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Some extrachromosomal circular DNAs containing the Alu family of dispersed repetitive sequences may be reverse transcripts.

A 300 base-pair (bp) size class of small polydisperse circular DNA (spcDNA) isolated from the BSC-1 line of African Green monkey kidney cells was cleaved with the restriction endonuclease Sau3A, and the resulting fragments (100 to 200 bp) were cloned in bacteriophage M13 mp7. The nucleotide sequence of each of 24 clones containing DNA sequences homologous to the Alu family of mobile, dispersed, repetitive elements was then determined. Analysis of these sequences revealed that many, and perhaps all, of the 300 bp Alu-containing spcDNAs had regions in which the 5' and 3' ends of the normal Alu element were juxtaposed and covalently joined. Although more than one model can explain the generation of such circular molecules, the most attractive one at this time involves their generation from reverse transcripts of Alu-specific RNAs.

Animals↗

Molecular characterization of extrachromosomal circular DNAs from differentiating embryonic stem cells.

Embryonic E14 stem cells were differentiated to parietal yolksac-like flat cells in vitro in the absence of added feeders and LIF (Leukemia Inhibitory Factor). We cloned circular DNAs from the differentiating E14 cells. Out of 9 DNA inserts with the unique sequence, one clone showed a chromosomal rearrangement which could have occurred between a pair of short inverted repeats. Recombination mechanism is discussed in view of two other circularization events of the flanking sequences between short inverted repeats shown in differentiated P19 embryonal carcinoma cells.

Base Sequence↗

Amplification of extrachromosomal small circular DNAs in a murine model of accelerated senescence. A brief note.

Extrachromosomal circular DNA complexes from peripheral blood lymphocytes from inbred mice of accelerated senescence, were detected by mica-press-adsorption method. In senescence-resistant series (SAM-R), polydisperse circular DNAs were observed at 7 weeks of age and a restricted size class of small circular forms of 0.4-0.8 microns in contour length was amplified several-fold at 26 months of age. In senescence-prone series (SAM-P), a similar amplification of small circular DNAs was observed at young age of 10 weeks and more progressive at 17 months of age.

Aging↗

Circle-seq analysis reveals the involvement of eccDNAs in salt stress response of bermudagrass (Cynodon dactylon).

Extrachromosomal circular DNAs (eccDNAs) have been identified in a wide variety of plant species and play a pivotal role in genomic plasticity, emerging as key drivers of stress adaptation. However, the putative roles of eccDNAs under environmental stress remain largely unexplored in plants. As a high-quality turfgrass, bermudagrass (Cynodon dactylon L.) is a pivotal species for the reclamation and improvement of saline-alkali soils. Therefore, we performed a comprehensive analysis of the eccDNA profiles in bermudagrass under salt stress. A total of 1,068 eccDNAs were identified across all chromosomes. These eccDNAs were characterized by short lengths (ranging from 100 bp to 1 kb) and low GC content. Their genomic distribution was not entirely random but rather exhibited a certain preference for intergenic regions and coding sequences (CDS). Crucially, null model analysis of A/T-rich junction sites revealed that these eccDNAs primarily originate from physically unstable scaffold/matrix attachment regions (S/MARs) via stochastic fragmentation, followed by opportunistic circularization predominantly mediated by the non-homologous end joining (NHEJ) pathway. Notably, salt stress specifically enriched eccDNAs derived from DNA transposons, including the Tc1/Mariner, CACTA and MITE superfamilies. Overall, our findings reveal complex extrachromosomal structural dynamics in bermudagrass, offering novel insights into its genomic adaptation under environmental stress.

Cynodon↗

Detection of extrachromosomal circular DNA sequences from tumor cells by an alkaline lysis, Alu-polymerase chain reaction technique.

Extrachromosomal circular DNAs ranging in size from submicroscopic molecules of approximately 100 kb to cytogenetically resolvable structures of 1000+ kb called minute and double-minute chromosomes have been shown to harbor amplified genes in primary tumor cells, tumor cell lines, and drug-resistant cells grown in vitro. The presence of these molecules in transformed and malignant cells trends to reflect genetic instability and also suggests that role in tumor progression. Using a colon carcinoma cell line, we developed a technique to detect extrachromosomal circular DNA-specific sequences by Alu-polymerase chain reaction. Circular DNA was enriched by selective alkaline denaturation of genomic DNA. We have successfully performed this procedure with a minimum of 5 x 10(5) cells. The technique does not require any prior knowledge of the sequences located on the covalent circular DNA molecules for their detection. The procedure should be useful as a routine screen of primary tumor cells for the presence of extrachromosomal circular DNA and should permit the preparation of specific probes ot aid in their detailed characterizations.

Base Sequence↗

Developmentally regulated extrachromosomal circular DNA formation in the mesozoan Dicyema japonicum.

The dicyemid mesozoans are simple multicellular parasites with a long cylindrical axial cell surrounded by a single outer layer of 20 to 30 ciliated peripheral somatic cells. Their larval development proceeds within the axial cell. Here we demonstrate the appearance of extrachromosomal circular DNAs and their fate during early embryogenesis in Dicyema japonicum. These DNAs are highly heterogeneous in sequence, suggesting that they consist of unique--not repetitive--elements. Potential open reading frames were not evident in the elements, so these DNAs are unlikely to have a protein-encoding function. In situ hybridization revealed that the circular DNA elements were restricted to the early embryonic larvae and gradually faded out as larvae approached maturity. Furthermore Southern blot analysis and polymerase chain reaction analysis using a high molecular weight DNA as a template provided evidence that the extrachromosomal DNA circles are originally present in chromosomes. These observations suggest DNA elimination--or selective replication--of the elements from chromosomes during early embryogenesis in dicyemid mesozoans.

Animals↗

Excision products of the T cell receptor gene support a progressive rearrangement model of the alpha/delta locus.

We have cloned extrachromosomal circular DNAs containing T cell receptor (TCR) delta gene segments in adult mouse thymocytes and splenocytes. We find that the frequency of circular DNA clones carrying germline delta sequences is lower than that of J alpha probe-positive clones, possibly related to increasing 5' distance from the most upstream J alpha segment. This suggests that the TCR alpha/delta locus is successively rearranged from within and that the delta-containing excision products are progressively diluted out by the subsequent cell division which includes further alpha gene rearrangements. In addition, examination of delta gene excision products revealed newly identified V delta subfamilies, the reciprocal joining of two D delta elements, J delta 2 usage in thymocytes and novel sequences homologous to the human delta-gene deleting elements.

Amino Acid Sequence↗

Absence of reverse transcriptase activity in human diploid fibroblasts.

The reverse flow of genetic information from RNA transcripts to DNA has been postulated to be the mechanism for the generation of pseudogenes, dispersed repetitious DNA families, and small extrachromosomal circular DNAs in eukaryotic cells. We were unable to detect reverse transcriptase-like activity in several strains of cultured human cells, with or without induction by a variety of chemical and physical agents known to induce latent retroviruses.

Cells, Cultured↗

Circular DNA is excised by immunoglobulin class switch recombination.

We have purified extrachromosomal circular DNAs from adult mouse spleen cells, and cloned into a phage vector the BamHl fragments hybridizing with C mu and S gamma 1 probes. We obtained 52 S mu+S gamma 1+ clones by screening 1.4 million phage clones derived from spleen cells stimulated with bacterial lipopolysaccharide and interleukin 4. We have identified the breakpoints of six clones that contain S gamma 1 and S mu sequences fused in the 5' to 3' orientation. All these switch recombination sites were assigned to the central repetitive sequences of the S mu and S gamma 1 regions. Since the common S mu-S gamma 1 sequences at the recombination sites are at most 2 bases long, typical homologous recombination cannot account for their joining. These findings provide direct evidence that mu-gamma 1 class switching can occur by the looping out and excision of chromosomal DNA, with formation of a circle.

Animals↗

Transforming growth factor-beta induced class switch recombination may be modified during the cell proliferation restored by IL-2 stimulation.

Mouse spleen cells were stimulated, first by transforming growth factor beta (TGF-beta) and then by interleukin-2 (IL-2) in the presence of bacterial lipopolysaccharide (LPS). LPS plus IL-2 stimulation restored the cell proliferation suppressed by TGF-beta and increased the number of B cells. Both TGF-beta alone or TGF-beta plus IL-2 enhanced production of surface IgA-positive (sIgA+) cells in LPS-stimulated B-cell cultures. We characterized extrachromosomal circular DNAs generated in TGF-beta-primed and IL-2-stimulated B cells and identified the breakpoints of S mu/S gamma 3 recombinants which were the major intermediates of S mu and S alpha switch recombination. All switch recombination sites were dispersed evenly within both S mu and S gamma 3 regions. This even distribution of S mu/S gamma 3 breakpoints is in contrast to the site preference of class switch breakpoints induced by TGF-beta alone. These results suggest that IL-2-stimulated cell proliferation may modify class switch recombination primed by TGF-beta.

Amino Acid Sequence↗

Efficient gene activation system on mammalian cell chromosomes using recombinant adenovirus producing Cre recombinase.

To develop a method for activating genes located on cell chromosomes, an on/off switching unit regulated by the site-specific recombinase Cre was constructed. The switching unit was designed to express firstly the neo gene and secondly the reporter lacZ gene by Cre-mediated excisional deletion of the neo gene. CV1 cell lines bearing the switching unit on a cell chromosome were isolated and activation of the lacZ gene was examined after infection with a Cre-producing recombinant adenovirus. In one cell line virtually 100% of the cells stably expressed the lacZ gene, whereas in another cell line lacZ-expressing cell populations reached only to about 90% and decreased after cell divisions. The Southern blot analyses showed that the latter type of cells contained a head-to-tail array of the switching units, and that consequently the lacZ-expressing units were excised from a cell chromosome and present as extrachromosomal circular DNAs. These results showed that the system offers efficient activation of genes introduced into cell chromosomes and that the organization of the reporter units are important for efficiency and duration of the activated gene expression.

Adenoviridae↗

Biased distribution of recombination sites within S regions upon immunoglobulin class switch recombination induced by transforming growth factor beta and lipopolysaccharide.

We have characterized extrachromosomal circular DNAs from adult mouse spleen cells that were induced to switch to immunoglobulin A (IgA) with bacterial lipopolysaccharide (LPS) and transforming growth factor beta (TGF-beta), and identified breakpoints of S mu/S gamma 3, S mu/S gamma 2, S mu/S alpha, S gamma 3/S alpha, and S gamma 2/S alpha recombinants. The S mu recombination donor sites clustered in the 3' half of the S mu region, while the S alpha recombination acceptor sites clustered in the 5' half of the S alpha region. In addition, donor and acceptor sites of S gamma regions also clustered in the 3' and 5' parts, respectively. These site preferences are in sharp contrast to the dispersed distribution of S mu/S gamma 1 breakpoints within both S mu and S gamma 1 regions upon IgG1 switch induced by LPS and interleukin 4. Our results support the hypotheses that TGF-beta increases the frequency of switch recombination events to IgA and that the switch recombination to IgA often proceeds by successive recombination of S mu/S gamma and S gamma/S alpha.

Animals↗

Illegitimate recombination in the histone multigenic family generates circular DNAs in Drosophila embryos.

From extrachromosomal covalently closed circular DNA molecules purified from Drosophila melanogaster embryos, we have isolated 24 clones homologous to the histone tandemly repeated gene family. Some of the clones harbor one of the two main types of genomic repeated units of 4.8 and 5.0 kb. and probably result from homologous recombination. The remaining clones have a size ranging from 0.2 to 2.5 kb. and most of them carry a single fragment of the repeated unit. Nucleotide sequences of the junction region of six of these clones indicate they are generated by illegitimate recombination between short (8-15 bp.) imperfect direct repeats. The data suggest that most of the histone homologous circular DNA molecules are deleted histone units.

Animals↗

Ongoing in vivo immunoglobulin class switch DNA recombination in chronic lymphocytic leukemia B cells.

Chronic lymphocytic leukemia (CLL) results from the expansion of malignant CD5(+) B cells that usually express IgD and IgM. These leukemic cells can give rise in vivo to clonally related IgG(+) or IgA(+) elements. The requirements and modalities of this process remain elusive. Here we show that leukemic B cells from 14 of 20 CLLs contain the hallmarks of ongoing Ig class switch DNA recombination (CSR), including extrachromosomal switch circular DNAs and circle transcripts generated by direct S micro -->Sgamma, S micro -->Salpha, and S micro -->Sepsilon as well as sequential Sgamma-->Salpha and Sgamma-->Sepsilon CSR. Similar CLL B cells express transcripts for activation-induced cytidine deaminase, a critical component of the CSR machinery, and contain germline I(H)-C(H) and mature V(H)DJ(H)-C(H) transcripts encoded by multiple Cgamma, Calpha, and Cepsilon genes. Ongoing CSR occurs in only a fraction of the CLL clone, as only small proportions of CD5(+)CD19(+) cells express surface IgG or IgA and lack IgM and IgD. In vivo class-switching CLL B cells down-regulate switch circles and circle transcripts in vitro unless exposed to exogenous CD40 ligand and IL-4. In addition, CLL B cells that do not class switch in vivo activate the CSR machinery and secrete IgG, IgA, or IgE upon in vitro exposure to CD40 ligand and IL-4. These findings indicate that in CLL at least some members of the malignant clone actively differentiate in vivo along a pathway that induces CSR. They also suggest that this process is elicited by external stimuli, including CD40 ligand and IL-4, provided by bystander immune cells.

B-Lymphocytes↗

H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability.

Investigations aimed at identifying regulators of nuclear architecture in Drosophila demonstrated that cells lacking H3K9 methylation and RNA interference (RNAi) pathway components displayed disorganized nucleoli, ribosomal DNA (rDNA) and satellite DNAs. The levels of H3K9 dimethylation (H3K9me2) in chromatin associated with repeated DNAs decreased dramatically in Su(var)3-9 and dcr-2 (dicer-2) mutant tissues compared with wild type. We also observed a substantial increase in extrachromosomal circular (ecc) repeated DNAs in mutant tissues. The disorganized nucleolus phenotype depends on the presence of Ligase 4 and ecc DNA formation is not induced by removal of cohesin. We conclude that the structural integrity and organization of repeated DNAs and nucleoli are regulated by the H3K9 methylation and RNAi pathways, and other regulators of heterochromatin-mediated silencing. In addition, repeated DNA stability involves suppression of non-homologous end joining (NHEJ) or other recombination pathways. These results suggest a mechanism for how local chromatin structure can regulate genome stability, and the organization of chromosomal elements and nuclear organelles.

Animals↗

DNA-mediated transport of the intermediate filament protein vimentin into the nucleus of cultured cells.

A number of characteristic properties of intermediate filament (IF) proteins, such as nucleic acid-binding activity, affinity for histones and structural relatedness to transcription factors and nuclear matrix proteins, in conjunction with the tight association of IFs with the nucleus, suggest that these proteins might also fulfill nuclear functions in addition to their structure-organizing and -stabilizing activities in the cytoplasm. Yet, cytoplasmic IF proteins do not possess nuclear localization signals. In a search for carriers capable of transporting the IF protein vimentin into the nucleus, complexes of FITC-vimentin with various DNAs were microinjected into the cytoplasm of cultured cells and the intracellular distribution of the protein was followed by confocal laser scanning microscopy. The single-stranded oligodeoxyribonucleotides oligo(dG)25, oligo[d(GT)12G] and oligo[d(G3T2A)4G] proved to be excellent nuclear carriers for vimentin. However, in fibroblasts, fluorescence-labeled vimentin taken up by the nuclei remained undetectable with affinity-purified, polyclonal anti-vimentin antibody, whereas it was readily identifiable in the nuclei of microinjected epithelial cells in this way. Moreover, when FITC-vimentin was preinjected into fibroblasts and allowed to assemble into the endogenous vimentin filament system, it was still transferred into the nucleus by post-injected oligo(dG)25, although to a lesser extent. Superhelical circular DNAs, like pBR322, SV40 and mitochondrial DNA, were also characterized by considerable capacities for nuclear vimentin transport; these transport potentials were totally destroyed by relaxation or linearization of the DNA molecules. Nevertheless, certain linear double-stranded DNA molecules with a high affinity for vimentin IFs, such as repetitive telomere and centromere or mobile long interspersed repeat (LINE) DNA, could carry FITC-vimentin into the nucleus. This was also true for a 375 bp extrachromosomal linear DNA fragment which occurs in the cytoplasm of mouse tumor cells and which is capable of immortalizing human lymphocytes. On the basis of these results, it appears very likely that cellular and viral products of reverse transcription as well as other extrachromosomal DNAs, which are circular, superhelical and apparently shuttling between the cytoplasm and the nucleus (eccDNA), are constantly loaded with vimentin in vimentin-positive cells. Since such DNAs are considered as markers of genomic instability, it is conceivable that vimentin directly participates as an architectural, chromatin-modifying protein in recombinatorial processes set off by these DNAs in the nucleus.

Animals↗

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↗

Electron microscopy of amplified DNA forms in antifolate-resistant Leishmania.

Three independently derived antifolate-resistant Leishmania major cell lines overproduce the bifunctional protein thymidylate synthase-dihydrofolate reductase (TS-DHFR) by amplification of a region of DNA (R-region DNA) that contains the gene for TS-DHFR. On orthogonal-field-alteration gel electrophoresis (OFAGE), the extrachromosomal R-region DNAs are circular molecules, and different forms of R-region DNA within these cell lines are resolved. The R-region DNAs migrate aberrantly on OFAGE with respect to linear DNA and supercoiled plasmid standards. We describe a method for the isolation of these R-region DNA forms from OFAGE. By electron microscopy, we show that the extrachromosomal elements are single supercoiled circular DNA molecules, and are predominantly circular monomers and dimers of the original R-region DNA amplification unit. Using OFAGE, an analysis of cloned isolates shows that individual cells may contain multiple forms of R-region DNA. Furthermore, within a given cell line, certain distinguishable forms appear to have the same size and restriction map, suggesting they may be topoisomers. The multiple forms of R-region DNA are in a dynamic state in the antifolate-resistant populations, and the relative amount of DNA in each form as well as the number of forms within each cell line change through time. As currently understood, the generation of amplified R-region DNA in L. major is summarized.

Animals↗