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Results for “extrachromosomal circular DNAs”

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At least 19 recordsLinked to original sources

PubMed1990

Tissue-specific and age-related variations in repetitive sequences of mouse extrachromosomal circular DNAs.

Extrachromosomal circular (ecc) DNA was isolated from mouse brain, liver, and heart tissues at different ages. To determine the abundance of repetitive sequences in eccDNAs, preparations were probed for short-interspersed (B1 and B2), long-interspersed (L1), endogenous retroviral-like (IAP), and tandemly repeated satellite sequences (SAT) of the mouse genome. Together these sequence families comprise approximately 15% of the mouse genome. The hybridization results showed that each tissue had a characteristic pattern of repetitive sequence elements in eccDNAs, and the abundance of repetitive sequences changed as a function of age. Repetitive sequences decreased in liver and brain eccDNAs from 1 month to 8 months of age but appeared to remain stable thereafter. In contrast, repetitive sequence families in heart eccDNAs were constant from 1 month to 16 months of age but declined in 24-month-old mice. The present studies indicate that extrachromosomal sequences exhibit greater flexibility than chromosomal sequences.

Aging↗

PubMed2026

Characterisation of whole-blood extrachromosomal circular DNAs in Kawasaki disease complicated by coronary artery aneurysm.

BACKGROUND: Extrachromosomal circular DNAs are critical regulators of stress responses, immunity, and inflammation pathways. However, their role and underlying mechanisms in Kawasaki disease complicated by coronary artery aneurysm remain poorly understood. METHODS: Whole blood samples from six children with Kawasaki disease, including three with coronary artery aneurysm group and three without coronary artery aneurysm (control group), were subjected to extrachromosomal circular DNA sequencing. Putative extrachromosomal circular DNAs were identified using Circle-Map. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on genes associated with upregulated extrachromosomal circular DNAs, and an exploratory immune-signature profiling was performed using the single-sample gene set enrichment analysis algorithm. RESULTS: We identified 4,790 differential extrachromosomal circular DNAs between the coronary artery aneurysm and control groups, of which 4,789 were upregulated in the CAA group. The extrachromosomal circular DNAs in the coronary artery aneurysm group were more concentrated and shorter in length than those in the control group. Upregulated extrachromosomal circular DNAs were mainly derived from autosomes, particularly chromosomes 3, 4, and 7. Functional enrichment analysis indicated that genes associated with upregulated extrachromosomal circular DNAs were mainly involved in response to stimulus-related terms and pathways, including chemokine signalling, cGMP-PKG signalling, and calcium signalling. Immune-signature analysis suggested that the coronary artery aneurysm group exhibited more specific immune responses, whereas the control group tended towards broader immune regulatory processes. CONCLUSIONS: Coronary artery aneurysm and control groups exhibited distinct extrachromosomal circular DNA profiles. These findings suggest that extrachromosomal circular DNA alterations are associated with coronary artery aneurysm in Kawasaki disease and may provide new insights into the molecular features underlying this condition.

Coronary artery aneurysm↗

PubMed1983

Extrachromosomal circular DNAs from murine hemopoietic tissue cells.

Extrachromosomal circular DNA complexes from cells of murine hemopoietic organs, bone marrow, thymus, spleen, and lymph nodes were examined by mica-press-adsorption method (H. Yamagishi, T. Kunisada, and T. Tsuda, 1982, Plasmid 8, 299-306). They showed wide size distribution, from 0.3 to 10 micron. The large-size DNAs of more than 1 micron (3.1 kb) in contour length were more abundant in bone marrow and thymus than they were in spleen and lymph nodes. The appearance of the large size DNAs was examined on splenocytes of athymic nude mice during ontogeny. The large-size DNAs first became detectable after 2 weeks of age and the amount increased thereafter until 9 weeks of age. It appears that large-size circular DNAs appear during differentiation from the hemopoietic stem cells into several descendent cells. Possible immunological implications for the appearance of extrachromosomal circular DNAs are discussed.

Age Factors↗

PubMed1987

Dispersed repetitive sequences of the mouse genome are differentially represented in extrachromosomal circular DNAs in vivo.

Eukaryotic cells contain extrachromosomal circular (ecc) DNAs which are homologous to chromosomal sequences. We have isolated eccDNAs from whole tissues of C57BL/6 mice. Using hybridization techniques, we show that R-, MIF-, B1-, and B2-dispersed repetitive sequences of the mouse genome are differentially represented in heart, brain, and liver tissues. Moreover, we show that the relative abundance of B2 sequences in heart and liver eccDNAs is higher than the relative abundance of the other repetitive sequence families studied.

Animals↗

PubMed1985

Appearance of extrachromosomal circular DNAs during in vivo and in vitro ageing of mammalian cells.

Appearance of extrachromosomal circular DNAs with in vivo and in vitro cellular ageing was examined by using a new technique of mica-press-adsorption for electron microscopy. The size distribution and the copy number of circular DNA complexes varied, depending on the cellular age. Extrachromosomal circular DNA complexes of variable length of more than 0.5 microns or 1.5 kilobase (kb) appeared during in vivo ageing of rat lymphocytes and in vitro ageing of cultured human lung fibroblasts. A restricted size class of circular forms of less than 0.5 microns in contour length was amplified in human skin fibroblasts from aged normal or Werner's syndrome subjects. These circular DNA molecules are suggested to be products of DNA rearrangements or gene amplification occurring in the chromosome.

Aging↗

PubMed1993

Molecular characterization of extrachromosomal circular DNAs from an embryonal carcinoma cell line induced to differentiate into neuron-like cells in vitro.

Extrachromosomal circular DNAs isolated from a P19 embryonal carcinoma cell line were induced to differentiate into neuron-like cells by retinoic acid and cloned into an EcoRI site of a phage vector. Of the 26 DNA inserts (2.1 kb in average length) analyzed, 16 contained repetitive sequences. Out of 10 DNA inserts with unique sequence, 6 carried linear chromosomal sequences and 4 showed chromosomal rearrangements in Southern blots. Two unique fragments with germline configuration were enriched in circular DNA clone libraries. We assigned the breakpoints of 3 circular DNA fragments to positions in the germline sequence. Patchy short inverted repeats were found in the vicinity of breakpoints. An intrastrand loop structure between such inverted short homology region may be required for the circularization of excised DNA.

Animals↗

PubMed1993

Identification of short tandemly repeated sequences in extrachromosomal circular DNAs from Drosophila melanogaster embryos.

A sequence (scl) belonging to the recently identified dodeca satellite family was found to be a major family of extrachromosomal circular DNA molecules from Drosophila melanogaster embryos. The basic unit consists of the 11-bp repeat 5' ACTGGTCCCGT 3', is 63% G + C rich, and shares some similarity with the Escherichia coli chi sequence. This family accounts for only about 0.06% of the genome but very likely for a higher proportion of the circular DNA molecules. It is organized in the genome into at least five main clusters contained in DNA fragments larger than 20 kb and several minor clusters. These clusters are located in the heterochromatic pericentromeric regions. Two other families of simple repeated sequences, the 1.686 g/cm3 (5' AATAACATAG 3') and the 1.705 g/cm3 (5' AAGAG 3') satellite DNAs, were also found in circular DNAs, while another family, the 1.672 g/cm3 (5' AATAT 3'), was not detected. The representation of the simple repeated sequences in circular molecules is not correlated to their genomic representation. Among the seven families of sequences identified to date in extrachromosomal circular DNAs from embryos, the dodeca satellite, the 240-bp repeat of the rDNA intergenic spacer, and the 1.688 and 1.705 g/cm3 satellite DNAs are the most represented families, while the 5S genes, the histone genes, and the 1.686 g/cm3 satellite DNA are present in a lower amount.

Animals↗

PubMed1991

Structure of extrachromosomal circular DNAs generated by immunoglobulin light chain gene rearrangements.

Recombination at the immunoglobulin kappa or lambda light chain locus generates extrachromosomal circular DNAs. We have isolated circular DNAs from adult mouse spleen cells and prepared a circular DNA clone library. We characterized four J kappa-positive and one J lambda 1-positive clones. The J kappa-clones contained both coding and signal joints of V kappa-J kappa joining, and the J lambda 1-clone contained a signal joint of V lambda 1-J lambda 1 joining. Genomic organization of the V kappa gene families used in these joints suggested the excision of circular DNA preceded by inversion. A specific dinucleotide (P) insertion in the coding joint was observed in two clones. Three coding joints were out of frame and one clone had an in-frame coding joint, although possibly combined with a pseudo-V kappa gene. These kappa-positive circular DNAs are possibly excised from the chromosome by secondary recombinations which replace non-productive primary rearrangements.

Amino Acid Sequence↗

PubMed1993

Despite its high representation in extrachromosomal circular DNAs from Drosophila embryos, the dodecasatellite does not allow autonomous replication in cultured cells.

The dodecasatellite is a 11/12 bp tandemly repeated sequence which is overrepresented, with regard to its genomic representation, in extrachromosomal circular DNAs from D melanogaster embryos. Here we show that a bacterial plasmid carrying a cluster of dodecasatellite is not able to replicate efficiently in cultured cells. This observation does not support the hypothesis that the overrepresentation results from an autonomous replication of dodecasatellite circular DNA molecules.

Animals↗

PubMed1988

Structure of extrachromosomal circular DNAs excised from T-cell antigen receptor alpha and delta-chain loci.

Small polydisperse circular (spc) DNA was isolated from mouse thymocytes, fragmented by HindIII digestion and cloned into the vector. Sixty DNA clones were randomly selected from the 10,400 phage library. The average size of insert was one-fifth of the original circular molecule. Twenty spc-DNA clones were homologous to DNA probes derived from T-cell antigen receptor (TCR) alpha-chain loci. We have characterized nine clones by DNA sequencing; they contain new germline sequences of the TCR alpha-chain variable (V alpha) and joining (J alpha) gene segments and the products out of the recombination of a V alpha with a J alpha gene segment. An additional four spc-DNA clones carried a new rearranging gene of the TCR delta-chain that is located between V alpha and J alpha genes. At least nine of 60 DNA clones carried the recombination junction of a heptamer-heptamer head-to-head structure expected from an excised product of V-J joining. This shows that most extrachromosomal circular DNAs in the thymus are formed by a sequence-dependent recombination mechanism. We suggest that a functional T-cell receptor V alpha gene can be constructed by somatic random rearrangements through successive looping-out, excision and deletion.

Animals↗

PubMed1990

Purification of eucaryotic extrachromosomal circular DNAs using exonuclease III.

A method for the isolation of eucaryotic extrachromosomal circular (ecc) DNA is described. Exonuclease III was used to preparatively digest linear and open circular forms of DNA; the resultant exonuclease-resistant molecules were then characterized by buoyant density gradient sedimentation and were found to be essentially covalently closed circular DNA. The efficiency of the exonuclease method was compared to ultracentrifugation techniques and was found to give yields greater than those obtained by two or more equilibrium density gradients. The utility of the exonuclease III technique was determined by purifying eccDNAs from mouse liver, brain, heart, and kidney tissues. The results showed that there are tissue-related differences in eccDNA content.

Animals↗

PubMed1984

Structure of extrachromosomal circular DNAs containing both the Alu family of dispersed repetitive sequences and other regions of chromosomal DNA.

Small polydisperse circular DNA (spcDNA) isolated from the BSC-1 line of African Green monkey kidney cells was digested with the restriction endonuclease BamHI and cloned in bacteriophage lambda. The resulting library of 25,000 phage was then screened for the presence of the Alu family of short interspersed nucleotide sequences, and four of the 100 Alu-positive clones were characterized. In summary: (1) all four clones contained regions other than Alu that were homologous to the BSC-1 chromosome. Two contained Alu plus unique chromosomal DNA, one contained Alu plus an uncharacterized repetitive chromosomal DNA, and one contained Alu plus both unique and a specific tandemly repeated chromosomal DNA (alpha-satellite); (2) all four clones were derived from extrachromosomal circular DNAs and not from the accidental cloning of a very small amount of contaminating chromosomal material assumed to be present in spcDNA preparations; and (3) one clone represented an intact circular DNA with a restriction endonuclease cleavage map that was a circularly permuted version of its chromosomal homologue.

Animals↗

PubMed1989

Extrachromosomal circular DNAs in Drosophila melanogaster: comparison between embryos and Kc0% cells.

We established the size distribution of extrachromosomal covalently closed circular DNA molecules from embryos of various Drosophila melanogaster strains and from Kc0% tissue culture cells. In embryos, more than 80% of the circular DNA molecules are smaller than 2.5 kb and all the distributions show a peak of molecules of between 200 and 400 bp. The Kc0% cell distribution differs mainly from that of embryos in that 48% of the molecules have a size between 4 and 8 kb. Correlating with this, circular molecules homologous to copia, 412 and 297 were detected only in Kc0% cells. The three tandemly repeated families containing the 5S genes, the histone genes and the 240 bp repeat of the ribosomal DNA intergenic spacer, which had previously been identified in circular DNAs from embryos, were also found in cultured cells. A fourth tandemly repeated family corresponding to the 1.688 g/cm3 satellite DNA was detected, both in embryos and Kc0% cells. It consists of circular multimeric molecules containing multiple copies of the 359 bp repeated unit. No circular DNA molecules homologous to the actin genes, the type I ribosomal DNA insertion, or the F and I transposable elements were found in embryos or Kc0% cells. Thus it appears that the extrachromosomal circular DNA molecules from embryos and from tissue culture cells differ mainly in the presence of circular copies of the copia-like transposable elements.

Animals↗

PubMed1984

Extrachromosomal circular DNAs in interspecific mouse-rat reconstituted cells.

Several clones of reconstituted cells were isolated by fusion of karyoplasts of mouse melanoma B16 cells with cytoplasts of rat myoblastic L6 cells and processed by the mica-press-adsorption method for electron microscopy. Extrachromosomal small circular DNAs of less than 1 micron in contour length (smaller circular DNA) were present in both parental cells, and circles larger than 1 micron (larger circular DNA) were found more frequently in reconstituted cells at an early stage after the clonal isolation. Mitochondrial DNA was not released from mitochondria by this method. The new phenotypes of reconstituted cells were stable, but larger circles were lost after prolonged cultivation of the cells. The possibility that the larger circular DNAs result from intrachromosomal DNA rearrangement induced by rat cytoplasts is discussed.

Animals↗

PubMed1987

Some extrachromosomal circular DNAs from Drosophila embryos are homologous to tandemly repeated genes.

In Drosophila melanogaster embryos we have identified three classes of extrachromosomal circular DNA molecules homologous to the three main families of tandemly repeated genes, 5 S, rDNA and histone. 5 S genes are present in circular multimeric molecules containing up to 16 copies of the 375(+/- 7) base-pair repeated unit. Circular molecules homologous to rDNA are also multimeric molecules, which contain up to ten copies of the 240 base-pair tandemly repeated sequence of the non-transcribed spacer. The two major genomic classes of histone units (4800 and 5000 bases) are found only as monomeric circular molecules. No circular intermediate of the I transposable element was detected in embryos laid by F1 dysgenic females produced by the I-R system of hybrid dysgenesis. As far as we know, it is the first time that genes have been identified among extrachromosomal circular molecules independently of any specific amplification phenomenon.

Animals↗

PubMedDate not supplied

Extrachromosomal circular DNAs and genomic sequence plasticity in eukaryotic cells.

The ability of eukaryotic organisms of the same genotype to vary in developmental pattern or in phenotype according to varying environmental conditions is frequently associated with changes in extrachromosomal circular DNA (eccDNA) sequences. Although variable in size, sequence complexity, and copy number, the best characterized of these eccDNAs contain sequences homologous to chromosomal DNA which indicates that they might arise from genetic rearrangements, such as homologous recombination. The abundance of repetitive sequence families in eccDNAs is consistent with the notion that tandem repeats and dispersed repetitive elements participate in intrachromosomal recombination events. There is also evidence that a fraction of this DNA has characteristics similar to retrotransposons. It has been suggested that eccDNAs could reflect altered patterns of gene expression or an instability of chromosomal sequences during development and aging. This article reviews some of the findings and concepts regarding eccDNAs and sequence plasticity in eukaryotic genomes.

Animals↗

PubMed2000

A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi.

We have determined that Borrelia burgdorferi strain B31 MI carries 21 extrachromosomal DNA elements, the largest number known for any bacterium. Among these are 12 linear and nine circular plasmids, whose sequences total 610 694 bp. We report here the nucleotide sequence of three linear and seven circular plasmids (comprising 290 546 bp) in this infectious isolate. This completes the genome sequencing project for this organism; its genome size is 1 521 419 bp (plus about 2000 bp of undetermined telomeric sequences). Analysis of the sequence implies that there has been extensive and sometimes rather recent DNA rearrangement among a number of the linear plasmids. Many of these events appear to have been mediated by recombinational processes that formed duplications. These many regions of similarity are reflected in the fact that most plasmid genes are members of one of the genome's 161 paralogous gene families; 107 of these gene families, which vary in size from two to 41 members, contain at least one plasmid gene. These rearrangements appear to have contributed to a surprisingly large number of apparently non-functional pseudogenes, a very unusual feature for a prokaryotic genome. The presence of these damaged genes suggests that some of the plasmids may be in a period of rapid evolution. The sequence predicts 535 plasmid genes >/=300 bp in length that may be intact and 167 apparently mutationally damaged and/or unexpressed genes (pseudogenes). The large majority, over 90%, of genes on these plasmids have no convincing similarity to genes outside Borrelia, suggesting that they perform specialized functions.

Base Sequence↗

PubMed1991

[Increase in the quantity of highly repetitive sequences in extrachromosomal circular DNAs under inhibition of translation by cycloheximide].

Small polydispersed circular DNA(spcDNA) was isolated from cultivated HeLa cells. Cells were treated by cycloheximide in concentrations of 1 and 50 micrograms/ml. Gradient fractions were dot blotted to nitrocellulose filters and were hybridized with different repetitive DNAs. The pool of repetitive DNA sequences in fraction of spcDNA increased for cycloheximide treated cells. The content of Alu sequences increased by 1.5-2.5 times, "classical" satellite DNA--by 5-7 times, alpha-satellite--by 3-5 times.

Cycloheximide↗