PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Extrachromosomal circular DNAs”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources
PubMed1986

The termini of extrachromosomal linear copia elements.

Extrachromosomal linear copia elements were isolated and cloned from cultured Drosophila melanogaster cells. Four full length copia recombinants were characterised. Each contains a full sized copy of copia bounded by its direct repeats. The sequences of the ends of the copia inserts were determined. All of the termini are identical to those of genomic copias except for a single base deletion from one end of one clone. These results suggest that the priming for initiation of copia reverse transcription differs from normal retroviral models. Southern blot analysis of uncloned full length copia circles shows that approximately 50% correspond to the predicted circularisation product of such linears. We propose that this class of circles and the linear DNAs described here are precursors to integrated genomic copia elements.

Animals↗
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↗
PubMed2006

Formation of non-random extrachromosomal elements during development, differentiation and oncogenesis.

Extrachromosomal elements (EEs) were first discovered as minute chromatin bodies [Cox et al. Minute chromatin bodies in malignant tumors of childhood. Lancet 1965;62:55-8], and subsequently characterized as small circular DNA molecules physically separated from chromosomes. They include episomes, minichromosomes, small polydispersed DNAs or double minutes. This review focuses on eukaryotic EEs generated by genome rearrangements under physiological or pathological conditions. Some of those rearrangements occur randomly, but others are strictly non-random, highly regulated, and involve specific chromosomal locations (V(D)J-recombination, telomere maintenance mechanisms, c-myc deregulation). The multiple mechanisms of EEs formation are strongly interconnected and frequently linked to gene amplification. Identification of genes located on EEs will undoubtedly allow a better understanding of genome dynamics and oncogenic pathways.

Animals↗
PubMed1986

Mode of transmission of human T-cell leukemia virus type I (HTLV I) in a human promyelocytic leukemia HL60 cell.

HTLV-I propagated in IMR90 human diploid fibroblasts was transmitted to human myeloid leukemia HL60 cells at a low efficiency. After co-cultivation for 3 months, the viral genome was detected in 14/48 HL60 cell clones. Among the 14 HTLV-I-infected clones, 8 contained subgenomic fragments alone or in addition to the complete HTLV-I genome. The frequency of deleted proviruses (9/24 total proviruses) was unexpectedly high. Hirt's supernatant of some of the clones harboring complete HTLV-I genome(s) in the chromosome contained both linear and circular HTLV-I proviral DNAs. The circular DNAs were composed of one LTR and 2 LTR closed circular proviruses. These clones produced infectious HTLV-I constitutively, which was proved by transmission of the viral genome into fresh IMR90 cells by co-cultivation. However, in these clones, re-integration of extrachromosomal provirus into their own chromosomes was not observed.

Cell Line↗
PubMedDate not supplied

Amplification of inter-Alu extrachromosomal DNA during cellular ageing: retraction and explanation.

We reported previously the age-dependent appearance of extrachromosomal circular DNA bands hybridizing to a human DNA fragment ('inter-Alu'), isolated from a genomic cluster of AluI repeats. Such bands appeared or increased at late passage in four out of six human fibroblast strains (six out of nine cell expansions); moreover, all DNAs (9/9) obtained from peripheral lymphocytes of aged donors, but none (0/8) from young donors, revealed a non-genomic inter-Alu band at congruent to 4.8 kilobases (kb). Subsequent data extended these numbers to 16/24 aged donors compared with 0/18 young donors. These results were interpreted as evidence of age-dependent DNA rearrangement in normal human cells. We now report that the 'extra' bands were of microbial origin, although clearly occurring in an age-dependent manner.

Aged↗
PubMed1973

Influence of thymine starvation on the integrity of episomal and chromosomal deoxyribonucleic acids in Escherichia coli CR34 (lambda ind-).

The effect of thymine deprivation on the integrity of phage lambda, sex factor, and chromosomal deoxyribonucleic acid (DNA) in Escherichia coli CR34 (lambda ind(-)) was examined by sedimenting cell lysates through alkaline sucrose gradients. Both sex factor and chromosomal DNAs showed evidence of being degraded during the starvation period. In contrast, no loss of closed circular lambda DNA was observed.

Carbon Radioisotopes↗
PubMed1985

[Genetic transformation of somatic cells. III. An analysis of the status of the plasmid nucleotide sequences in the extrachromosomal DNA of transformant clone cells and the rescue of extrachromosomal molecules of the plasmid DNA].

Extrachromosomal DNAs from TK+ transformant clones of A238 Chinese hamster cells isolated after the treatment with plasmid pST826 containing thymidine kinase gene (TK-gene) of Herpes simplex virus (HSV1) and 1.8 kb insert of human satellite III DNA (HSIII) were studied by hybridization technique. In two TK+-clones (2T301 and 2T16) large quantities of rearranged plasmid DNA molecules were found. Electron microscopy show in clone 2T301 the presence of circular DNAs with average length being 4.64 +/- 0.27 kb. These molecules were rescued by retransformation into E. coli and analysed by restriction mapping and hybridization. All of them contain deletions spanning the entire TK gene of HSV1 and pBR325 sequences situated just downstream from the ORI of replication. The origin of extra-replicating circular DNA in 2T301 clone is discussed.

Animals↗
PubMed1996

HIV-1 protein expression from synthetic circles of DNA mimicking the extrachromosomal forms of viral DNA.

We have constructed circular forms of human immunodeficiency virus type 1 viral DNA in vitro that closely resemble the single and double long terminal repeat circular forms of unintegrated viral DNA formed in the nuclei of infected cells. We have analyzed viral protein expression after transient transfection of these circular DNAs into HeLa cells and compared it with expression from a transfected linearized plasmid containing an integrated provirus. Both circular forms are expressed, as judged by the appearance of extracellular p24, and expression is trans-activated by human immunodeficiency virus type 1 Tat. Viral p24 production, however, is approximately an order of magnitude lower than that obtained with transfected integrated viral DNA. Similar data were obtained when a luciferase reporter gene was substituted for the coding regions of the viral DNA. Positional effects of the transcriptional initiation and termination signals in the long terminal repeat appear to account for some of the low expression levels. These data suggest that unintegrated circular viral DNAs are transcriptionally active, although at low levels, and may contribute to overall viral replication in infected people under some conditions.

Base Sequence↗
PubMed1992

DNA methylation inhibits propagation of tomato golden mosaic virus DNA in transfected protoplasts.

The effects of methylation on plant viral DNA replication have been studied in Nicotiana tabacum protoplasts transfected with DNA of the geminivirus tomato golden mosaic virus (TGMV). The transfected cells were also used to determine whether experimentally introduced methylation patterns are maintained in extrachromosomal viral DNA. Replacement of cytosine residues with 5-methylcytosine (m5C) reduced the amount of viral DNA which accumulated in transfected protoplasts. The reduction was observed whether m5C residues were substituted for cytosine residues in vitro in either the viral strand or the complementary strand of double-stranded circular inoculum DNAs containing tandemly repeated copies of the A component of the TGMV genome. Both limited and extensive cytosine methylation of TGMV DNA sequences in vitro was not propagated in progeny viral DNA. The absence of detectable maintenance-type methylation of the transfecting TGMV DNA sequences may be related to the lack of methylation observed in double-stranded TGMV DNA isolated from infected plants.

Blotting, Southern↗
PubMed1995

Analysis of recombination junctions in extrachromosomal circular DNA obtained by in-gel competitive reassociation.

Essentially all eukaryotic cells contain circular extrachromosomal DNA as a result of excision from the chromosomes. To obtain insight into the nature of recombination associated with the occurrence of such DNA species and its biological significance, we analyzed a library enriched in recombination junctions which was constructed by a novel DNA subtraction technique; in-gel competitive reassociation (IGCR). Furthermore, we also introduced inverse PCR to characterize chromosomal DNA fragments containing the recombination junctions. At least 45% of the clones in the library constructed by the IGCR procedure comprised DNA with recombination junctions. Nucleotide sequence analysis of the recombination junctions indicated that three of four extrachromosomal DNAs thus analyzed were produced through recombination between sequences with a 3-5 bp homology in the chromosomes. One extrachromosomal DNA was apparently generated through non-homologous recombination, possibly by end-to-end joining. These results have demonstrated the usefulness of IGCR in concentrating recombination junctions, which provide the most direct evidence for the mechanism of the recombinational events involved, from highly complex genomes.

Base Sequence↗
PubMed1988

Amplified DNAs in laboratory stocks of Leishmania tarentolae: extrachromosomal circles structurally and functionally similar to the inverted-H-region amplification of methotrexate-resistant Leishmania major.

We describe the structure of amplified DNA that was discovered in two laboratory stocks of the protozoan parasite Leishmania tarentolae. Restriction mapping and molecular cloning revealed that a region of 42 kilobases was amplified 8- to 30-fold in these lines. Southern blot analyses of digested DNAs or chromosomes separated by pulsed-field electrophoresis showed that the amplified DNA corresponded to the H region, a locus defined originally by its amplification in methotrexate-resistant Leishmania major (S. M. Beverley, J. A. Coderre, D. V. Santi, and R. T. Schimke, Cell 38:431-439, 1984). Similarities between the amplified DNA of the two species included (i) extensive cross-hybridization; (ii) approximate conservation of sequence order; (iii) extrachromosomal localization; (iv) an overall inverted, head-to-head configuration as a circular 140-kilobase tetrameric molecule; (v) two regions of DNA sequence rearrangement, each of which was closely associated with the two centers of the inverted repeats; (vi) association with methotrexate resistance; and (vii) phenotypically conservative amplification, in which the wild-type chromosomal arrangement was retained without apparent modification. Our data showed that amplified DNA mediating drug resistance arose in unselected L. tarentolae, although the pressures leading to apparently spontaneous amplification and maintenance of the H region are not known. The simple structure and limited extent of DNA amplified in these and other Leishmania lines suggests that the study of gene amplification in Leishmania spp. offers an attractive model system for the study of amplification in cultured mammalian cells and tumors. We also introduced a method for measuring the size of large circular DNAs, using gamma-irradiation to introduce limited double-strand breaks followed by sizing of the linear DNAs by pulsed-field electrophoresis.

Animals↗
PubMed2006

Extrachromosomal DNA isolated from tomato big bud and Candidatus Phytoplasma australiense phytoplasma strains.

The nucleotide sequences of two extrachromosomal elements from tomato big bud (TBB) and one extrachromosomal element from Candidatus Phytoplasma australiense (Ca. P. australiense) phytoplasmas were determined. Both TBB plasmids (3319 and 4092 bp) contained an open reading frame ( approximately 570 bp) with homology to the rolling circle replication initiator protein (Rep). This gene was shorter than the rep genes identified from other phytoplasma plasmids, geminiviruses and bacterial plasmids. Both TBB extrachromosomal DNAs (eDNAs) encoded a putative DNA primase (dnaG) gene, a chromosomal gene required for DNA replication and which contains the conserved topoisomerase/primase domain. We speculate that the replication mechanism for the TBB phytoplasma eDNA involves the dnaG gene instead of the rep gene. The Ca. P. australiense eDNA (3773 bp) was shown to be circular and contained four open reading frames. The rep gene was encoded on ORF 1 and had homology to both plasmid (pLS1) and geminivirus-like domains.

Amino Acid Sequence↗
PubMed1985

Expression of a human U1 RNA gene introduced into mouse cells via bovine papillomavirus DNA vectors.

We introduced a gene for human U1 small nuclear RNA, HU1-1, into mouse C127 cells via bovine papillomavirus (BPV) vectors. After transfection, up to 15% of the total U1 RNA in transformed cells was encoded by the introduced human genes. High levels of expression of the human gene were observed when the recombinant viral DNAs were maintained either as plasmids or after integration into high-molecular-weight DNA. As few as 400 and 35 base pairs of 5' and 3' flanking region sequences, respectively, were sufficient for transcription of human U1 RNA, and no increase in the level of expression was observed with HU1-1 DNA containing several kilobases of flanking region sequences. Several of the transformed cell lines contained the recombinant BPV DNA apparently integrated into the host genome. Integration or rearrangement or both of the U1-BPV DNA was promoted when the HU1-1 gene was positioned at the BamHI site downstream of the BPV transforming region. At least two variants of the U1-BPV DNAs were able to cause morphological transformation of cells despite the fact that these DNAs lacked a BPV transcriptional enhancer element.

Animals↗
PubMedDate not supplied

Isolation of an excision product of T-cell receptor alpha-chain gene rearrangements.

The genes for the T-cell receptor, like the immunoglobulin genes, are rearranged as DNA. The mechanism of this rearrangement is not clear; unequal crossover between chromosomes and the looping-out and excision of the excess DNA have both been suggested. We isolated small polydisperse circular (spc) DNAs from mouse thymocytes and cloned them into a phage vector. Of the 56 clones we analysed, nine contained sequences homologous to T-cell receptor alpha-chain joining (J alpha) segments. We have characterized one of these clones; it contains one J alpha segment, and the product out of the recombination of a variable region of the alpha-chain gene (V alpha) with a J alpha gene segment. This is the first demonstration of the presence in extrachromosomal DNA of a reciprocal recombination product of any rearranging immunoglobulin or T-cell receptor gene. The finding verifies that V alpha-J alpha joining can occur by the looping-out and excision of chromosomal DNA.

Animals↗
PubMed1996

Engineering a mini-herpesvirus as a general strategy to transduce up to 180 kb of functional self-replicating human mini-chromosomes.

The engineering of therapeutic human artificial episomal chromosomes, HAECs, requires the development of strategies to deliver large functional self-replicating extrachromosomal DNA in target cells. Members of the herpesviral family are among the largest episomal double-stranded DNA viruses. As model systems of this family of endemic infectious agents, vectors derived from the human herpes 4 Epstein-Barr virus (EBV) were constructed which transferred up to 180 kb of DNA packaged as infectious virions. Such a transduction strategy was based on a non-oncogenic helper-dependent mini-EBV carrying minimal cis elements for latent replication and virus production. After exposure of human B lymphoma and lymphoblastoid cells to mini-EBVs transducing lacZ and human HPRT minigenes, stable cell transformants were selected which carried the delivered multimeric linear DNAs as circular episomes up to 160-180 kb in size. Following transduction of Lesch-Nyhan disease cells with a mini-EBV/HPRT, normal human HPRT function was restored in cells carrying large episomal HPRT minigenes. Direct visualization of the therapeutic mini-EBV by fluorescent in situ hybridization (FISH) on metaphase and interphase nuclei indicated that 99% (556/563) of the transduced mini-EBV DNA was episomal with an average copy number of one to two per nucleus. This system should allow the delivery of large genes in common diseases such as hemophilia A and codelivery of multiple genes in cells from polygenic diseases such as cancer. The extrachromosomal mini-EBV-based strategy offers an alternative to integrative or non-replicating gene therapy infectious vectors, which may be generally applicable to other herpesviruses characterized by different tropisms.

B-Lymphocytes↗
PubMed1982

Persistence of freely replicating SV40 recombinant molecules carrying a selectable marker in permissive simian cells.

We have demonstrated that a SV40-pBR322 recombinant vector (pSV2-gpt) carrying a bacterial gene of selectable phenotype (Eco-gpt) may persist extrachromosomally in COS1 cells, a simian cell line that endogenously produces SV40 large T antigen. The amount of circular (supercoiled) recombinant DNA was estimated to be between 5 and 2000 copies per cell among several pSV2-transformed COS1 clonal lines examined. Complete pSV2 molecules were found in the majority of the transformants, although some of the pSV2 DNAs recovered were shown to have deletions in the pBR322 region. Our results indicate that removal of the pBR322 "inhibitory sequence" in pSV2 is not necessary for stable maintenance of these recombinant molecules in COS1 cells. In addition, large amounts of pSV2-related high molecular weight DNAs, probably concatemers of pSV2, were detected in the transformed lines.

Animals↗
PubMed1995

Amplification of a circular episome carrying an inverted repeat of the DFR1 locus and adjacent autonomously replicating sequence element of Saccharomyces cerevisiae.

Lack of suitable amplification markers has hindered the use of the yeast system for investigating the mechanism of gene amplification in a eukaryote with a simple genome and well defined genetic system. Recently, methotrexate has been used to select for Saccharomyces cerevisiae mutants with de novo amplification of the dihydrofolate reductase gene (DFR1) (Huang, T. (1993) In Vivo Disruption and de Novo Amplification of the DFR1 Gene Encoding Dihydrofolate Reductase in Saccharomyces cerevisiae. Ph. D. thesis, University of Alberta, Edmonton, Canada). We report here the detailed structure of a DFR1 episome amplified in methotrexate-resistant strain 25-1. The extrachromosomal DNA is found predominantly as a single 11-kilobase circular molecule. It consists of a 5.5-kilobase inverted duplication that contains the DFR1 locus and adjacent ARS (autonomously replicating sequence) element. This molecular configuration mimics the inferred structure of double minute chromosomes observed in a number of mammalian amplification systems and suggests that mechanisms that generate amplified DNAs are conserved from yeast to mammals.

Antimycin A↗