Nuclear and mitochondrial DNA from wild-type and petite yeast: circularity, length, and buoyant density

Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing

Extrachromosomal circular DNAs (eccDNAs) are enigmatic DNA molecules that have been detected in a range of organisms. In plants, eccDNAs have various genomic origins and may be derived from transposable elements. The structures of individual eccDNA molecules and their dynamics in response to stress are poorly understood. In this study, we showed that nanopore sequencing is a useful tool for the detection and structural analysis of eccDNA molecules. Applying nanopore sequencing to the eccDNA molecules of epigenetically stressed Arabidopsis plants grown under various stress treatments (heat, abscisic acid, and flagellin), we showed that TE-derived eccDNA quantity and structure vary dramatically between individual TEs. Epigenetic stress alone did not cause eccDNA up-regulation, whereas its combination with heat stress triggered the generation of full-length and various truncated eccDNAs of the ONSEN element. We showed that the ratio between full-length and truncated eccDNAs is TE- and condition-dependent. Our work paves the way for further elucidation of the structural features of eccDNAs and their connections with various biological processes, such as eccDNA transcription and eccDNA-mediated TE silencing.

Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer

Extrachromosomal circular DNA (eccDNA) refers to a type of circular DNA that originate from but are likely independent of chromosomes. Due to technological advancements, eccDNAs have recently emerged as multifunctional molecules with numerous characteristics. The unique topological structure and genetic characteristics of eccDNAs shed new light on the monitoring, early diagnosis, treatment, and prediction of cancer. EccDNAs are commonly observed in both normal and cancer cells and function via different mechanisms in the stress response to exogenous and endogenous stimuli, aging, and carcinogenesis and in drug resistance during cancer treatment. The structural diversity of eccDNAs contributes to the function and numerical diversity of eccDNAs and thereby endows eccDNAs with powerful roles in evolution and in cancer initiation and progression by driving genetic plasticity and heterogeneity from extrachromosomal sites, which has been an ignored function in evolution in recent decades. EccDNAs show great potential in cancer, and we summarize the features, biogenesis, evaluated functions, functional mechanisms, related methods, and clinical utility of eccDNAs with a focus on their role in evolution and cancer.

Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters

Interest in extrachromosomal circular DNA (eccDNA) molecules has increased recently because of their widespread presence in normal cells across every species ranging from yeast to humans, their increased levels in cancer cells and their overlap with oncogenic and drug-resistant genes. However, the majority of eccDNA (microDNA) in mammalian tissues and cell lines are too small to carry protein coding genes. We have tested functional capabilities of microDNA by creating artificial microDNA molecules mimicking known microDNA sequences and have discovered that they express functional small regulatory RNA including microRNA and novel si-like RNA. MicroDNA are transcribed in vitro and in vivo independent of a canonical promoter sequence. MicroDNA that carry miRNA genes form transcripts that are processed by the endogenous RNA-interference pathway into mature miRNA molecules, which repress a luciferase reporter gene as well as endogenous mRNA targets of the miRNA. Further, microDNA that contain sequences of exons repress the endogenous gene from which the microDNA were derived through the formation of novel si-like RNA. We also show that endogenous microDNA associate with RNA polymerases subunits, POLR2H and POLR3F. Together, these results suggest that microDNA may modulate gene expression through the production of both known and novel regulatory small RNA.

Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells

While the vast majority of cellular DNA in eukaryotes is contained in long linear strands in chromosomes, we have long recognized some exceptions like mitochondrial DNA, plasmids in yeasts, and double minutes (DMs) in cancer cells where the DNA is present in extrachromosomal circles. In addition, specialized extrachromosomal circles of DNA (eccDNA) have been noted to arise from repetitive genomic sequences like telomeric DNA or rDNA. Recently eccDNA arising from unique (nonrepetitive) DNA have been discovered in normal and malignant cells, raising interesting questions about their biogenesis, function and clinical utility. Here, we review recent results and future directions of inquiry on these new forms of eccDNA.

Cascade DNA logic device programmed ratiometric DNA analysis and logic devices based on a fluorescent dual-signal probe of a G-quadruplex DNAzyme

Two fluorescence sensitive substrates of G4 DNAzyme with inverse responses were simultaneously used to a cascade advanced DNA logic device based DNA analysis for the first time.

A Pt(II)-Dip complex stabilizes parallel c-myc G-quadruplex

A new G-quadruplex (GQ) stabilizer, [Pt(Dip)2](PF6)2 (Dip: 4,7-diphenyl-1,10-phenanthroline), is prepared by the microwave irradiation method. The complex can highly stabilize G-quadruplex, but has negligible interactions with duplex DNA. Aromatic anchors on the polypyridyl ligands bestow the stabilizer with a high binding preference towards parallel GQ.

Saccharomyces cerevisiae plasmid, Scp or 2 mum: intracellular distribution, stability and nucleosomal-like packaging

Cell fractions from yeast strains known to harbor the plasmic 2 mum or Scp were treated with nucleases used to probe eukaryotic chromosome structure. Scp and subfragments were identified by hybridization to natural or cloned Scp probes according to Southern (34). Specificity was confirmed with non-Scp probes. Copy/haploid nuclear genome(n) was estimated from reconstructions at a resolution of 0.5/n. About 43-67% of the total cellular copy exists as nucleoprotein complexes which separate from other debris on isokinetic sucrose gradients with s-values of 67-110. These complexes are totally degraded by DNAase I. Digestion with micrococcal nuclease produced integral-sized fragments; they are not generated by direct mixing of pure Scp with nuclear chromatin from a[cir] strain. Initial digests gave a repeat of 168 +/- 3 base pairs (bp) for both Scp and nuclear nucleoprotein; advanced digests reduced the nuclear repeat relative to Scp by 8 bp. Of a potential 37 repeat units/plasmid, 31-32 were directly measured. A strain difference in Scp autodegradation was found. A partial nuclease resistant form was also demonstrated whose abundance was cell strain and growth stage dependent. Both Scp isomers exist in these complexes which are structurally similar to simian viral 40 minichromosomes.

Small circular deoxyribonucleic acid of Drosophila melanogaster: homologous transcripts in the nucleus and cytoplasm

We have recently characterized small circular DNA of Drosophila cultured cells in terms of its average size, sequence complexity, and homology to intermediate repetitive DNA. We show here that transcripts homologous to small circular DNA are present in various RNA fractions. Nuclear poly(A+), nuclear poly(A-), and polysomal poly(A+) RNA drive 10, 7, and 20%, respectively, of in vitro labeled small circular DNA tracer into hybrid. Sequences complementary to small circular DNA are at least 10-fold more concentrated in nuclear poly(A+) RNA than in nuclear poly(A-) or polysomal poly(A+) RNA. We do not detect significant homology between poly(A-) cytoplasmic RNA and small circular DNA. Assuming that only the least complex component of small circular DNA is driven into hybrid and that transcription is asymmetric, we use the results obtained here and previously published data to calculate the sequence complexity and relative concentration of nuclear poly(A+), nuclear poly(A-), and polysomal poly(A+) RNA homologous to small circular DNA.

Small circular DNA of Drosophila melanogaster: chromosomal homology and kinetic complexity

Nucleic acid reassociation techniques were used to determine the kinetic complexity of small circular DNA in cultured cells of Drosophila melanogaster. Two kinetic components are present. One of these constitutes 82% of the mass of the circular DNA and has a complexity of 1.8 x 10(4) nucleotide pairs; the other constitutes 18% of the mass and the a significantly higher but undefined sequence complexity. We have demonstrated that these circular molecules hybridize to middle repetitive chromosomal sequences by hybridization of in vitro-labeled circular DNA tracer with a vast excess of Drosophila chromosomal DNA. Thermal stability measurements indicate that base-pair mismatch between small circular DNA and middle repetitive chromosomal DNA does not exceed 2%. We discuss possible functions of these small circular DNAs in light of the above findings.

2 micrometer covalently closed non-mitochondrial circular DNA in the petite-negative yeast Schizosaccharomyces pombe

A population of small covalently closed non-mitochondrial circular DNA molecules was isolated from the petite-negative yeast Schizosaccharomyces pombe. The mean length of these molecules, possessing the same density as nuclear DNA (1.695 g/cm3) is 1.95 +/- 0.18 micrometer. The presence of these minicircles in crude mitochondrial preparations indicates their tight association with mitochondrial particles. Their disappearance after DNase treatment of mitochondria demonstrates their extramitochondrial location.

Circular molecules of heterogeneous size from mitochondrial fractions of the petite-negative yeast Schizosaccharomyces pombe

Size and shape of mitochondrial DNA molecules of Schizosaccharomyces pombe were analyzed by electron microscopy. Besides numerous linear molecules, circular molecules ranging from 0.83 micron to 12.81 micron were found. Depending on the method of preparation, both closed and open circular molecules were found. Most of the circular molecules could be assigned to five major size classes of 0.83 +/- 0.05 micron, 1.7 +/- 0.05 micron, 4.74 +/- 0.04 micron, 5.74 +/- 0.04 micron, and 8.32 +/- 0.07 micron. Possible explanations for the different size classes of mitochondrial DNA molecules are discussed.

A map of the restriction targets in yeast 2 micron plasmid DNA cloned on bacteriophage lambda

The 2 micron circular DNA from S. cerevisiae has been cloned on bacteriophage lambda. The two forms of circular DNA which exist in equilibrium due to recombination between inverted repeat sequences were separated as stable clones, and a map of targets for restriction endonucleases EcoRI, HindIII and HpaI was constructed. The circular DNAs isolated from a particular oligomycin resistant strain and its parent oligomycin snesitive strain were compared by restriction endonuclease analysis, and no difference was detected. The potential uses of cloned 2 micron DNA in determining the possible biological role of these plasmids are considered.