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Wenyi Gu, Surong Sun, Andrew Kahn, Dalton Dacus, Sebastian O Wendel, Nigel McMillan, Nicholas A Wallace
High risk human papillomavirus (HPV) infections are the causative agent in virtually every cervical cancer as well as a host of other anogenital and oropharyngeal malignancies. These viruses must activate DNA repair pathways to facilitate their replication, while avoiding the cell cycle arrest and apoptosis that can accompany DNA damage. HPV oncoproteins facilitate each of these goals, but also reduce genome stability. Our data dissect the cytotoxic and cytoprotective characteristics of HPV oncogenes in cervical cancer cells...
December 2, 2018: Gene
Michal Sobecki, Charbel Souaid, Jocelyne Boulay, Vincent Guerineau, Daan Noordermeer, Laure Crabbe
Mapping the binding sites of DNA- or chromatin-interacting proteins is essential to understanding biological processes. DNA adenine methyltransferase identification (DamID) has emerged as a comprehensive method to map genome-wide occupancy of proteins of interest. A caveat of DamID is the specificity of Dam methyltransferase for GATC motifs that are not homogenously distributed in the genome. Here, we developed an optimized method named MadID, using proximity labeling of DNA by the methyltransferase M.EcoGII...
December 4, 2018: Cell Reports
Hongbo Ling, Lirong Peng, Jianbo Wang, Raneen Rahhal, Edward Seto
The protein deacetylase SIRT1 (Sirtuin 1) regulates many cellular processes, including cell-cycle progression, DNA damage response, and metabolism. Although the centrosome is a key regulator of cell-cycle progression and genome stability, little is known concerning SIRT1 controlled centrosome-associated events. Here we report that the centrosome protein Plk2 is acetylated and undergoes deacetylation by SIRT1. Acetylation protects Plk2 from ubiquitination, and SIRT1-mediated deacetylation promotes ubiquitin-dependent degradation of Plk2...
December 4, 2018: Cell Reports
Elmar W Tobi, Joost van den Heuvel, Bas J Zwaan, L H Lumey, Bastiaan T Heijmans, Tobias Uller
An adverse intrauterine environment is associated with long-term physiological changes in offspring. These are believed to be mediated by epigenomic marks, including DNA methylation (DNAm). Changes in DNAm are often interpreted as damage or plastic responses of the embryo. Here, we propose that stochastic DNAm variation, generated during remodeling of the epigenome after fertilization, contributes to DNAm signatures of prenatal adversity through differential survival of embryos. Using a mathematical model of re-methylation in the early embryo, we demonstrate that selection, but not plasticity, will generate a characteristic reduction in DNAm variance at loci that contribute to survival...
December 4, 2018: Cell Reports
Anindya Biswas, Semanti Ghosh, Debabrata Sinha, Anindya Dutta, Soham Seal, Anshuman Bagchi, Subrata Sau
The lysogenic growth of phage ф11 in Staphylococcus aureus is controlled by a repressor (CI) that harbors an N-terminal domain (NTD), and a C-terminal domain (CTD). Previously, NTD, like CI, showed DNA binding activity and dimerized in the aqueous solution. To precisely understand the folding mechanism, function, and the stability of CI, NTD, and CTD, we have investigated their recombinant forms, rCI, rNTD, and rCTD, using various probes. The data reveal that rCTD, like rCI and rNTD, is a well-structured protein and produces dimers in the aqueous environment...
December 2, 2018: International Journal of Biological Macromolecules
Lufen Chang, Lei Shen, Hu Zhou, Jing Gao, Hangyi Pan, Li Zheng, Brian Armstrong, Yang Peng, Guang Peng, Binhua P Zhou, Steven T Rosen, Binghui Shen
The downregulation of the DNA damage response (DDR) enables aggressive tumors to achieve uncontrolled proliferation against replication stress, but the mechanisms underlying this process in tumors are relatively complex. Here, we demonstrate a mechanism through which a distinct E3 ubiquitin ligase, ITCH, modulates DDR machinery in triple-negative breast cancer (TNBC). We found that expression of a nuclear form of ITCH was significantly increased in human TNBC cell lines and tumor specimens. Phosphorylation of ITCH at Ser257 by AKT led to the nuclear localization of ITCH and ubiquitination of H1...
December 4, 2018: Nucleic Acids Research
Rebekah L Rogers, Long Zhou, Chong Chu, Roberto Márquez, Ammon Corl, Tyler Linderoth, Layla Freeborn, Matthew D MacManes, Zijun Xiong, Jiao Zheng, Chunxue Guo, Xu Xun, Marcus R Kronforst, Kyle Summers, Yufeng Wu, Huanming Yang, Corinne L Richards-Zawacki, Guojie Zhang, Rasmus Nielsen
We sequenced the genome of the strawberry poison frog, Oophaga pumilio, at a depth of 127.5× using variable insert size libraries. The total genome size is estimated to be 6.76 Gb, of which 4.76 Gb are from high copy number repetitive elements with low differentiation across copies. These repeats encompass DNA transposons, RNA transposons, and LTR retrotransposons, including at least 0.4 and 1.0 Gb of Mariner/Tc1 and Gypsy elements, respectively. Expression data indicate high levels of gypsy and Mariner/Tc1 expression in ova of O...
December 1, 2018: Molecular Biology and Evolution
Arthur R Gorter de Vries, Lucas G F Couwenberg, Marcel van den Broek, Pilar de la Torre Cortés, Jolanda Ter Horst, Jack T Pronk, Jean-Marc G Daran
Targeted DNA double-strand breaks (DSBs) with CRISPR-Cas9 have revolutionized genetic modification by enabling efficient genome editing in a broad range of eukaryotic systems. Accurate gene editing is possible with near-perfect efficiency in haploid or (predominantly) homozygous genomes. However, genomes exhibiting polyploidy and/or high degrees of heterozygosity are less amenable to genetic modification. Here, we report an up to 99-fold lower gene editing efficiency when editing individual heterozygous loci in the yeast genome...
December 5, 2018: Nucleic Acids Research
Daniel O'Reilly, Zachary J Kartje, Eman A Ageely, Elise Malek-Adamian, Maryam Habibian, Annabelle Schofield, Christopher L Barkau, Kushal J Rohilla, Lauren B DeRossett, Austin T Weigle, Masad J Damha, Keith T Gagnon
CRISPR (clustered regularly interspaced short palindromic repeat) endonucleases are at the forefront of biotechnology, synthetic biology and gene editing. Methods for controlling enzyme properties promise to improve existing applications and enable new technologies. CRISPR enzymes rely on RNA cofactors to guide catalysis. Therefore, chemical modification of the guide RNA can be used to characterize structure-activity relationships within CRISPR ribonucleoprotein (RNP) enzymes and identify compatible chemistries for controlling activity...
December 4, 2018: Nucleic Acids Research
Jun Xiong, Tian-Tian Ye, Cheng-Jie Ma, Qing-Yun Cheng, Bi-Feng Yuan, Yu-Qi Feng
In addition to DNA cytosine methylation (5-methyl-2'-deoxycytidine, m5dC), DNA adenine methylation (N6-methyl-2'-deoxyadenosine, m6dA) is another DNA modification that has been discovered in eukaryotes. Recent studies demonstrated that the content and distribution of m6dA in genomic DNA of vertebrates and mammals exhibit dynamic regulation, indicating m6dA may function as a potential epigenetic mark in DNA of eukaryotes besides m5dC. Whether m6dA undergoes the further oxidation in a similar way to m5dC remains elusive...
December 4, 2018: Nucleic Acids Research
Wataru Kobiayashi, Enwei Liu, Hajime Ishii, Sachihiro Matsunaga, Peter Schlögelhofer, Hitoshi Kurumizaka
In eukaryotes, homologous recombination plays a pivotal role in both genome maintenance and generation of genetic diversity. Eukaryotic RecA homologues, RAD51 and DMC1, are key proteins in homologous recombination that promote pairing between homologous DNA sequences. Arabidopsis thaliana is a prominent model plant for studying eukaryotic homologous recombination. However, A. thaliana RAD51 and DMC1 have not been biochemically characterized. In the present study, we purified A. thaliana RAD51 (AtRAD51) and DMC1 (AtDMC1)...
December 5, 2018: Journal of Biochemistry
Pierre Dupuy, Laurent Sauviac, Claude Bruand
DNA double-strand breaks (DSB) in bacteria can be repaired by non-homologous end-joining (NHEJ), a two-component system relying on Ku and LigD. While performing a genetic characterization of NHEJ in Sinorhizobium meliloti, a representative of bacterial species encoding several Ku and LigD orthologues, we found that at least two distinct functional NHEJ repair pathways co-exist: one is dependent on Ku2 and LigD2, while the other depends on Ku3, Ku4 and LigD4. Whereas Ku2 likely acts as canonical bacterial Ku homodimers, genetic evidences suggest that Ku3-Ku4 form eukaryotic-like heterodimers...
December 4, 2018: Nucleic Acids Research
Marius Gheorghe, Geir Kjetil Sandve, Aziz Khan, Jeanne Chèneby, Benoit Ballester, Anthony Mathelier
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most popular assay to identify genomic regions, called ChIP-seq peaks, that are bound in vivo by transcription factors (TFs). These regions are derived from direct TF-DNA interactions, indirect binding of the TF to the DNA (through a co-binding partner), nonspecific binding to the DNA, and noise/bias/artifacts. Delineating the bona fide direct TF-DNA interactions within the ChIP-seq peaks remains challenging. We developed a dedicated software, ChIP-eat, that combines computational TF binding models and ChIP-seq peaks to automatically predict direct TF-DNA interactions...
December 4, 2018: Nucleic Acids Research
Weina Ke, Enping Hong, Renata F Saito, Maria Cristina Rangel, Jian Wang, Mathias Viard, Melina Richardson, Emil F Khisamutdinov, Martin Panigaj, Nikolay V Dokholyan, Roger Chammas, Marina A Dobrovolskaia, Kirill A Afonin
Nucleic acid-based assemblies that interact with each other and further communicate with the cellular machinery in a controlled manner represent a new class of reconfigurable materials that can overcome limitations of traditional biochemical approaches and improve the potential therapeutic utility of nucleic acids. This notion enables the development of novel biocompatible 'smart' devices and biosensors with precisely controlled physicochemical and biological properties. We extend this novel concept by designing RNA-DNA fibers and polygons that are able to cooperate in different human cell lines and that have defined immunostimulatory properties confirmed by ex vivo experiments...
December 4, 2018: Nucleic Acids Research
Dmitry Sutormin, Natalia Rubanova, Maria Logacheva, Dmitry Ghilarov, Konstantin Severinov
An important antibiotic target, DNA gyrase is an essential bacterial enzyme that introduces negative supercoils into DNA and relaxes positive supercoils accumulating in front of moving DNA and RNA polymerases. By altering the superhelical density, gyrase may regulate expression of bacterial genes. The information about how gyrase is distributed along genomic DNA and whether its distribution is affected by drugs is scarce. During catalysis, gyrase cleaves both DNA strands forming a covalently bound intermediate...
December 4, 2018: Nucleic Acids Research
Lex Flagel, Yaniv Brandvain, Daniel R Schrider
Population-scale genomic datasets have given researchers incredible amounts of information from which to infer evolutionary histories. Concomitant with this flood of data, theoretical and methodological advances have sought to extract information from genomic sequences to infer demographic events such as population size changes and gene flow among closely related populations/species, construct recombination maps, and uncover loci underlying recent adaptation. To date most methods make use of only one or a few summaries of the input sequences and therefore ignore potentially useful information encoded in the data...
December 4, 2018: Molecular Biology and Evolution
Luca Boeri, Paolo Capogrosso, Eugenio Ventimiglia, Filippo Pederzoli, Walter Cazzaniga, Francesco Chierigo, Edoardo Pozzi, Massimo Clementi, Paola Viganò, Emanuele Montanari, Francesco Montorsi, Andrea Salonia
STUDY QUESTION: Does the presence of human papillomavirus (HPV) in semen impact seminal parameters and sperm DNA quality in white European men seeking medical help for primary couple's infertility? SUMMARY ANSWER: HPV seminal infections involving high-risk (HR) genotypes are associated with impaired sperm progressive motility and sperm DNA fragmentation (SDF) values. WHAT IS KNOWN ALREADY: HPV is commonly present in semen samples. However, whether the presence of HPV in semen is actually associated with impaired sperm parameters and SDF values have yet to be elucidated...
December 4, 2018: Human Reproduction
Isabelle Accoceberry, Célia Couzigou, Valérie Fitton-Ouhabi, Nicolas Biteau, Thierry Noël
Objectives: A strain of the opportunistic pathogenic yeast Candida lusitaniae was genetically engineered for full-length replacement of the FKS1 gene encoding the target of echinocandin antifungals in order to assess the impact of FKS mutations on echinocandin resistance and reduced echinocandin susceptibility (RES). Methods: FKS1 allelic exchange was achieved by transforming C. lusitaniae with two DNA fragments covering the entire FKS1 ORF. Both fragments overlap a 40 bp region where SNPs or small indels of interest were inserted...
December 4, 2018: Journal of Antimicrobial Chemotherapy
Ricardo Roberto de Souza Fonseca, Ana Cláudia Braga Amoras Alves, Thalita de Almeida Amanajás, Brenna Magdalena Lima Nogueira, Tatiany Oliveira de Alencar Menezes, Leonardo Quintão Siravenha, Danilo Leôncio Aguiar Pereira, Luiz Fernando Almeida Machado, Luciana Campêlo da Silva Gilet, Silvio Augusto Fernandes de Menezes
INTRODUCTION: The influence of cytomegalovirus (CMV) on the progression of chronic periodontitis in HIV patients is poorly investigated. METHODS: ELISA was used for anti-CMV antibody IgG titer measurements and real-time polymerase chain reaction for qualitative and quantitative CMV detection. Data on the CD4 + T lymphocyte count and plasma HIV viral load were obtained from patient records. RESULTS: CMV DNA was detected in samples of subgingival biofilm in only three individuals, two of them with chronic periodontitis (4%) and one with gingivitis (3...
November 2018: Revista da Sociedade Brasileira de Medicina Tropical
Leticia Amésquita, María Nimia Cruz-Briceño, Zulita Prieto
The objective of the study was to evaluate the effect of chloroquine (CQ) on human lymphocytes through the Comet Assay. Lymphocytes were isolated from peripheral blood samples obtained from three healthy, non-smoking donors aged 24 to 30 years. The isolated lymphocytes were exposed for one hour to various treatments: hydrogen peroxide 2.5% (positive control), saline buffer phosphate 1X (negative control) and chloroquine at concentrations of 0 µg/ml, 0.25 µg/ml; 5 µg/ml and 300 µg/ml. The averages of the percentage of DNA in the comet tail, moment of tail and moment of Olive's tail were recorded, with significant differences between the different concentrations of CQ (p<0...
July 2018: Revista Peruana de Medicina Experimental y Salud Pública
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