Showing papers on "Genome published in 1982"
25 Apr 1982
TL;DR: The bovine 12 S and 16 S Ribosomal RNA genes, when compared with those from human mitochondrial DNA, show conserved features that are consistent with proposed secondary structure models for the ribosomal RNAs.
Abstract: We present here the complete 16,338 nucleotide DNA sequence of the bovine mitochondrial genome. This sequence is homologous to that of the human mitochondrial genome (Anderson et al., 1981) and the genes are organized in virtually identical fashion. The bovine mitochondrial protein genes are 63 to 79% homologous to their human counterparts, and most of the nucleotide differences occur in the third positions of codons. The minimum rate of base substitution that accounts for the nucleotide differences in the codon third positions is very high: at least 6 × 10−9 changes per position per year. The bovine and human mitochondrial transfer RNA genes exhibit more interspecies variation than do their cytoplasmic counterparts, with the “TΨC” loop being the most variable part of the molecule. The bovine 12 S and 16 S ribosomal RNA genes, when compared with those from human mitochondrial DNA, show conserved features that are consistent with proposed secondary structure models for the ribosomal RNAs. Unlike the pattern of moderate-to-high homology between the bovine and human mitochondrial DNAs found over most of the genome, the DNA sequence in the bovine D-loop region is only slightly homologous to the corresponding region in the human mitochondrial genome. This region is also quite variable in length, and accounts for the bulk of the size difference between the human and bovine mitochondrial DNAs.
1,407 citations
TL;DR: The distribution of other rare codons in the genes of the left arm suggests that they may have a controlling function on the relative amounts of the proteins produced, and the genome is fairly compact with comparatively little non-coding DNA.
1,099 citations
TL;DR: A huge number of stretches of dT-dG alternating sequence, a sequence that has been shown to adopt the Z-DNA conformation under some conditions, are found in eukaryotic genomes, indicating extraordinary evolutionary conservation.
Abstract: By Southern blotting and hybridization analysis using 32P-labeled poly(dT-dG) . poly(dC-dA) as a probe, we have found, in eukaryotic genomes, a huge number of stretches of dT-dG alternating sequence, a sequence that has been shown to adopt the Z-DNA conformation under some conditions. This sequence was found in all eukaryotic genomes examined from yeast to human, indicating extraordinary evolutionary conservation. The number of the sequence ranged from about 100 in yeast to tens of thousands in higher eukaryotes. Comparison of nucleotide sequences of dT-dG alternating regions and its flanking regions in several cloned genes showed that the repeated element [the Z(T-G) element]] consists only of dT-dG alternating sequence with variable length. The presence of another purine-pyrimidine alternating sequence was also surveyed in eukaryotic genomes by Southern blot hybridization using 32P-labeled poly(dG-dC) . poly(dG-dC) as the probe. The stretches of dC-dG alternating sequence [the Z(C-G) element] were found to be moderately repetitive in human, mouse, and salmon genomes. However, a few and no copies of the Z(C-G) element were found in yeast and calf genomes, respectively. These results provide evidence for the abundance of potential Z-DNA-forming sequences in nature.
731 citations
TL;DR: This chapter discusses the structure and organization of mammalian, highly repeated sequences at the molecular level with a description of tandemly repeated sequences, that are, satellites, and the segments that are interspersed among other genomic DNA sequences.
Abstract: Publisher Summary This chapter discusses the structure and organization of mammalian, highly repeated sequences at the molecular level. There is a description of tandemly repeated sequences, that are, satellites, and the segments that are interspersed among other genomic DNA sequences. The methods for the analysis of repeated DNA sequences are measurement of DNA renaturation kinetics and isopycnic centrifugation in gradients of CsCl and CsSO4. Eukaryote genomes can be divided into classes of DNA sequences according to the reiteration frequency. Many highly repeated sequences are in long tandem arrays. Some repetitive sequences are dispersed throughout major portions of genomes amid either other repeated sequences or sequences present only once per genome, that are, uniquesequences. The characteristic organizational feature of satellites and cryptic satellites is the tandem repetition of a unit DNA sequence. Satellite arrays resist separation by isopycnic centrifugation and instead remain within the main density fraction of genomic DNA. The repeat unit and its tandem organization can be revealed by restriction endonuclease digestion.
590 citations
TL;DR: Retroviruses have proved to be useful reagents for studying genetic and epigenetic changes in eukaryotic cells, and their capacity to establish a DNA (proviral) form of their RNA genomes as a stable component of host chromosomes, in either somatic or germinal cells.
Abstract: Retroviruses have proved to be useful reagents for studying genetic and epigenetic (such as regulatory) changes in eukaryotic cells, for assessing functional and structural relationships between transposable genetic elements, for inducing insertional mutations, including some important in oncogenesis, and for transporting genes into eukaryotic cells, either after natural transduction of putative cellular oncogenes or after experimental construction of recombinant viruses. Many of these properties of retroviruses depend on their capacity to establish a DNA (proviral) form of their RNA genomes as a stable component of host chromosomes, in either somatic or germinal cells.
555 citations
TL;DR: The findings suggest that the tandem repeat elements may interact with host-specific molecules and, furthermore, may constitute one of the elements determining the host range of these eukaryotic viruses.
Abstract: The simian virus (SV40) 72-base pair (bp) tandem repeated sequences have recently been shown to function as activators or enhancers of early viral transcription. A recombinant viral genome was recently constructed by inserting 72-bp tandem repeats from the Moloney murine sarcoma virus (MSV) in place of the 72-bp repeats of SV40. Although this genome replicates in monkey kidney cells, its rate of large tumor antigen expression and replication is considerably slower than that of wild-type SV40. In mouse cells, however, equivalent levels of large tumor antigen appear to be expressed from both wild-type and recombinant genomes, suggesting a relationship between the level of enhancer activity and the host cell. To confirm this observation, we have applied a sensitive quantitative assay for gene expression based on the conversion of chloramphenicol to its acetylated forms. The gene encoding the enzymatic function chloramphenicol acetyltransferase was inserted into two vectors in which the enhancer sequences from SV40 or MSV were placed adjacent to the early SV40 promoter. The SV40 tandem repeats appear to activate gene expression to significantly higher levels in monkey kidney cells, but the MSV repeats are more active in two lines of mouse cells. These findings suggest that the tandem repeat elements may interact with host-specific molecules and, furthermore, may constitute one of the elements determining the host range of these eukaryotic viruses.
471 citations
TL;DR: Polyadenylated RNAs of certain human tumour cell lines are shown to contain transcripts related to the cell-derived transforming onc genes of molecularly cloned primate, murine or avian transforming retrovirus genomes.
Abstract: Polyadenylated RNAs of certain human tumour cell lines are shown to contain transcripts related to the cell-derived transforming onc genes of molecularly cloned primate, murine or avian transforming retrovirus genomes. Thus, analogues of retroviral transforming genes are both present and frequently expressed in human neoplastic cells.
459 citations
TL;DR: Researchers have studied overlapping cosmids covering two separate regions of the genome, and the gene order in each of these regions was found to be γ–γ–ε–α, which implies an evolutionary duplication in this multigene family involving γ, ε and α genes.
Abstract: Cosmid clones containing the human γ, e and α heavy chain constant region genes and an e pseudogene have been isolated All these genes have a switch sequence detectable by hybridization We have studied overlapping cosmids covering two separate regions of the genome, and the gene order in each of these regions was found to be γ–γ–e–α This implies an evolutionary duplication in this multigene family involving γ, e and α genes
394 citations
TL;DR: There is a relatively stable arrangement of sequences in those genomes with the inverted repeat and a much more dynamic arrangement in those that have lost it, including the possibility that the invertedrepeat may play a direct role in maintaining a conserved arrangement of chloroplast DNA sequences.
394 citations
TL;DR: A 12-kilobase DNA sequence has been identified in the maize mitochondrial genome which is homologous to part of the inverted repeat of the maize chloroplast genome.
Abstract: A 12-kilobase DNA sequence has been identified in the maize mitochondrial genome which is homologous to part of the inverted repeat of the maize chloroplast genome. In chloroplasts the sequence contains a 16S rRNA gene, and also the coding sequences for tRNAIle and tRNAVal. Mitochondrial DNA from the male-sterile cytoplasms of maize is altered in this region.
356 citations
Patent•
08 Dec 1982
TL;DR: In this paper, the authors described methods for modifying the genome of vaccinia virus to produce vaccinia mutants, particularly by the introduction into the vaccinia genome of exogenous DNA; modified vaccinia prepared by such methods; certain DNA sequences and unmodified and genetically modified microorganisms involved as intermediates in such methods.
Abstract: What are disclosed are methods for modifying the genome of vaccinia virus to produce vaccinia mutants, particularly by the introduction into the vaccinia genome of exogenous DNA; modified vaccinia prepared by such methods; certain DNA sequences and unmodified and genetically modified microorganisms involved as intermediates in such methods; and methods for infecting cells and host animals with such vaccinia mutants to provoke the amplification of exogenous DNA and proteins encoded by the exogenous DNA, including antigenic proteins, by said cells and host animals.
TL;DR: A sequence comparison indicates the genomic organization of the bovine papillomavirus and that of the members of the simian virus 40-polyomvirus subgroup to be distinct, suggesting that these two groups of viruses are evolutionarily unrelated.
Abstract: The complete nucleotide sequence of the double-stranded circular DNA of bovine papillomavirus type 1 (BPV-1) was determined. Analysis of this sequence in conjunction with known transcriptional data for the virus provides a basis for determining the organization of the papillomavirus genome. All the major open reading frames are located on the same DNA strand. The region transcribed in BPV-transformed cells contains open frames in all three translational frames whereas the region transcribed in productively infected bovine fibropapillomas is characterized by two large open reading frames partitioned by a single translational stop codon. The localization of sequences diagnostic of promoters and polyadenylation sites suggests that splicing is involved in the biosynthesis of the viral mRNAs. A sequence comparison indicates the genomic organization of the bovine papillomavirus and that of the members of the simian virus 40-polyomavirus subgroup to be distinct, suggesting that these two groups of viruses are evolutionarily unrelated.
TL;DR: Restriction mapping experiments and heteroduplex analysis show that c-myc sequences of this locus are interrupted by one intron, suggesting that lambda-LMC-12 and -41 contain the complete functional c- myc gene.
Abstract: We have studied the genomic organization of human cellular sequences (c-myc) homologous to the transforming gene (v-myc) of avian myelocytomatosis virus (MC29). Southern blotting experiments using v-myc probes showed that several fragments of the human genome contain sequences related to the central part of v-myc but only few of them are homologous to the 3' portion of the viral gene. Several recombinant phages which represent different regions of the genome containing c-myc-related sequences were isolated from a human DNA library. Two clones (lambda-LMC-12 and -41) overlap over approximately 17 kilobases of DNA where a sequence homologous to that of the entire v-myc is present. Restriction mapping experiments and heteroduplex analysis show that c-myc sequences of this locus are interrupted by one intron, suggesting that lambda-LMC-12 and -41 contain the complete functional c-myc gene. Three other clones (lambda-LMC-3, -4, and -26) do not overlap and contain sequences related to only approximately 0.3 kilobase of v-myc but lack 5' and 3' portions of the gene. These sequences are not interrupted by introns and are more divergent from v-myc than is the complete gene, suggesting that they may represent either pseudogenes or parts of distantly related genes.
TL;DR: The exons in c-myc may define two functional domains in the gene and may therefore facilitate the dissection of the different oncogenic potentials of the MC29 virus.
Abstract: The chicken genome contains nucleotide sequences homologous to transforming genes (oncogenes) of a number of avian retroviruses. We have isolated chicken DNA (c-myc) that is homologous to the oncogene (v-myc) of the avian myelocytomatosis virus MC29 and have compared the structures of the cellular and viral genes. Results from restriction endonuclease mapping of c-myc and from analysis of heteroduplexes between the DNAs of the cellular and viral genes show that c-myc is homologous to 1,500 nucleotides in v-myc DNA. This homologous region is interrupted in c-myc by an intron-like sequence of 1,100 nucleotides which is absent from v-myc. Nuclear RNA from normal chicken cells contains at least five species of transcripts from c-myc ranging from 2.5 to 6.5 kilobases in length. By contrast, cytoplasm contains only the 2.5-kilobase c-myc RNA. These features of the c-myc gene and its nuclear transcripts are characteristic of normal cellular genes and suggest that the myc gene is of cellular rather than viral origin. The exons in c-myc may define two functional domains in the gene and may therefore facilitate the dissection of the different oncogenic potentials of the MC29 virus.
TL;DR: A cluster of amino acid changes is located in the viral coat proteins, especially in the NH2-terminal half of the viral capsid protein VP1, which may imply that the mutations in the VP1 coding region contribute to attenuation.
Abstract: The complete nucleotide sequence of the genome of the type 1 poliovirus vaccine strain (LSc,2ab) was determined by using molecular cloning and rapid sequence analysis techniques. The restriction fragments of double-stranded cDNA synthesized from the vaccine strain RNA were inserted into the adequate sites of cloning vector pBR322. Sequence analysis of the cloned DNAs revealed that the virion RNA molecule was 7,441 nucleotides long and polyadenylylated at the 3' terminus. When the nucleotide sequence was compared with that of the genome of the virulent parental strain (Mahoney), 57 base substitutions were observed to be scattered all over the genome. Of these, 21 resulted in amino acid changes in a number of viral proteins. A cluster of amino acid changes is located in the viral coat proteins, especially in the NH2-terminal half of the viral capsid protein VP1. These results may imply that the mutations in the VP1 coding region contribute to attenuation.
TL;DR: The sequence of 15,441 nucleotides from the adenovirus-2 genome has been determined and includes the regions between coordinates 0-32% and 89-100%, as well as the two virus-associated RNAs and the leader sequences for the major late mRNAs.
TL;DR: Self-priming and de novo start replication models, which involve a site-specific nick in one DNA strand proximal to the 104 nucleotide loop, account for the observed sequence inversions and incomplete base-pairing.
TL;DR: Findings indicate that the c-erb loci are normal vertebrate genes rather than genes of cryptic endogenous retroviruses, and that they may have a role in the metabolism of normal cells.
TL;DR: The properties of B1 and B2 repeats suggest that they may represent a novel class of transposon-like elements in eukaryotic genome, and a possible role of B-type repeats in genome reorganization, DNA replication and pre-mRNA processing is discussed.
Abstract: Mouse genome contains two major families of short interspersed repeats in more than 10(5) copies scattered throughout the whole genome. They are referred to as B1 and B2 sequences since they were first isolated from the genome library by means of a dsRNA-B probe /1/. In this work, two copies of the B2 family were sequenced and compared with the previously sequenced B1 repeat /2/. A B2 ubiquitous repeat is ca. 190 bp long. The members of the family deviate in 3-5% of nucleotides from the consensus sequence. B2 contains regions of homology to the RNA polymerase III split promoter and to 4.5S snRNA I. Both B1 and B2 contain regions which resemble junctions between exons and introns. In contrast to B1, B2 does not contain apparent homologies to papova viral replication origins and a human Alu sequence. One side of the B2 repeat is represented by a very AT-rich sequence (ca. 30 bp long) followed with an oligo (dA) stretch 10-15 nucleotides long. This region of the repeat is the most variable one. The whole unit is flanked with 15-16 bp direct repeats different in sequenced copies of B2. The same is true of some copies of the B1 family. The properties of B1 and B2 repeats suggest that they may represent a novel class of transposon-like elements in eukaryotic genome. A possible role of B-type repeats in genome reorganization, DNA replication and pre-mRNA processing is discussed.
TL;DR: From the complete nucleotide sequence of the genome of the avian sarcoma virus Y73, predicted amino acid sequence of p90gag-yes, the product of the transforming gene, suggests that the cellular counterparts of the two (c-yes and c-src) originated from a common prototype sequence.
Abstract: From the complete nucleotide sequence of the genome of the avian sarcoma virus Y73, we have predicted amino acid sequence of p90gag-yes, the product of the transforming gene. Contrary to previous evidence from molecular hybridization studies, p90gag-yes was found to have much homology with the transforming gene product p60src of Rous sarcoma virus, suggesting that the cellular counterparts of the two (c-yes and c-src) originated from a common prototype sequence.
TL;DR: The nucleotide sequence of the genomic termini of the herpes simplex virus genome is determined and it is shown that insertion of either the free S terminus or the L terminus causes inversions in the viral genome.
TL;DR: A 72-bp repeat derived from the long terminal repeat (LTR) of cloned Moloney murine sarcoma virus (MSV) DNA can substitute functionally for the SV40 repeats and generate a viable virus in monkey kidney cells.
Abstract: The simian virus 40 (SV40) 72-base pair (bp) tandem-repeated sequences have a crucial role as an activator element in viral gene expression. We replaced the SV40 72-bp repeat with a 72-bp repeat derived from the long terminal repeat (LTR) of cloned Moloney murine sarcoma virus (MSV) DNA. Although there is no detectable sequence homology to SV40, the MSV repeats can substitute functionally for the SV40 repeats and generate a viable virus in monkey kidney cells.
TL;DR: The complete nucleotide sequence of human papillomavirus type 1a (7811 nucleotides) has been established and putative signals for regulation of gene expression, and homologies with the Alu family of human ubiquitous repeats and the SV40 72‐bp repeat are outlines.
Abstract: The complete nucleotide sequence of human papillomavirus type 1a (7811 nucleotides) has been established. The overall organization of the viral genome is different from that of other related papovaviruses (SV40, BKV, polyoma). Firstly, genetic information seems to be coded by one strand. Secondly, no significant homology is found with SV40 or polyoma coding sequence for either DNA or deducted protein sequences. The relatedness of human and bovine papillomaviruses is revealed by a conserved coding sequence in the two species. Two regions can be defined on the viral genome: the putative early region contains two large open reading frames of 1446 and 966 nucleotides, together with several split ones, and corresponds to the transforming part of the bovine papillomavirus type 1 genome, and the remaining sequences, which include two open reading frames likely to encode structural polypeptide(s). The DNA sequence is analysed and putative signals for regulation of gene expression, and homologies with the Alu family of human ubiquitous repeats and the SV40 72-bp repeat are outlines.
TL;DR: The distribution of VSG genes in the genome is analysed using probes for the sequences at the edges of the transposed segment which are partially homologous among these genes, and it is concluded that the VSGs genes are highly clustered and share common sequence at the borders of thetransposed segment.
Abstract: Trypanosoma brucei contains more than a hundred genes coding for the different variant surface glycoproteins (VSGs). Activation of some of these genes involves the duplication of the gene (the basic copy or BC) and transposition of the duplicate to an expression site (yielding the expression-linked copy or ELC). We have cloned large fragments of genomic DNA in cosmid vectors in Escherichia coli. Cosmids containing the BCs of genes 117, 118 and 121 were readily obtained, but DNA containing the ELCs was strongly selected against in the cosmid and plasmid cloning systems used. We have analysed the distribution of VSG genes in the genome using probes for the sequences at the edges of the transposed segment which are partially homologous among these genes. In genomic cosmid clone banks, about 9% of all colonies hybridize with probes from the 5'- and 3'-edges of the transposed segment, showing that these sequences are linked in the genome. Moreover, the 117 and 118 BC cosmids contain several additional putative VSG genes in tandem, as deduced from hybridization and sequence analyses. We conclude that the VSG genes are highly clustered and share common sequences at the borders of the transposed segment.
TL;DR: The study of T-DNA transmission from Agrobacterium Ti or Ri plasmid into the genomes of higher plant cells has revealed much about the consequences of transformation and it is now clear that the transformed phenotype is caused by hormonal changes produced directly or indirectly by T- DNA genes.
Abstract: The study of T-DNA transmission from Agrobacterium Ti or Ri plasmid into the genomes of higher plant cells has revealed much about the consequences of transformation. It is now clear that the transformed phenotype is caused by hormonal changes produced directly or indirectly by T-DNA genes. The opine synthases are enzymes encoded in T-DNA that function in the plant cell. Our level of understanding of T-DNA-encoded functions is already sufficient to reveal clear and feasible ways to exploit T-DNA as a gene vector. What remains to challenge the crown gall investigator are many questions of fundamental importance: What is the mechanism of the seemingly illegitimate recombination between T-DNA and plant DNA, and is this process catalyzed by bacterial or host plant enzymes, or both? Do T-DNA genes encode enzymes that catalyze biosynthesis of auxin- and cytokinin-active substances? What gene in T-DNA confers immunity to A. tumefaciens, and what is its mode of action? Does T-DNA insert into random or specific sites in the host plant genome? Did T-DNA derive from plant genetic information or has prokaryotic DNA arrived at functional eukaryotic gene structure by convergent evolution? Although there is keen interest in T-DNA as a vector for genetic engineering, it holds equal interest as a unique interface between the biology of prokaryotes and eukaryotes.
TL;DR: These experiments demonstrate directly the amplification of mitochondrial DNA in mammalian oocytes and are consistent with models which could generate mitochondrial DNA polymorphisms by unequal amplification of mitochondria genomes within an animal.
TL;DR: Mouse and human DNA used as in vitro-labeled "high-complexity" probes revealed hybridization between specific herpesvirus DNA fragments on Southern transfers and repetitive sequences present at 10(3) to 10(5) copies per mammalian cell genome.
TL;DR: A dispersed immunoglobulin pseudogene carries two hallmarks of RNA processing—spliced J and C regions and a poly (A)-rich tail and its discovery strengthens the notion that processed genes are a significant feature of the mammalian genome and that genetic information can return to the genome via an RNA intermediate.
Abstract: A dispersed immunoglobulin pseudogene carries two hallmarks of RNA processing—spliced J and C regions and a poly (A)-rich tail. Its discovery strengthens the notion that processed genes are a significant feature of the mammalian genome and that genetic information can return to the genome via an RNA intermediate.