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At least 181 records · Page 10Linked to original sources
PubMed1985

Inheritance of extrachromosomal ribosomal DNA during the asexual life cycle of Dictyostelium discoideum: examination by use of DNA polymorphisms.

Wild-type isolates of Dictyostelium discoideum exhibited differences in the size of restriction fragments of the extrachromosomal 88-kilobase ribosomal DNA (rDNA) palindrome. Polymorphisms in rDNA also were found among strains derived solely from the NC4 wild-type isolate. These variations involved EcoRI fragments II, III, and V; they included loss of the EcoRI site separating fragments II and V and deletion and insertion of DNA. More than one rDNA form can coexist in the same diploid or haploid cell. However, one or another parental rDNA tended to predominate in diploids constructed, using the parasexual cycle, between haploid NC4-derived strains and haploid wild-type isolates. In some cases, most if not all of the rDNA of such diploids were of one form after ca. 50 generations of growth. Segregant haploids, derived from diploids that possessed predominantly a single rDNA allele, possessed the same allele as the diploid and did not recover the other form. This evidence implies that replication does not proceed from a single chromosomal or extrachromosomal copy of the rDNA during the asexual life cycle of D. discoideum.

Alleles↗
PubMed1981

Mouse cells transformed by bovine papillomavirus contain only extrachromosomal viral DNA sequences.

The viral DNA sequences in mouse C127 cells transformed by bovine papillomavirus type 1 (BPV-1) virions, by full-length linear BPV-1 DNA, or by a defined transforming subgenomic DNA segment of BPV-1 were examined by reassociation kinetics and blot hybridization. In all cases, the transformed cells contained multiple copies of BPV-1 DNA, present exclusively as supercoiled or nicked circular extrachromosomal molecules or as a slowly migrating complex of circular viral DNA molecules. In the transformed cell lines established from cells transfected with full-length linear BPV-1 DNA, there was recircularization of the input DNA which in some cases resulted in the loss of the restriction site used in the linearization of the DNA. In the transformed cell lines established with the defined subgenomic segment there was circularization of the DNA accompanied by the acquisition of new sequences or duplication and rearrangement of the BPV-1 sequences. In contrast to other well-studied virus transformation systems, no integration of the BPV-1 genome into the host chromosome could be detected under conditions sensitive enough to detect 0.1-0.2 viral genome equivalent. It was concluded that maintenance of transformation may be mediated by nonintegrated viral DNA.

Animals↗
PubMed1986

Gene reorganization during serial divisions of normal human cells.

We have followed during serial divisions of human fibroblasts the presence in chromosomal and extrachromosomal DNA, of two genes that are expressed in fibroblasts, actin and interferon, and of one that is not expressed, globin. The intensity of the blot hybridization of the actin and globin probes with chromosomal DNA diminished during serial divisions of diploid fibroblasts. The interferon gene remained constant throughout the human fibroblast life span. Chromosomal DNA sequences were present in extrachromosomal circular DNA which appeared at the end of the fibroblast life span. The results could explain some functional changes that occur in these cell populations when their division potential declines.

Actins↗
PubMed1992

Preferential usage of JH2 in D-J joinings with DQ52 is determined by the primary DNA sequence and is largely dependent on recombination signal sequences.

Rearrangement of DQ52 with JH in IgH genes takes place in a large part of lymphocytes at a very early stage of differentiation although usage of DQ52 seems to be limited in the functional IgH genes of mature B cells. A possible and likely explanation for this, is secondary D-JH joinings occurring after the initial DQ52-JH joinings, which becomes possible only when DQ52 segments join 5'-located JH segments. Previously we reported the non-random use of JH in joinings with DQ52, in which DQ52-JH2 joinings are dominant. We questioned how the preferential usage of JH2 in DQ52-JH joinings is determined by utilizing extrachromosomal DNA substrates. Extrachromosomal DNA substrates with a combination of DQ52 and multiple JH segments were prepared. These plasmids with a polyoma-derived replication system were transfected into pre-B cell lines and recombination profiles of recovered plasmids were analyzed semi-quantitatively. Experiments with plasmids containing all four JH segments in normal configuration showed an apparent high frequency of JH2 usage, similar to the rearrangement previously observed in thymocyte genomes. In plasmids containing two JH segments, when one was JH2, it was rearranged more frequently than the other, independent of its proximity to DQ52. The JH3 with recombination signal sequences (RSS) substituted for JH2 was rearranged more frequently than the naive JH2 itself indicating the importance of RSS. A JH3 hybrid with the 200 bp upstream sequence of JH2 but excluding RSS, however, failed to increase JH3 use. The addition of one nucleotide to the 22-bp spacer of JH1 RSS increased the frequency of JH1 usage. These observations suggest that the preferential usage of JH2 is determined by the primary DNA sequence and is largely dependent on RSS.

Animals↗
PubMed1988

Epigenetic control and reintegration of extrachromosomal proviral DNA in HL60 cells chronically infected with human T cell leukaemia virus type 1.

Extrachromosomal human T cell leukaemia virus type 1 (HTLV-I) proviruses are persistently maintained in HTLV-I-infected human promyelocytic leukaemia (HL60) cells even 24 months after viral infection. By successive recloning of these HTLV-I-infected clones, and by Southern blot analysis of their HTLV-I proviruses, we concluded the following. The copy number of extrachromosomal proviruses fluctuated, and this fluctuation was probably dependent on the epigenetic conditions in the host cell, HL60. The transient appearance of a high copy number of extrachromosomal proviruses was followed by an increase in the copy number of integrated proviruses. Persistence of extrachromosomal proviruses appeared to be caused by an intracellular rather than an intercellular mechanism.

DNA, Viral↗
PubMed1983

Benzo[a]pyrene induction of extrachromosomal viral DNA synthesis in rat cells transformed by polyoma virus.

The effect of the carcinogen benzo[a]pyrene (BP) on the production of specific extrachromosomal DNAs has been studied in transformed rat cells containing integrated polyoma virus DNA. Exposure of cells previously transformed by the polyoma virus mutant ts-a, which codes for a temperature sensitive T antigen, to a non-toxic dose of BP (0.25 micrograms/ml) enhanced the production of free polyoma DNA at the population level. This occurred at 33 degrees C (the permissive temperature) but not at 39 degrees C, indicating that the BP effect was dependent on the function of the T antigen of polyoma virus. In the same cell system, BP did not induce the production of extrachromosomal copies of two endogenous rat retrovirus genomes, the 30S RNA virus and rat leukemia virus. Thus, the effects on integrated polyoma DNA are quite specific and do not reflect a generalized increase in asynchronous DNA replication and excision. Further studies utilizing a carcinogenic metabolite of BP, benzo[a]pyrene trans-7,8-dihydrodiol-9,10-epoxide (anti) (BPDE), on a rat cell line transformed by wild type (WT) polyoma virus demonstrate that the enhancement of polyoma DNA synthesis persists for at least 5 days after a single exposure to BPDE, despite the rapid decay of this compound. In addition, enhanced synthesis of polyoma DNA can be induced by fusion of normal rat fibroblasts previously exposed to BPDE with polyoma transformed rat fibroblasts not exposed to BPDE. It appears, therefore, that the effects we have observed are not due solely to direct carcinogen damage at the level of the integrated polyoma virus DNA, but may instead involve the induction of cellular factor(s) that act indirectly to enhance asynchronous replication of polyoma DNA.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1992

Extrachromosomal ribosomal DNA of Didymium iridis: sequence analysis of the large subunit ribosomal RNA gene and sub-telomeric region.

The ribosomal DNA of the myxomycete Didymium iridis is organized as extrachromosomal linear molecules of about 20 kb, containing only one transcription unit of the ribosomal RNA genes. We have determined the sequence of the large subunit ribosomal RNA (LSU rRNA) gene as well as the sub-telomeric and telomeric regions. The LSU rRNA gene was found to encode a 3857 nucleotide-long LSU rRNA, interrupted by a transcribed spacer and two group I introns. A complete secondary structure model of D. iridis LSU rRNA has been constructed. The compact sub-telomeric region of D. iridis rDNA was found to contain several directly repeated sequence elements that include the simple telomere motif TTAGGG. Based on pairwise comparisons of LSU rRNA sequences, the time of divergence between the two myxomycete genera Didymium and Physarum was estimated.

Animals↗
PubMed1992

Isolation of telomerelike sequences from Cryptococcus neoformans and their use in high-efficiency transformation.

Development of a transformation system for the fungal human pathogen Cryptococcus neoformans is an important prerequisite for the identification of genes involved in virulence. It has previously been reported that low-efficiency transformation can be achieved by using the cloned C. neoformans URA5 gene and ura5 mutants. The introduction of linearized URA5 vectors into C. neoformans resulted in unstable transformants which apparently harbored linear extrachromosomal DNA molecules. In this paper, the nature of these molecules is confirmed to be linear by exonuclease digestion. Recovery of the extrachromosomal DNA in Escherichia coli and sequence analysis demonstrates that repeats characteristic of telomeric DNA have been added to the ends of the introduced DNA. The recovered plasmids are capable of transforming at much higher efficiencies either in the supercoiled state (up to 200 transformants per microgram) or the linear state (up to 90,000 transformants per microgram).

Base Sequence↗
PubMed1979

Restriction endonuclease mapping of unintegrated proviral DNA of Snyder-Theilen feline sarcoma virus: localization of sarcoma-specific sequences.

Extrachromosomal DNA purified from mink cells acutely infected with the Snyder-Theilen strain of feline sarcoma virus (FeSV) was digested with restriction endonucleases, and the DNA fragments were electrophoretically separated, transferred to a solid substrate, and hybridized with radiolabeled DNA transcripts complementary to different portions of the FeSV RNA genome. Major DNA species 8.4 and 5.0 kilobase pairs (kbp) long represent the linear, unintegrated proviruses of Snyder-Theilen feline leukemia virus and FeSV, respectively. Transfection experiments performed with electroeluted DNAs showed that the 8.4-kbp form led to the production of replicating nontransforming virus in mink and cat cells; in contrast, the 5.0-kbp DNA produced helper virus-independent foci of transformation in mouse NIH/3T3 cells and helper virus-dependent foci in mink cells at an efficiency comparable to that obtained with unfractionated extrachromosomal DNA. Sites of restriction endonuclease cleavage for six enzymes were oriented with respect to one another within the FeSV provirus. EcoRI recognized cleavage sites at 0.3 to 0.4 kbp from each terminus of FeSV DNA, reducing the 5.0-kbp DNA to molecules 4.3 kbp long; this enzyme excised a large internal proviral DNA fragment of corresponding size from the DNA of FeSV-transformed mink nonproducer cells. By using DNA transcripts complementary to different portions of the FeSV genome, sarcoma-specific sequences (the FeSV src gene) were positioned within 2.1 and 3.4 kbp from the 5' end of the proviral DNA with respect to the viral RNA genome. The src gene is flanked at both ends by sequences shared in common with feline leukemia virus. The localization of src sequences to this region suggests that a portion of an FeSV polyprotein which contains feline oncornavirus-associated cell membrane antigen (FOCMA-S) is the major product of this gene.

Animals↗
PubMed1991

Tunicamycin-resistant variants from five species of Leishmania contain amplified DNA in extrachromosomal circles of different sizes with a transcriptionally active homologous region.

Twelve independent variants were selected from five species of Leishmania for resistance to tunicamycin by exposure of cultured promastigotes to increasing concentrations of this antibiotic, an inhibitor of the microsomal N-acetylglucosamine-1-phosphate transferase in the dolichol pathway of N-glycosylation. All variants obtained from all species, as found previously with Leishmania amazonensis, contain amplified chromosomal DNA exclusively as extrachromosomal circles. These circular amplicons hybridize with amplified DNAs cloned previously from tunicamycin-resistant Leishmania amazonensis, but not with those from Leishmania resistant to other drugs. The amplicons from tunicamycin-resistant cells vary with different species in size from 30 to 70 kb, but all share a homologous region of 20 kb. Multiple independent transcripts are overexpressed from this region. Elevation of the microsomal glycosyltransferase activity is demonstrated in these variants from representative species. The results thus provide further evidence that this enzyme is overexpressed due to amplification of the gene in these cells. The consistent observation of this event in all cases studied also suggests that this is the predominant, if not the only mechanism of tunicamycin resistance in Leishmania.

Animals↗
PubMed1989

DNA restriction patterns and DNA-DNA solution hybridization studies of Frankia isolates from Myrica pennsylvanica (bayberry).

Sixteen Frankia strains were isolated from Myrica pennsylvanica (bayberry) root nodules collected at diverse sites in New Jersey. Restriction pattern analysis of total genomic DNA was used to group the isolates into gel groups, and the genetic relatedness among the isolates was evaluated by DNA-DNA solution hybridization studies. Restriction pattern analysis provided a distinctive reproducible fingerprint for each isolate. Isolates fell into nine separate groups (strain types). More than one strain type was isolated from most sites. Isolates from two different gel groups were found in 3 of 10 nodules examined. Of the 16 isolates, 10 contained extrachromosomal DNA. Six different extrachromosomal DNA banding patterns were found. Genomically similar isolates carried related, but different, banding patterns. DNA hybridization studies indicated that isolates from a single plant species can be minimally related as determined by total genome homology. Homology ranged from 12 to 99%. Highly divergent strains were isolated from the same plant and found to cohabit the same nodule. Thus, this study demonstrated that Frankia strains which infect the same host plant are not only phenotypically different but also genetically diverse.

Actinomycetales↗
PubMed2026

Hypertranscription caused by p53 deficiency triggers nucleotide insufficiency that induces replication stress and genomic instability.

p53 plays a central role in the DNA damage response, inducing repair, cell-cycle arrest or apoptosis. Its loss is associated with replication stress and genomic instability. While several underlying mechanisms were suggested, the primary triggers of catastrophic genomic events like chromothripsis, a known driver of tumorigenesis linked with p53 loss, are still unclear. Using p53-depleted epithelial cells and fibroblasts, as well as patient-derived fibroblasts with germline p53 variants that spontaneously undergo chromothripsis, we found that p53 loss causes hypertranscription and increased nucleotide consumption. The resulting nucleotide shortage induces replication stress, causing telomere dysfunction, micronuclei formation, and chromothripsis. These effects were rescued by nucleoside supplementation or normalization of transcription levels, demonstrating a causal link between transcriptional activity, nucleotide availability, and genome stability. Emerging chromothriptic clones displayed restored DNA replication, telomere stabilization, and extrachromosomal DNA, suggesting key features that support clonal selection. We identify nucleotide pool homeostasis as a critical p53 function that suppresses replication stress, prevents chromothripsis, and protects against early tumorigenesis.

Genomic Instability↗
PubMed1996

Selective capture of acentric fragments by micronuclei provides a rapid method for purifying extrachromosomally amplified DNA.

The amplification and overexpression of a number of oncogenes is strongly associated with the progression of a variety of different cancers. We now present a strategy to purify amplified DNA on double minute chromosomes (DMs) to enable analysis of their prevalence and contribution to tumourigenesis. Using cell lines derived from four different tumour types, we have developed a general and rapid method to purify micronuclei that are known to entrap extrachromosomal elements. The isolated DNA is highly enriched in DM sequences and can be used to prepare probes to localize the progenitor single copy chromosomal regions. The capture of DMs by micronuclei appears to be dependent on their lack of a centromere rather than their small size.

Cell Fractionation↗
PubMed1988

Extrachromosomal elements in the lower eukaryote Leishmania.

Extrachromosomal DNA elements have been identified in wild-type populations of the parasitic protozoan Leishmania. Elements from L. major and L. tropica were detected using orthogonal-field-alternation-gel electrophoresis. They are nonhomologous, supercoiled circular DNA molecules derived from different chromosomes in the Leishmania genome. Electron microscopy revealed that the elements have very similar physical properties; both are 80-kilobase supercoiled DNA molecules that contain large inverted repeat structures. The extrachromosomal DNAs are amplified in the Leishmania populations and show a fluctuation in copy number, from undetectable to around 20 copies per cell. After exposure of the L. tropica population to the drug methotrexate (MTX), a second amplified DNA was observed that is homologous to the extrachromosomal DNA found in L. major. Furthermore, wild-type Leishmania populations containing extrachromosomal DNA adapt more readily to MTX selection than populations with no amplified DNA. From these observations, there appears to be a relationship between the presence of extrachromosomal elements in wild-type Leishmania and the genesis and maintenance of MTX resistance in these organisms.

Animals↗
PubMed1972

Selective inhibition of nuclear DNA synthesis by 9- -D-arabinofuranosyl adenine in rat cells transformed by Rous sarcoma virus.

The drug, 9-beta-D-arabinofuranosyl adenine, selectively inhibits the synthesis of nuclear DNA without affecting extrachromosomal DNA synthesis in rat cells transformed by Rous sarcoma virus (B-mix K-44/6). The inhibition was linear with respect to drug concentration over the range of 37-600 muM. Mitosis and total synthesis of DNA per cell were also depressed. DNA synthesis was determined by measurement of [(3)H]thymidine incorporation into DNA. Covalently-closed circular DNA was extracted by the Hirt procedure and separated from residual chromosomal DNA by buoyant density gradient ultracentrifugation in CsCl-propidium diiodide. On the basis of buoyant density and sedimentation velocity centrifugation, the covalently-closed circular DNA formed in the presence of the drug was indistinguishable from that formed in its absence.

Adenine↗
PubMed2003

The papillomavirus E8-E2C protein represses DNA replication from extrachromosomal origins.

Carcinogenic DNA viruses such as high-risk human papillomaviruses (HPV) and Epstein-Barr-Virus (EBV) replicate during persistent infections as low-copy-number plasmids. EBV DNA replication is restricted by host cell replication licensing mechanisms. In contrast, copy number control of HPV genomes is not under cellular control but involves the viral sequence-specific DNA-binding E2 activator and E8-E2C repressor proteins. Analysis of HPV31 mutant genomes revealed that residues outside of the DNA-binding/dimerization domain of E8-E2C limit viral DNA replication, indicating that binding site competition or heterodimerization among E2 and E8-E2C proteins does not contribute to copy number control. Domain swap experiments demonstrated that the amino-terminal 21 amino acids of E8-E2C represent a novel, transferable DNA replication repressor domain, whose activity requires conserved lysine and tryptophan residues. Furthermore, E8-E2C (1-21)-GAL4 fusion proteins inhibited the replication of the plasmid origin of replication of EBV, suggesting that E8-E2C functions as a general replication repressor of extrachromosomal origins. This finding could be important for the development of novel therapies against persistent DNA tumor virus infections.

Base Sequence↗