Showing papers on "Genome published in 1985"

Isolation and characterization of rat and human glyceraldehyde-3-phosphate dehydrogenase cDNAs: genomic complexity and molecular evolution of the gene

Abstract: Full length cDNAs encoding the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from rat and man have been isolated and sequenced. Many GAPDH gene-related sequences have been found in both genomes based on genomic blot hybridization analysis. Only one functional gene product is known. Results from genomic library screenings suggest that there are 300-400 copies of these sequences in the rat genome and approximately 100 in the human genome. Some of these related sequences have been shown to be processed pseudogenes. We have isolated several rat cDNA clones corresponding to these pseudogenes indicating that some pseudogenes are transcribed. Rat and human cDNAs are 89% homologous in the coding region, and 76% homologous in the first 100 base pairs of the 3'-noncoding region. Comparison of these two cDNA sequences with those of the chicken, Drosophila and yeast genes allows the analysis of the evolution of the GAPDH genes in detail.

Structure and transcription of human papillomavirus sequences in cervical carcinoma cells

Abstract: DNA of human papillomavirus (HPV) types 16 and 18 has been found closely associated with human genital cancer, supporting the concept that members of this virus group are key factors in the aetiology of genital cancer. HPV 18 DNA sequences were also detected in cell lines derived from cervical cancer. We have now analysed these cell lines, HeLa, C4-1 and 756, for the structural organization and transcription of the HPV 18 genome and we find that the HPV 18 DNA is integrated into the cellular genome and is amplified in HeLa and 756 cells. Almost the complete HPV 18 genome seems to be present in 756 cells, with the early region being disrupted into two portions in each integrated copy. In HeLa and C4-1 cells, a 2-3 kilobase (kb) segment of HPV 18-specific sequences is missing from the E2 to L2 region. HPV 18 sequences are specifically transcribed from the E6-E7-E1 region into poly(A)+ RNAs of 1.5-6.5 kb. Hybridization analysis of cDNA clones indicated that some of the transcripts are composed of HPV 18 and cellular sequences. In addition, poly(A)+ RNA hybridizing with HPV 16 DNA was found in two out of three cervical carcinoma biopsies.

The mosaic genome of warm-blooded vertebrates.

Abstract: Most of the nuclear genome of warm-blooded vertebrates is a mosaic of very long (much greater than 200 kilobases) DNA segments, the isochores; these isochores are fairly homogeneous in base composition and belong to a small number of major classes distinguished by differences in guanine-cytosine (GC) content. The families of DNA molecules derived from such classes can be separated and used to study the genome distribution of any sequence which can be probed. This approach has revealed (i) that the distribution of genes, integrated viral sequences, and interspersed repeats is highly nonuniform in the genome, and (ii) that the base composition and ratio of CpG to GpC in both coding and noncoding sequences, as well as codon usage, mainly depend on the GC content of the isochores harboring the sequences. The compositional compartmentalization of the genome of warm-blooded vertebrates is discussed with respect to its evolutionary origin, its causes, and its effects on chromosome structure and function.

Gene gating: a hypothesis

Abstract: It is assumed that the genome of a higher eukaryotic organism is organized into a number of distinct three-dimensional (3-D) structures, each characteristic for a given differentiated state. These discrete 3-D structures are envisioned to develop in a hierarchical and largely irreversible manner from an omnipotent 3-D structure of the zygotic genome. The information for these processes is assumed to reside in the genome. The nuclear pore complexes, the peripheral nuclear lamina, and components of the nuclear core are proposed to be among the topologically most proximal organelles that interpret this information and thereby serve in the maintenance and the alteration of the 3-D structure of the genome during development, differentiation, and the cell cycle. The nuclear pore complexes are envisioned to serve as gene-gating organelles capable on interacting specifically with expanded (transcribable) portions of the genome. Their nonrandom distribution on the nuclear surface would reflect the underlying periodic organization of the genome into expanded and compacted domains, alternating with each other. All transcripts of a given gated gene would leave the nucleus by way of that pore complex to which the gene is gated. Implications for cell asymmetry and polarity are discussed and evolutionary considerations are presented.

The physical state of human papillomavirus type 16 DNA in benign and malignant genital tumours.

Abstract: Summary Cloned DNA from human papillomavirus (HPV) type 16 was subjected to restriction enzyme analysis. A genome size of 7.8 ± 0.1 kb was determined and restriction maps were prepared. Fragments of HPV 16 DNA were nick-translated and hybridized with fragments of HPV 6b DNA. The two genomes appeared to be colinear. The physical state of HPV 16 DNA in genital tumours was analysed. In each of six benign tumours the viral DNA was detected exclusively as 8 kb circles. In four malignant tumours the viral DNA appeared to be integrated within the host genome but one cervical carcinoma and one case of Bowen's disease also contained oligomeric episomal molecules of viral DNA. One cervical carcinoma (WV 2965), containing only integrated viral DNA, was examined in detail. HPV 16 DNA was integrated as head-to-tail tandem repeats at more than one site. Three virus/cell junction fragments from this tumour were cloned. Two contained lengths of repetitive cellular DNA and one a length of apparently single copy cellular DNA.

Complete nucleotide sequence of the genome of bovine leukemia virus: its evolutionary relationship to other retroviruses.

Abstract: We report the complete 8714-nucleotide sequence of the integrated bovine leukemia virus genome and deduce the following genomic organization: 5' LTR-gag-pol-env-pXBL-3' LTR, where LTR represents a long terminal repeat and pXBL represents a region containing unidentified open reading frames. This genomic structure is similar to that of human T-cell leukemia virus. The LTR contains a putative splice donor site in the R region. The gag gene encodes a precursor protein with the form NH2-p15-p24-p12-COOH. The NH2- and COOH-terminal regions of the pol product show stronger homologies with those of avian, rather than murine, type C retrovirus, and its structure is identical to that of avian virus. The env gene encodes a surface glycoprotein (gp51) and a transmembrane protein (gp30). In contrast to the pol product, the gp30 shows stronger sequence homology with a murine, rather than avian homologue, indicating the chimeric nature of the bovine leukemia virus genome. Comparisons of the best conserved pol sequences and overall genomic organizations between several major oncoviruses allow us to propose that bovine leukemia and human T-cell leukemia viruses constitute a group, designated as type "E," of Oncovirinae.

The Evolution of genome size

Abstract: Genes consist of DNA, and their main function is to code for proteins. Therefore one might expect that the amount of DNA per cell would depend mainly on the number of different proteins an organism makes during its life: highly complex organisms with lots of different genes should have much more DNA than simple ones. But in eukaryotes measurements of the amount of DNA per haploid nucleus (an organism's 'genome size' or 'C-value') show no such simple pattern. The fact that some very simple unicellular organisms have huge amounts of DNA per genome, whereas some highly complex multicellular ones have many times less therefore poses a fundamental biological problem known as the 'C-value paradox'. Do the massive amounts of 'extra' DNA in organisms like some salamanders and lilies that have exceptionally large genomes have some function? If so what? Or is the extra DNA merely useless junk or a 'selfish' parasite ('selfish DNA') of the cells replication machinery? This book discusses both the evolutionary causes and the molecular mechanisms of changes in genome size. It emphasises the universal positive correlation between genome size and cell volume, and discusses both natural and experimentally induced changes in genome size.

Dissection of Mycobacterium tuberculosis antigens using recombinant DNA

Abstract: A recombinant DNA strategy has been used systematically to survey the Mycobacterium tuberculosis genome for sequences that encode specific antigens detected by monoclonal antibodies. M. tuberculosis genomic DNA fragments with randomly generated endpoints were used to construct a large lambda gt11 recombinant DNA expression library. Sufficient numbers of recombinants were produced to contain inserts whose endpoints occur at nearly every base pair in the pathogen genome. Protein antigens specified by linear segments of pathogen DNA and produced by the recombinant phage of Escherichia coli were screened with monoclonal antibody probes. This approach was coupled with an improved detection method for gene isolation using antibodies to clonally isolate DNA sequences that specify polypeptide components of M. tuberculosis. The methodology described here, which is applicable to other pathogens, offers possibilities for the development of more sensitive and specific immunodiagnostic and seroepidemiological tests for tuberculosis and, ultimately, for the development of more effective vaccines.

Genetics, cytology and evolution of Gossypium.

Abstract: Publisher Summary This chapter presents a comprehensive review of the published information on the cytology, genetics, and evolution of Gossypium . In addition, it presents recent data and information on genome organization with which a hypothesis is proposed for the origin of the allotetraploid species that is different from that generally assumed. The genus Gossypium consists of 35 diploid species that are divided into seven genome groups and six allotetraploid species, each with the same two subgenomes. The genome relationships are also discussed in the chapter. Moreover, with the advent of the new technology of genetic engineering and its potential for improving the commercial cottons by inter- and intra- genomic transfer of desirable genetic segments, the basic genetic analyses should have even greater application in the future. The successful application of genetic engineering is greatly enhanced by the availability of fundamental knowledge of the genetic organization of the chromosomes gained through the classical genetic and cytogenetic approaches. Thus, to utilize the full potential of the new technology, it is of utmost importance that the classical approaches to the genetic analysis of the chromosomes of cotton be augmented.

Mitochondrial protein synthesis is required for maintenance of intact mitochondrial genomes in Saccharomyces cerevisiae.

Abstract: The genes of Saccharomyces cerevisiae coding for the mitochondrial threonine and tryptophan tRNA synthetases and for a putative mitochondrial ribosomal protein have been cloned. These, and the previously cloned gene for a mitochondrial elongation factor, were used to disrupt or partially delete the wild-type chromosomal copies of the genes in the respiratory-competent strain W303. In each case, inactivation of a gene whose product is required for mitochondrial protein synthesis causes an instability in mitochondrial DNA. Although intact mitochondrial genomes are rapidly and quantitatively eliminated in the protein synthesis defective strains, specific rho- genomes can be maintained stably over many generations. These results indicate that mitochondrial protein synthesis is required for the propagation of wild-type mitochondrial DNA in yeast.

An estimate of unique DNA sequence heterozygosity in the human genome.

Abstract: Fifteen different restriction fragment length polymorphisms (RFLPs) were detected in the human genome using 19 cloned DNA segments, derived from flow-sorted metaphase chromosomes or total genomic DNA, as hybridization probes. Since these clones were selected at random with respect to their coding potential, their analysis permitted an unbiassed estimate of single-copy DNA sequence heterozygosity in the human genome. Since our estimate (h=0.0037) is an order of magnitude higher than previous estimates derived from protein data, most of the polymorphic variation present in the genome must occur in non-coding sequences. In addition, it was confirmed that enzymes containing the dinucleotide CpG in their recognition sequence detect more polymorphic variation than those that do not contain CpG.

Effects of genomic position on the expression of transduced copies of the white gene of Drosophila.

Abstract: The white gene of Drosophila is expressed normally when introduced at many different sites in the genome by P-element-mediated DNA transformation, but is expressed abnormally when inserted at two particular genomic positions It is now demonstrated that the mutant expression in these two cases is caused by the surrounding chromosomal region into which the white gene has been inserted The white gene could be moved from these two positions, where it confers a mutant phenotype, to other positions in the genome where it confers a wild-type phenotype However, flies in which white has been moved to one new location have an unusual mosaic phenotype

Rapid Genomic Change in Higher Plants

Abstract: INTR ODUCTI ON 367 EXAMPLES OF RAPID OR PR OGRAMMED GENOMIC CHANGE 368 Chromosome Rearrangements 368 Chromosome Imprint ing 370 Gene Ampli ficat ion and Loss 370 Transposable Elements 372 LIFE HIST ORY DIFFERENCES BE TWEEN HIGHER PLANTS AND ANIMALS.... 374 PHENO TYPIC AND GENO TYPIC PLASTICITY IN HIGHER PLANTS 377 Plastid Genome ...... 377 Mitochondrial Genome 378 Nuclear Genome 380 C ONCLUDING REMARKS 391

DNA polymorphism and molecular pathology of the human globin gene clusters

Abstract: In the past few years there has been intensive study of the human globin genes. This study has provided important insights into normal gene structure and function and the nature of molecular defects leading to a set of inherited diseases. In turn, this information forms the basis for rational design of specific tests for prenatal diagnosis of particular forms of β-gene cluster in which recombination appears to be more frequent than in areas surrounding it. This will provide new insights into the evolution of a segment of the genome and aid in explaining how particular mutations are dispersed to numerous chromosome types. Second, study of additional β-thalassemia genes from human populations not previously studied will provide new gene defects, some of which may yield further clues about RNA transcription and processing. In addition, some (e.g., the coding region substitutions that affect RNA processing) may allow identification of new mechanisms of gene dysfunction. Third, we need further refinement of prenatal diagnostic tests so that early, accurate, and simplified assessment of pregnancies at risk can be accomplished widely, particularly in those geographic regions where β-thalassemia is especially prevalent.

Genomic diversity of the acquired immune deficiency syndrome virus HTLV-III: different viruses exhibit greatest divergence in their envelope genes

Abstract: Converging lines of research have linked human T-cell lymphotropic virus type III (HTLV-III) to the pathogenesis of the acquired immune deficiency syndrome. A characteristic feature of this virus is its genomic heterogeneity, which occurs to varying degrees in different viral isolates. To define further the nature and extent of these genomic changes, we compared the molecularly cloned genomes of two variant HTLV-III isolates by extensive restriction enzyme mapping and heteroduplex thermal melt analysis. Both viral isolates were found to be highly related to each other throughout their entire genomic complement, yet they differed markedly in their restriction enzyme maps. Electron microscopic heteroduplex analysis revealed several distinct regions of divergence located almost exclusively in the part of the genome that encodes the viral envelope gene. In vitro culture of one of these viruses over a period of 3 months did not result in any genomic changes as determined by restriction analysis of viral DNA. These results, as well as the recently published nucleotide sequences of other HTLV-III isolates, indicate that the most substantial variation among HTLV-III isolates is located in the envelope. These findings raise the possibility that viral isolates from different individuals could have important biological differences in their envelope antigens, a consideration relevant to ongoing attempts to develop a vaccine against HTLV-III.

Molecular cloning of the a1 locus of Zea mays using the transposable elements En and Mu1

Abstract: The a1 locus of Zea mays has been cloned using transposable elements as gene tags. The strategy was to make genomic libraries from maize stocks with a1 mutations induced either by En(Spm) or by Robertson's Mutator-system. These libraries were then screened with either Spm-I8 and En1, for the En-containing mutant, or with Mu1 for the Mu-induced mutation. There are many En and Mu1 hybridizing sequences present in the maize genome, however, by a process of cross-screening of the positives from the two libraries and by molecular analysis of the En-positive clones it was possible to identify clones in both libraries carrying all or part of the a1 gene.

Chloroplast dna variation and evolution in pisum: patterns of change and phylogenetic analysis

Abstract: Variation in 30 chloroplast DNAs, representing 22 wild and cultivated accessions in the genus Pisum, was analyzed by comparing fragment patterns produced by 16 restriction endonucleases. Three types of mutations were detected. First, an inversion of between 2.2 kilobase pairs (kb) and 5.2 kb distinguished a population of P. humile from all other Pisum accessions examined. Second, deletions and insertions of between 50 and 1200 base pairs produced small restriction fragment length variations in four regions of the 120-kb chloroplast genome. Two of these regions—one of which is located within the sequence that is inverted in P. humile—showed a high degree of size polymorphism, to the extent that size differences were detected between individuals from the same accession. Finally, a total of only 11 restriction site mutations were detected among the 165 restriction sites sampled in the 30 DNAs. Based on these results and previous data, we conclude that the chloroplast genome is evolving very slowly relative to nuclear and mitochondrial DNAs. The Pisum chloroplast DNA restriction site mutations define two major lineages: One includes all tested accessions of P. fulvum, which is known to be cytogenetically quite distinct from all other Pisum taxa. The second includes 12 of 13 cultivated lines of the garden pea (P. sativum) and a wild population of P. humile from northern Israel. These observations strongly reinforce an earlier conclusion that the cultivated pea was domesticated primarily from northern populations of P. humile. A 13th P. sativum cultivar has a chloroplast genome that is significantly different from those of the aforementioned lines and somewhat more similar to those of P. elatius and southern populations of P. humile. This observation indicates that secondary hybridization may have occurred during the domestication of the garden pea.

A Drosophila Minute gene encodes a ribosomal protein.

Abstract: Minute genes have long constituted a special problem in Drosophila genetics. For at least 50-60 different genes scattered throughout the genome, dominant mutations and/or deficiencies have been recognized which result in a common phenotype consisting of short thin bristles, slow development, reduced viability, rough eyes, small body size and etched tergites. Schultz proposed that the Minute loci encode similar but separate functions involved in growth and division common to all cells. Atwood and Ritossa suggested that Minute loci encode components of the protein synthetic machinery, specifically the transfer RNA genes; this now seems unlikely on grounds of both mapping and mutability studies. More recently, we and others suggested that the Minute loci are ribosomal protein genes. We report here that transformation with a cloned 3.3-kilobase (kb) region containing the gene encoding the large subunit ribosomal protein 49 (rp49) suppresses the dominant phenotypes of Minute (3)99D, a previously undescribed Minute associated with a chromosomal deficiency of the 99D interval. This activity is specific to the 99D Minute as it does not suppress other Minute loci elsewhere in the genome. This result provides direct evidence that the Minute locus at the 99D interval encodes the ribosomal protein 49.

Primary structure and gene organization of human hepatitis A virus.

Abstract: The RNA genome of human hepatitis A virus (HAV) was molecularly cloned. Recombinant DNA clones representing the entire HAV RNA were used to determine the primary structure of the viral genome. The length of the viral genome is 7478 nucleotides. An open reading frame starting at nucleotide 734 and terminating at nucleotide 7415 encodes a polyprotein of Mr 251,940. Comparison of the HAV nucleotide sequence with that of other picornaviruses has failed to reveal detectable areas of homology. However, a computer analysis of the putative amino acid sequence of HAV and poliovirus demonstrated the existence of short areas of homology in virion protein 3 (VP3) and throughout the carboxyl-terminal portion of the polyproteins. In addition, extensive protein structural homologies with poliovirus were detected.

Human gamma-chain genes are rearranged in leukaemic T cells and map to the short arm of chromosome 7.

Abstract: Three gene families that rearrange during the somatic development of T cells have been identified in the murine genome. Two of these gene families (alpha and beta) encode subunits of the antigen-specific T-cell receptor and are also present in the human genome. The third gene family, designated here as the gamma-chain gene family, is rearranged in murine cytolytic T cells but not in most helper T cells. Here we present evidence that the human genome also contains gamma-chain genes that undergo somatic rearrangement in leukaemia-derived T cells. Murine gamma-chain genes appear to be encoded in gene segments that are analogous to the immunoglobulin gene variable, constant and joining segments. There are two closely related constant-region gene segments in the human genome. One of the constant-region genes is deleted in all three T-cell leukaemias that we have studied. The two constant-region gamma-chain genes reside on the short arm of chromosome 7 (7p15); this region is involved in chromosomal rearrangements identified in T cells from individuals with the immunodeficiency syndrome ataxia telangiectasia and observed only rarely in routine cytogenetic analyses of normal individuals. This region is also a secondary site of beta-chain gene hybridization.

Tissue-specific expression of rat myosin light-chain 2 gene in transgenic mice

Abstract: One approach to determining how the differential expression of specific genes is regulated in higher organisms is to introduce cloned copies of the genes (or parts of the genes) into the genomes of individual organisms from the very beginning of their development. The way in which the exogenous genetic information behaves during the development of the experimental organisms can then provide a means of defining the DNA sequences that restrict the expression of the gene to specific cell types and times of development. So far, several different genes have been introduced into the genomes of mice1–15, but in only a few cases have the exogenous genes retained the tissue specificity of expression of the equivalent endogenous genes12,14,15. I report here that in two out of three ‘transgenic’ mice carrying copies of the rat gene for skeletal muscle myosin light chain 2, the exogenous gene is expressed specifically in skeletal muscle cells. The sequences contained in the cloned copy of the myosin light-chain 2 gene used in these experiments are thus sufficient to confer a tissue-specific pattern of expression.