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PubMed1991

Transient occurrence of extrachromosomal DNA of an Arabidopsis thaliana transposon-like element, Tat1.

Analysis of 11 genomic clones containing the S-adenosylmethionine synthetase 1 gene (sam1) of Arabidopsis thaliana revealed the presence of a 431-base-pair (bp) insertion in the 3' end of sam1 in one of these clones. The inserted sequence, called Tat1, shows structural features of a transposon. It is flanked by a 5-bp duplication of the target site DNA and has 13-bp inverted repeats at its termini. Two highly homologous elements situated in a different genomic context were isolated from a genomic library. Genomic Southern analysis indicates that there are at least four copies of Tat1 present in the A. thaliana ecotype Columbia genome. Different hybridization patterns are observed with DNAs derived from different ecotypes of Arabidopsis thaliana, indicating that the element has moved since the divergence of these ecotypes. In two populations of A. thaliana, linear extrachromosomal Tat1-homologous DNA has been observed. The presented data are consistent with the hypothesis that Tat1 is an active transposable element.

Base Sequence↗
PubMedDate not supplied

[Induction of saccharomyces cerevisiae extrachromosomal-DNA].

In Saccharomyces yeast the significant portion of rRNA genes may be located as extrachromosomal copies. Extrachromosomal rDNA is represented by covalently-closed circular molecules with a major class contour length of 3.3 micrometer (the same as the length of one rDNA repeating unit). Covalently-closed circular rDNA can only be isolated from the stationary phase yeast culture (more than 60 hours of growth). Electron microscopy revealed several discrete length classes of circular molecules. Three of them are 3.3, 6.6 and 9.9 micrometers. Circular molecules were found with contour length less than 3.3 micrometers (1.1, 2.0 and 2.6 micrometers). The proportion of these molecules is 8% from the total number.

DNA↗
PubMed2025

Modern biology of extrachromosomal DNA: A decade-long voyage of discovery.

Genomic instability is a hallmark of cancer and is a major driving force of tumorigenesis. A key manifestation of genomic instability is the formation of extrachromosomal DNAs (ecDNAs) - acentric, circular DNA molecules ranging from 50 kb to 5 Mb in size, distinct from chromosomes. Ontological studies have revealed that ecDNA serves as a carrier of oncogenes, immunoregulatory genes, and enhancers, capable of driving elevated transcription of its cargo genes and cancer heterogeneity, leading to rapid tumor evolution and therapy resistance. Although ecDNA was documented over half a century ago, the past decade has witnessed a surge in breakthrough discoveries about its biological functions. Here, we systematically review the modern biology of ecDNA uncovered over the last ten years, focusing on how discoveries during this pioneering stage have illuminated our understanding of ecDNA-driven transcription, heterogeneity, and cancer progression. Furthermore, we discuss ongoing efforts to target ecDNA as a novel approach to cancer therapy. This burgeoning field is entering a new phase, poised to reshape our knowledge of cancer biology and therapeutic strategies.

Humans↗
PubMed1997

Nuclear extrachromosomal DNA of higher plants.

Recent reports indicate that minichromosomes and other small genetic entities may occur in the nuclei of uninfected higher plants. They become especially abundant under some special growth conditions and, sometimes, resemble extrachromosomal genes of ciliated protozoa. An example of such gene-sized DNA species was isolated from resting wheat embryos. The presence of telomeric sequences at its termini and the ability to replicate autonomously in wheat nuclei made it possible to distinguish this nuclear minichromosome from chromosomal DNA fragmentation products. The biological significance of plant minichromosomes remains to be elucidated.

Cell Nucleus↗
PubMed1985

Extrachromosomal DNA forms of copia-like transposable elements, F elements and middle repetitive DNA sequences in Drosophila melanogaster. Variation in cultured cells and embryos.

Drosophila melanogaster embryos and cells in culture were screened for the presence of unintegrated covalently closed circular DNA forms that hybridize to copia-like transposable elements, the F element and uncharacterized dispersed middle repetitive DNA elements. Our results indicate that the majority of copia-like elements (including copia, 297, 412, mdg1, mdg3 and gypsy), the F elements, and 9 of 12 middle repetitive DNA elements are present as free DNA forms in cultured cells and embryos. An 18 base-pair inverted repeat has been reported to flank the long direct repeat of mdg3, implying that mdg3 is not an orthodox copia-like element; however, we have sequenced two independently isolated mdg3 clones and shown that the inverted repeat is not part of the element. The relative abundance with which free DNA forms are found varies between the cultured cells used, and between cultured cells and embryos. This variation, which can be up to 20-fold for some elements, does not correlate well with either the amount of element-specific poly(A)+ RNA present per cell or the number of element-specific sequences integrated in the genome.

Animals↗
PubMed2006

Role of the silkworm argonaute2 homolog gene in double-strand break repair of extrachromosomal DNA.

The argonaute protein family provides central components for RNA interference (RNAi) and related phenomena in a wide variety of organisms. Here, we isolated, from a Bombyx mori cell, a cDNA clone named BmAGO2, which is homologous to Drosophila ARGONAUTE2, the gene encoding a repressive factor for the recombination repair of extrachromosomal double-strand breaks (DSBs). RNAi-mediated silencing of the BmAGO2 sequence markedly increased homologous recombination (HR) repair of DSBs in episomal DNA, but had no effect on that in chromosomes. Moreover, we found that RNAi for BmAGO2 enhanced the integration of linearized DNA into a silkworm chromosome via HR. These results suggested that BmAgo2 protein plays an indispensable role in the repression of extrachromosomal DSB repair.

Amino Acid Sequence↗
PubMed1976

Extrachromosomal DNA and RNA-synthesis in oocytes of Creophilus maxillosus (Staphylinidae, Coleoptera, Polyphaga).

It has been found that the transcriptional activity of nuclear extra DNA in Creophilus maxillosus oocytes, as examined by autoradiography, increases parallel with its dispersion during the previtellogenic period of oocyte growth. The RNA, after being synthesized in the greatly enlarged oocyte nucleus, is subsequently transported into the cytoplasm. The oocyte chromosomes form a karyosphere and synthesize the RNA more weakly than other parts of the nucleus, which contain the extra DNA in a highly dispersed condition.

Animals↗
PubMed1985

Extrachromosomal DNA transformation of Caenorhabditis elegans.

DNA was introduced into the germ line of the nematode Caenorhabditis elegans by microinjection. Approximately 10% of the injected worms gave rise to transformed progeny. Upon injection, supercoiled molecules formed a high-molecular-weight array predominantly composed of tandem repeats of the injected sequence. Injected linear molecules formed both tandem and inverted repeats as if they had ligated to each other. No worm DNA sequences were required in the injected plasmid for the formation of these high-molecular-weight arrays. Surprisingly, these high-molecular-weight arrays were extrachromosomal and heritable. On average 50% of the progeny of a transformed hermaphrodite still carried the exogenous sequences. In situ hybridization experiments demonstrated that approximately half of the transformed animals carried foreign DNA in all of their cells; the remainder were mosaic animals in which some cells contained the exogenous sequences while others carried no detectable foreign DNA. The presence of mosaic and nonmosaic nematodes in transformed populations may permit detailed analysis of the expression and function of C. elegans genes.

Animals↗
PubMed1991

Human epithelial cells immortalized by SV40 retain differentiation capabilities in an in vitro raft system and maintain viral DNA extrachromosomally.

Carcinomas are the predominant type of cancer found in man, yet in vitro studies on the transformation of epithelial cells have been limited. In an attempt to extend our knowledge of the mechanisms involved in the development of epithelial cancers, we have examined the effects of oncogenes on keratinocytes in vitro using both the ability to immortalize and the ability to alter differentiation as criteria for transformation. SV40 T-antigen was observed to be an efficient immortalizing agent in human keratinocytes consistent with previous studies in other human cell types. Using an in vitro cell culture system (rafts) for epithelial stratification at the air-liquid interface, we observed that the morphology of rafts of SV40-immortalized keratinocytes was similar to that of untransfected epithelial cells, demonstrating that although immortal these cells retain differentiation capabilities. The ability to differentiate was lost only upon prolonged passage in culture, suggesting that this effect is separable from immortalization. In these immortalized epithelial cells, SV40 genomes were found to be maintained as a heterogeneous population of extrachromosomal molecules dependent upon the SV40 origin of replication. It is not clear whether these molecules arise continuously as a result of excision events from integrated copies or are stably maintained as episomes.

Antigens, Polyomavirus Transforming↗
PubMed1993

Convenient plasmid for extrachromosomal DNA recombination in mouse cells.

We constructed a convenient plasmid for DNA recombination assay. The plasmid, pMR1, contains a double prokaryotic terminator to decrease the background and two unique restriction enzyme sites on both sides of the double terminator to allow for easy construction. The assay is capable of selecting the bacterial cells containing recombined plasmid DNA on a selective plate containing ampicillin and chloramphenicol. We adapted pMR1 for V(D)J recombination and homologous recombination and detected both types of recombination in murine PreB cell line. As pMR1 has the double terminator, background on the selective plate decreases effectively and we select only the recombined clones. We consider the vector, pMR1, to be convenient for the analysis of homologous and non-homologous recombinations.

Abelson murine leukemia virus↗
PubMed1983

Biosynthetic mechanism of ribulose-1,5-bisphosphate carboxylase in the purple photosynthetic bacterium, Chromatium vinosum. III. Absence of extrachromosomal DNA.

Inducible formation of ribulose-1,5-bisphosphate (RuBP) carboxylase in the cells of Chromatium vinosum under autotrophic conditions was not affected by six different inhibitors of DNA synthesis. Photosynthetic CO2 fixation and RuBP carboxylase activities were not influenced by seven reagents known to eliminate plasmids. Plasmids were not detectable by agarose gel electrophoresis employing either the cleared lysate or alkaline sodium dodecyl sulfate method, nor were they detected by ethidium bromide-CsCl density gradient centrifugation. Overall experimental results tend to indicate that plasmids are absent in the Chromatium cells and that the induction of RuBP carboxylase is presumably not regulated in the DNA replication process.

Carboxy-Lyases↗