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Extrachromosomal DNA

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https://www.readbyqxmd.com/read/28324510/analysis-of-telomere-homologous-dna-with-different-conformations-using-2d-agarose-electrophoresis-and-in-gel-hybridization
#1
Zepeng Zhang, Qian Hu, Yong Zhao
In mammalian cells, in addition to double-stranded telomeric DNA at chromosome ends, extra telomere-homologous DNA is present that adopts different conformations, including single-stranded G- or C-rich DNA, extrachromosomal circular DNA (T-circle), and telomeric complex (T-complex) with an unidentified structure. The formation of such telomere-homologous DNA is closely related to telomeric DNA metabolism and chromosome end protection by telomeres. Conventional agarose gel electrophoresis is unable to separate DNA based on conformation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28239156/cancer-genomics-ecdetect-hunts-extrachromosomal-dna
#2
Shimona Starling
No abstract text is available yet for this article.
April 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28230082/tubz-filament-assembly-dynamics-requires-the-flexible-c-terminal-tail
#3
Maria E Fuentes-Pérez, Rafael Núñez-Ramírez, Alejandro Martín-González, David Juan-Rodríguez, Oscar Llorca, Fernando Moreno-Herrero, Maria A Oliva
Cytomotive filaments are essential for the spatial organization in cells, showing a dynamic behavior based on nucleotide hydrolysis. TubZ is a tubulin-like protein that functions in extrachromosomal DNA movement within bacteria. TubZ filaments grow in a helical fashion following treadmilling or dynamic instability, although the underlying mechanism is unclear. We have unraveled the molecular basis for filament assembly and dynamics combining electron and atomic force microscopy and biochemical analyses. Our findings suggest that GTP caps retain the filament helical structure and hydrolysis triggers filament stiffening upon disassembly...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28213352/extrachromosomal-dna-amplifications-increase-oncogene-copy-number
#4
(no author information available yet)
Circular extrachromosomal DNA (ecDNA) amplifications promote tumor heterogeneity and evolution.
February 17, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28212615/molecular-pathways-underlying-inhibitory-effect-of-antimicrobial-peptide-nal-p-113-on-bacteria-biofilms-formation-of-porphyromonas-gingivalis-w83-by-dna-microarray
#5
Hong-Yan Wang, Li Lin, Li-Si Tan, Hui-Yuan Yu, Jya-Wei Cheng, Ya-Ping Pan
BACKGROUND: Wound-related infection remains a major challenge for health professionals. One disadvantage in conventional antibiotics is their inability to penetrate biofilms, the main protective strategy for bacteria to evade irradiation. Previously, we have shown that synthetic antimicrobial peptides could inhibit bacterial biofilms formation. RESULTS: In this study, we first delineated how Nal-P-113, a novel antimicrobial peptide, exerted its inhibitory effects on Porphyromonas gingivalis W83 biofilms formation at a low concentration...
February 17, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28212378/sequencing-the-extrachromosomal-circular-mobilome-reveals-retrotransposon-activity-in-plants
#6
Sophie Lanciano, Marie-Christine Carpentier, Christel Llauro, Edouard Jobet, Dagmara Robakowska-Hyzorek, Eric Lasserre, Alain Ghesquière, Olivier Panaud, Marie Mirouze
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28178237/extrachromosomal-oncogene-amplification-drives-tumour-evolution-and-genetic-heterogeneity
#7
Kristen M Turner, Viraj Deshpande, Doruk Beyter, Tomoyuki Koga, Jessica Rusert, Catherine Lee, Bin Li, Karen Arden, Bing Ren, David A Nathanson, Harley I Kornblum, Michael D Taylor, Sharmeela Kaushal, Webster K Cavenee, Robert Wechsler-Reya, Frank B Furnari, Scott R Vandenberg, P Nagesh Rao, Geoffrey M Wahl, Vineet Bafna, Paul S Mischel
Human cells have twenty-three pairs of chromosomes. In cancer, however, genes can be amplified in chromosomes or in circular extrachromosomal DNA (ecDNA), although the frequency and functional importance of ecDNA are not understood. We performed whole-genome sequencing, structural modelling and cytogenetic analyses of 17 different cancer types, including analysis of the structure and function of chromosomes during metaphase of 2,572 dividing cells, and developed a software package called ECdetect to conduct unbiased, integrated ecDNA detection and analysis...
March 2, 2017: Nature
https://www.readbyqxmd.com/read/28137853/binding-sliding-and-function-of-cohesin-during-transcriptional-activation
#8
Melinda S Borrie, John S Campor, Hansa Joshi, Marc R Gartenberg
The ring-shaped cohesin complex orchestrates long-range DNA interactions to mediate sister chromatid cohesion and other aspects of chromosome structure and function. In the yeast Saccharomyces cerevisiae, the complex binds discrete sites along chromosomes, including positions within and around genes. Transcriptional activity redistributes the complex to the 3' ends of convergently oriented gene pairs. Despite the wealth of information about where cohesin binds, little is known about cohesion at individual chromosomal binding sites and how transcription affects cohesion when cohesin complexes redistribute...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096488/novel-superspreader-bacteriophages-promote-horizontal-gene-transfer-by-transformation
#9
Eric C Keen, Valery V Bliskovsky, Francisco Malagon, James D Baker, Jeffrey S Prince, James S Klaus, Sankar L Adhya
Bacteriophages infect an estimated 10(23) to 10(25) bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28068490/food-analysis-using-organelle-dna-and-the-effects-of-processing-on-assays
#10
Jane M Caldwell
Extrachromosomal DNA such as organelle DNA are increasingly targeted in molecular detection assays where samples have been degraded by physical or chemical means. Owing to multiple organelles per cell and greater copy numbers than nuclear genes, organelle gene targets provide a more robust signal in polymerase chain reaction (PCR), quantitative PCR (qPCR), and other emerging molecular technologies. Because of these advantages, direct analysis of organelle DNA in food matrices is used for detection of contaminants and identification and authentication of food ingredients and allergens...
February 28, 2017: Annual Review of Food Science and Technology
https://www.readbyqxmd.com/read/28042541/rational-development-of-a-polycistronic-plasmid-with-a-cpg-free-bacterial-backbone-as-a-potential-tool-for-direct-reprogramming
#11
Kianoush Dormiani, Hamid Mir Mohammad Sadeghi, Hojjat Sadeghi-Aliabadi, Mahboobeh Forouzanfar, Hossein Baharvand, Kamran Ghaedi, Mohammad Hossein Nasr-Esfahani
OBJECTIVE: Induced pluripotent stem cells are generated from somatic cells by direct reprogramming. These reprogrammed pluripotent cells have different applications in biomedical fields such as regenerative medicine. Although viral vectors are widely used for efficient reprogramming, they have limited applications in the clinic due to the risk for immunogenicity and insertional mutagenesis. Accordingly, we designed and developed a small, non-integrating plasmid named pLENSO/Zeo as a 2A-mediated polycistronic expression vector...
2017: Cell Journal
https://www.readbyqxmd.com/read/27911392/optogenetic-random-mutagenesis-using-histone-minisog-in-c-elegans
#12
Kentaro Noma, Yishi Jin
Forward genetic screening in model organisms is the workhorse to discover functionally important genes and pathways in many biological processes. In most mutagenesis-based screens, researchers have relied on the use of toxic chemicals, carcinogens, or irradiation, which requires designated equipment, safety setup, and/or disposal of hazardous materials. We have developed a simple approach to induce heritable mutations in C. elegans using germline-expressed histone-miniSOG, a light-inducible potent generator of reactive oxygen species...
November 14, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27893790/detection-of-a-cfr-b-variant-in-german-enterococcus-faecium-clinical-isolates-and-the-impact-on-linezolid-resistance-in-enterococcus-spp
#13
Jennifer K Bender, Carola Fleige, Ingo Klare, Stefan Fiedler, Alexander Mischnik, Nico T Mutters, Kate E Dingle, Guido Werner
The National Reference Centre for Staphylococci and Enterococci in Germany has received an increasing number of clinical linezolid-resistant E. faecium isolates in recent years. Five isolates harbored a cfr(B) variant gene locus the product of which is capable of conferring linezolid resistance. The cfr(B)-like methyltransferase gene was also detected in Clostridium difficile. Antimicrobial susceptibility was determined for cfr(B)-positive and linezolid-resistant E. faecium isolates and two isogenic C. difficile strains...
2016: PloS One
https://www.readbyqxmd.com/read/27879331/brd4-activates-early-viral-transcription-upon-human-papillomavirus-18-infection-of-primary-keratinocytes
#14
Caleb C McKinney, Min Jung Kim, Dan Chen, Alison A McBride
Human papillomaviruses (HPVs) replicate in the cutaneous and mucosal epithelia, and the infectious cycle is synchronous with the differentiation program of the host keratinocytes. The virus initially infects dividing cells in the lower layers of the epithelium, where it establishes a persistent infection. The viral genome is maintained as a low-copy-number, extrachromosomal element in these proliferating cells but switches to the late stage of the life cycle in differentiated cells. The cellular chromatin adaptor protein Brd4 is involved in several stages and processes of the viral life cycle...
November 22, 2016: MBio
https://www.readbyqxmd.com/read/27741255/complete-circular-genome-sequence-of-successful-st8-sccmeciv-community-associated-methicillin-resistant-staphylococcus-aureus-oc8-in-russia-one-megabase-genomic-inversion-is256-s-spread-and-evolution-of-russia-st8-iv
#15
Tsai-Wen Wan, Olga E Khokhlova, Yasuhisa Iwao, Wataru Higuchi, Wei-Chun Hung, Ivan V Reva, Olga A Singur, Vladimir V Gostev, Sergey V Sidorenko, Olga V Peryanova, Alla B Salmina, Galina V Reva, Lee-Jene Teng, Tatsuo Yamamoto
ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split...
2016: PloS One
https://www.readbyqxmd.com/read/27733851/dynamics-of-a-class-1-integron-located-on-plasmid-or-chromosome-in-two-aeromonas-spp-strains
#16
Abigail Pérez-Valdespino, Alfredo Lazarini-Martínez, Alejandro X Rivera-González, Normand García-Hernández, Everardo Curiel-Quesada
Integrons are non-mobile bacterial genetic elements that carry different cassettes conferring antibiotic resistance. Cassettes can excise or integrate by action of an integron-encoded integrase, enabling bacteria to face environmental challenges. In this work, the functionality and dynamics of two integrons carrying the same cassette arrangement (dfrA12-orfF-aadA2), but located on plasmid or chromosome in two different strains were studied. In order to demonstrate the functionality of the Class 1 integrase, circular cassette integration intermediaries were PCR amplified by PCR using extrachromosomal DNA extracted from bacteria grown in the presence or absence of cassette-encoded antibiotics...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27716469/characterization-of-nonpathogenic-listeria-species-isolated-from-food-and-food-processing-environment
#17
Dorota Korsak, Magdalena Szuplewska
A total of 127 Listeria isolates from food and food processing environments, including 75 L. innocua, 49 L. welshimeri, 2 L. seeligeri and 1L. grayi were tested for susceptibility to eight antimicrobials, benzalkonium chloride (BC), cadmium and arsenic. The isolates were also screened for the presence of extrachromosomal genetic elements - plasmids, and their restriction pattern types were determined. All strains were susceptible to ampicillin, ciprofloxacin, erythromycin, gentamicin, rifampicin, trimethoprim and vancomycin...
December 5, 2016: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/27709566/mutagenesis-and-genome-engineering-of-epstein-barr-virus-in-cultured-human-cells-by-crispr-cas9
#18
Kit-San Yuen, Chi-Ping Chan, Kin-Hang Kok, Dong-Yan Jin
The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 nuclease (Cas9) system is a powerful genome-editing tool for both chromosomal and extrachromosomal DNA. DNA viruses such as Epstein-Barr virus (EBV), which undergoes episomal replication in human cells, can be effectively edited by CRISPR/Cas9. We have demonstrated targeted editing of the EBV genome by CRISPR/Cas9 in several lines of EBV-infected cells. CRISPR/Cas9-based mutagenesis and genome engineering of EBV provides a new method for genetic analysis, which has some advantages over bacterial artificial chromosome-based recombineering...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27705914/extrachromosomal-hpv-16-lcr-transcriptional-activation-by-hdaci-opposed-by-cellular-differentiation-and-dna-integration
#19
Ekaterina Dimitrova Bojilova, Christine Weyn, Marie-Hélène Antoine, Véronique Fontaine
Histone deacetylase inhibitors (HDACi) have been shown to render HPV-carrying cells susceptible to intrinsic and extrinsic apoptotic signals. As such, these epigenetic drugs have entered clinical trials in the effort to treat cervical cancer. Here, we studied the effect of common HDACi, with an emphasis on Trichostatin A (TSA), on the transcriptional activity of the HPV-16 Long Control Region (LCR) in order to better understand the impact of these agents in the context of the HPV life cycle and infection. HDACi strongly induced transcription of the firefly luciferase reporter gene under the control of the HPV-16 LCR in a variety of cell lines...
September 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27699529/hpv-integration-in-head-and-neck-squamous-cell-carcinomas-cause-and-consequence
#20
REVIEW
Ernst Jan M Speel
Human papillomaviruses (HPVs) are a necessary cause of anogenital squamous cell carcinomas (SCC) and a subgroup of head and neck SCC, i.e., those originating in the oropharynx. The key events in high-risk HPV (HRHPV)-associated neoplastic progression include persistent infection, deregulated expression of virus early genes in basal epithelial cells, local immune suppression and the accumulation of chromosomal alterations. Evidence for these events particularly comes from studies of uterine cervical carcinogenesis; primary premalignant HRHPV-positive lesions of the head and neck mucosa are seldomly detected...
2017: Recent Results in Cancer Research
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