses that circulated during the previous influenza season. Fewer oligonucleotide changes were observed between the 1986 A/Taiwan/86-like and H1N1 viruses isolated before 1983, however, suggesting that the former evolved from viruses that circulated before the 1983 antigenic variants became the predominant H1N1 epidemic virus strains. This was confirmed by sequencing the HA1 domain of the haemagglutinin genes of three A/Taiwan/86-like viruses. These studies provide evidence that other genes of influenza A viruses, in addition to the haemagglutinin gene, may evolve concurrently along two or more separate pathways.

Amino Acid Sequence↗
PubMed1990

The beta-lactam biosynthesis genes for isopenicillin N epimerase and deacetoxycephalosporin C synthetase are expressed from a single transcript in Streptomyces clavuligerus.

Isopenicillin N isomerase (epimerase) has been purified from Streptomyces clavuligerus, and the amino acid sequence of the N-terminus has been determined. By using single oligonucleotide probes based on high GC codon bias ("guessmers"), the translation start codons were determined for two successive genes in the beta-lactam-biosynthetic pathway and mapped within a 3.6-kilobase-pair KpnI restriction fragment. The epimerase gene (cefD) was located immediately upstream of the deacetoxycephalosporin C synthetase (expandase) gene (cefE) that was characterized previously. cefD was sequenced and expressed in Escherichia coli; the resulting cell extracts contained epimerase activity. Western immunoblots demonstrated that a protein comigrated with purified S. clavuligerus epimerase at 44 kilodaltons. cefD and cefE were separated by an 81-base-pair segment. The DNA sequence upstream of the epimerase gene had a high AT content, suggestive of a promoter region. Primer extension analysis of S. clavuligerus mRNA showed that the start of transcription occurred approximately 130 base pairs upstream of the epimerase translation start site; Northern (RNA blot) analysis revealed a hybridization signal large enough to code for both epimerase and expandase, and nuclease S1 protection assays showed that a single message may code for epimerase, expandase, and another unknown protein. When cefD and cefE were placed in an expression vector, concomitant synthesis of both epimerase and expandase occurred in E. coli.

Amino Acid Isomerases↗
PubMed1998

High-resolution structural analysis of chromatin at specific loci: Saccharomyces cerevisiae silent mating type locus HMLalpha.

Genetic studies have suggested that chromatin structure is involved in repression of the silent mating type loci in Saccharomyces cerevisiae. Chromatin mapping at nucleotide resolution of the transcriptionally silent HMLalpha and the active MATalpha shows that unique organized chromatin structure characterizes the silent state of HMLalpha. Precisely positioned nucleosomes abutting the silencers extend over the alpha1 and alpha2 coding regions. The HO endonuclease recognition site, nuclease hypersensitive at MATalpha, is protected at HMLalpha. Although two precisely positioned nucleosomes incorporate transcription start sites at HMLalpha, the promoter region of the alpha1 and alpha2 genes is nucleosome free and more nuclease sensitive in the repressed than in the transcribed locus. Mutations in genes essential for HML silencing disrupt the nucleosome array near HML-I but not in the vicinity of HML-E, which is closer to the telomere of chromosome III. At the promoter and the HO site, the structure of HMLalpha in Sir protein and histone H4 N-terminal deletion mutants is identical to that of the transcriptionally active MATalpha. The discontinuous chromatin structure of HMLalpha contrasts with the continuous array of nucleosomes found at repressed a-cell-specific genes and the recombination enhancer. Punctuation at HMLalpha may be necessary for higher-order structure or karyoskeleton interactions. The unique chromatin architecture of HMLalpha may relate to the combined requirements of transcriptional repression and recombinational competence.

Base Sequence↗
PubMed1989

Hepatitis B virus transcript produced by RNA splicing.

A new hepatitis B virus (HBV) transcript of about 2.2 kilobases was identified in HBV DNA-transfected human hepatoma cells. The 5' terminus of this viral RNA appears to map at one or more of the precore initiation sites, contains a deletion of 1,223 bases corresponding to the last codon of the core gene to the middle of the surface antigen gene, and terminates at the 3' polyadenylation site used by the other known HBV RNAs. The junction region of the deleted sequences showed the conserved splice donor and acceptor GT-AG sequences. Moreover, when a mutant HBV DNA in which the splice acceptor site was changed from AG to CG was transfected into human hepatoma cells, no 2.2-kilobase RNA was detected, further suggesting that this RNA represents a spliced transcript. The core gene, although an amino acid shorter, still encoded a functional viral core protein in complementation experiments. Sequence analysis of the cDNA of the 2.2-kilobase RNA suggests that this transcript can potentially encode a new protein that comprises the reverse transcriptase domain of HBV. However, genetic analysis using a transient DNA transfection system suggests that the gene product(s) of this transcript is not essential for viral replication. The function of this transcript remains to be studied.

Base Sequence↗
PubMed1989

Activation of the ret-II oncogene without a sequence encoding a transmembrane domain and transforming activity of two ret-II oncogene products differing in carboxy-termini due to alternative splicing.

We previously reported the cloning of a transforming gene, ret-II, which contains the proto-ret kinase domain. In the present study ret-II cDNAs were cloned from a transformant and analyzed. The restriction map and nucleotide sequence indicated that the sequence upstream of the proto-ret kinase domain was replaced by another sequence, which encoded a fusion protein composed of 899 amino acids. This non-proto-ret sequence differed from that of the ret previously reported and had no hydrophobic amino acid stretch for a transmembrane domain. Furthermore, we obtained two kinds of ret-II cDNAs differing in their 3' regions and found that the differences were generated by alternative splicing. From these cDNAs, two types of oncogene products differing in their carboxy-terminal amino acid residues were predicted. The two products exhibited similar transforming activity in NIH3T3 cells. These data indicate that activation of proto-ret can occur as a result of replacement of the extra-cellular and transmembrane domains with the hydrophilic sequence. In addition, differences in the carboxy-terminal amino acid residues in the two types of ret-II oncogene products have no influence on the transforming activity of the ret-II oncogene.

Amino Acid Sequence↗
PubMed1989

Isolation and characterization of the human chromosomal gene for polypeptide chain elongation factor-1 alpha.

The cDNA for human elongation factor-1 alpha was isolated from a cDNA library of human fibroblast cells. Using the cDNA as a probe, a number of chromosomal genes encoding the human elongation factor-1 alpha were isolated. Characterization of the clones by restriction enzyme mapping and nucleotide sequence analysis has revealed that only one of them is an active gene, whereas all of the other genes are processed pseudogenes. The active gene consists of 8 exons and 7 introns spanning about 3.5 kilobases, and the sequence of its exons is completely identical to that of the human elongation factor-1 alpha cDNA. The first non-coding exon of 33 base pairs is separated by a 943-base pair intron from the coding exons. The primer extension of human elongation factor-1 alpha mRNA has indicated that the transcription of human elongation factor-1 alpha gene starts from a C residue, and a "TATA" box was found 24 base pairs upstream of the initiation site. Three and five Sp1 binding sites are present on the 5'-flanking region and the 1st intron, respectively. Furthermore, one Ap-1 binding site is located in the 1st intron. By using nuclear extracts from HeLa cells, the promoter of human elongation factor-1 alpha gene could stimulate in vitro transcription better than the adenovirus major late promoter.

Amino Acid Sequence↗