scholarly journals Ethidium bromide-mediated renaturation of denatured closed circular DNAs. The nature of denaturation-resistant fractions of bacteriophage PM2 closed circular DNA

1980 ◽  
Vol 8 (3) ◽  
pp. 673-701 ◽  
Author(s):  
Paul P. Lau ◽  
Horace B. Gray
Keyword(s):  
Ethidium Bromide ◽  
Circular Dna ◽  
Circular Dnas

scholarly journals Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA

2019 ◽  
Vol 47 (18) ◽  
pp. 9741-9760 ◽  
Author(s):  
V Talya Yerlici ◽  
Michael W Lu ◽  
Carla R Hoge ◽  
Richard V Miller ◽  
Rafik Neme ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Rearrangement ◽  
Genome Instability ◽  
Genome Rearrangements ◽  
Circular Dna ◽  
Dna Elimination ◽  
Circular Dnas ◽  
Bona Fide ◽  
Polymerase Chain ◽  
2D Gel

Abstract Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.

scholarly journals Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Iñigo Prada-Luengo ◽  
Anders Krogh ◽  
Lasse Maretty ◽  
Birgitte Regenberg
Keyword(s):  
Real Data ◽  
Circle Map ◽  
Sequencing Data ◽  
Rna Detection ◽  
Short Read ◽  
Circular Dna ◽  
Dna And Rna ◽  
Command Line Tool ◽  
Circular Dnas ◽  
Nucleotide Resolution

Abstract Background Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limiting their detection from short-read sequencing data. Results Here, we propose a new method, Circle-Map that guides the realignment of partially aligned reads using information from discordantly mapped reads to map the short unaligned portions using a probabilistic model. We compared Circle-Map to similar up-to-date methods for circular DNA and RNA detection and we demonstrate how the approach implemented in Circle-Map dramatically increases sensitivity for detection of circular DNA on both simulated and real data while retaining high precision. Conclusion Circle-Map is an easy-to-use command line tool that implements the required pipeline to accurately detect circular DNA from circle enriched next generation sequencing experiments. Circle-Map is implemented in python3.6 and it is freely available at https://github.com/iprada/Circle-Map.

scholarly journals Sequence characterization of eccDNA content in glyphosate sensitive and resistant Palmer amaranth from geographically distant populations

2021 ◽  
Author(s):  
Hailey Spier Camposano ◽  
Christopher A Saski ◽  
William Molin
Keyword(s):  
Ribosomal Proteins ◽  
Genome Structure ◽  
Genetic Resistance ◽  
Palmer Amaranth ◽  
Gene Copy ◽  
Circular Dna ◽  
Sequence Characterization ◽  
Epsps Gene ◽  
Repeat Content ◽  
Circular Dnas

The discovery of non-chromosomal circular DNA offers new directions in linking genome structure with function in plant biology.  Glyphosate resistance through  EPSPS  gene copy amplification in Palmer amaranth was due to an autonomously replicating extra-chromosomal circular DNA mechanism (eccDNA).  CIDER-Seq analysis of geographically distant glyphosate sensitive (GS) and resistant (GR) Palmer Amaranth ( Amaranthus palmeri ) revealed the presence of numerous small extra-chromosomal circular DNAs varying in size and with degrees of repetitive content, coding sequence, and motifs associated with autonomous replication. In GS biotypes, only a small portion of these aligned to the 399 kb eccDNA replicon, the vehicle underlying gene amplification and genetic resistance to the herbicide glyphosate. The aligned eccDNAs from GS were separated from one another by large gaps in sequence. In GR biotypes, the eccDNAs were present in both abundance and diversity to assemble into a nearly complete eccDNA replicon.  Mean sizes of eccDNAs were similar in both biotypes and were around 5kb with larger eccDNAs near 25kb.  Gene content for eccDNAs ranged from 0 to 3 with functions that include ribosomal proteins, transport, metabolism, and general stress response genetic elements. Repeat content among smaller eccDNAs indicate a potential for recombination into larger structures. Genomic hotspots were also identified in the Palmer amaranth genome with a disposition for gene focal amplifications as eccDNA. The presence of eccDNA may serve as a reservoir of genetic heterogeneity in this species and may be functionally important for survival.

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

Genome ◽  
1993 ◽  
Vol 36 (2) ◽  
pp. 244-254 ◽  
Author(s):  
S. Renault ◽  
F. Degroote ◽  
G. Picard
Keyword(s):  
Drosophila Melanogaster ◽  
Satellite Dna ◽  
Intergenic Spacer ◽  
Repeated Sequences ◽  
Basic Unit ◽  
Dna Molecules ◽  
Satellite Dnas ◽  
Circular Dna ◽  
Chi Sequence ◽  
Circular Dnas

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.Key words: D. melanogaster, extrachromosomal circular DNAs, repeated sequences, satellite DNA.

scholarly journals ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines

2020 ◽  
Vol 6 (20) ◽  
pp. eaba2489 ◽  
Author(s):  
Pankaj Kumar ◽  
Shashi Kiran ◽  
Shekhar Saha ◽  
Zhangli Su ◽  
Teressa Paulsen ◽  
...  
Keyword(s):  
Cell Lines ◽  
Inverse Pcr ◽  
Driver Genes ◽  
Circular Dna ◽  
Cancer Driver ◽  
Genome Wide ◽  
Number Variation ◽  
Circular Dnas ◽  
Tumor Types ◽  
Pan Cancer

Extrachromosomal circular DNAs (eccDNAs) are somatically mosaic and contribute to intercellular heterogeneity in normal and tumor cells. Because short eccDNAs are poorly chromatinized, we hypothesized that they are sequenced by tagmentation in ATAC-seq experiments without any enrichment of circular DNA. Indeed, ATAC-seq identified thousands of eccDNAs in cell lines that were validated by inverse PCR and by metaphase FISH. ATAC-seq in gliomas and glioblastomas identify hundreds of eccDNAs, including one containing the well-known EGFR gene amplicon from chr7. More than 18,000 eccDNAs, many carrying known cancer driver genes, are identified in a pan-cancer analysis of ATAC-seq libraries from 23 tumor types. Somatically mosaic eccDNAs are identified by ATAC-seq even before amplification is recognized by genome-wide copy number variation measurements. Thus, ATAC-seq is a sensitive method to detect eccDNA present in a tumor at the pre-amplification stage and can be used to predict resistance to therapy.

scholarly journals Repair of a synthetic abasic site in DNA in a Xenopus laevis oocyte extract.

1989 ◽  
Vol 9 (9) ◽  
pp. 3750-3757 ◽  
Author(s):  
Y Matsumoto ◽  
D F Bogenhagen
Keyword(s):  
Dna Damage ◽  
Xenopus Laevis ◽  
Dna Synthesis ◽  
Patch Repair ◽  
Synthetic Analog ◽  
Xenopus Laevis Oocyte ◽  
Synthesis Reaction ◽  
Abasic Site ◽  
Circular Dna ◽  
Circular Dnas

Covalently closed circular DNA containing a synthetic analog of an abasic site at a unique position was used as a substrate to study DNA repair. Incubation of this DNA in Xenopus laevis oocyte extracts resulted in rapid cleavage of the DNA at the abasic site by a class II apurinic-apyrimidinic endonuclease, followed by complete repair within 40 min. Nicked circular DNAs persisted for several minutes before repair by an ATP-dependent DNA synthesis reaction. The repair-related DNA synthesis was localized within 3 or 4 nucleotides surrounding the abasic site. These results are consistent with the short-patch repair reported for DNA damage at heterogeneous sites in human cells (J. D. Regan and R. B. Setlow, Cancer Res. 34:3318-3325, 1974).

Repair of a synthetic abasic site in DNA in a Xenopus laevis oocyte extract

1989 ◽  
Vol 9 (9) ◽  
pp. 3750-3757
Author(s):  
Y Matsumoto ◽  
D F Bogenhagen
Keyword(s):  
Dna Damage ◽  
Xenopus Laevis ◽  
Dna Synthesis ◽  
Patch Repair ◽  
Synthetic Analog ◽  
Xenopus Laevis Oocyte ◽  
Synthesis Reaction ◽  
Abasic Site ◽  
Circular Dna ◽  
Circular Dnas

Covalently closed circular DNA containing a synthetic analog of an abasic site at a unique position was used as a substrate to study DNA repair. Incubation of this DNA in Xenopus laevis oocyte extracts resulted in rapid cleavage of the DNA at the abasic site by a class II apurinic-apyrimidinic endonuclease, followed by complete repair within 40 min. Nicked circular DNAs persisted for several minutes before repair by an ATP-dependent DNA synthesis reaction. The repair-related DNA synthesis was localized within 3 or 4 nucleotides surrounding the abasic site. These results are consistent with the short-patch repair reported for DNA damage at heterogeneous sites in human cells (J. D. Regan and R. B. Setlow, Cancer Res. 34:3318-3325, 1974).

scholarly journals Mitochondrial genetics, circular DNA and the mechanism of thepetitemutation in yeast

1974 ◽  
Vol 24 (1) ◽  
pp. 43-57 ◽  
Author(s):  
G. D. Clark-Walker ◽  
George L. Gabor Miklos
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Structural Rearrangements ◽  
Dna Molecules ◽  
Mitochondrial Genetics ◽  
General Hypothesis ◽  
Mitochondrial Recombination ◽  
Circular Dna ◽  
Bacterial Plasmids ◽  
Circular Dnas

SUMMARYWe propose a general hypothesis involving properties of circular DNA which can explain such phenomena as thepetitemutation, suppressiveness, and the polarity observed in mitochondrial recombination in the yeastSaccharomyces cerevisiae. This hypothesis involves excision and insertion events between circular DNA molecules as well as structural rearrangements in the DNA generated by these events. The special properties of circular DNA have been considered in analysing recombination, and a number of results are obtained which are not intuitively apparent.This hypothesis can be applied to any situation involving circular DNA such as bacterial plasmids and cytoplasmic circular DNAs, where the opportunity exists for recombination and rearrangement events.

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