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https://www.readbyqxmd.com/read/29453899/the-role-of-dna-pk-in-aging-and-energy-metabolism
#1
REVIEW
Jay H Chung
DNA-dependent protein kinase (DNA-PK) is a very large holoenzyme comprised of the p470 kDa DNA-PK catalytic subunit (DNA-PK cs ) and the Ku heterodimer consisting of the p86 (Ku 80) and p70 (Ku 70) subunits. It is best known for its non-homologous end joining (NHEJ) activity, which repairs double-strand DNA (dsDNA) breaks (DSBs). As expected, the absence of DNA-PK activity results in sensitivity to ionizing radiation, which generates DSBs and defect in lymphocyte development, which requires NHEJ of the V(D)J region in the immunoglobulin and T cell receptor loci...
February 17, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29453254/development-of-a-versatile-cas9-driven-subpopulation-selection-toolbox-in-lactococcus-lactis
#2
Simon van der Els, Jennelle K James, Michiel Kleerebezem, Peter A Bron
CRISPR-Cas9 technology has been exploited for the removal or replacement of genetic elements in a wide range of prokaryotes and eukaryotes. Here we describe the extension of the Cas9 application toolbox to the industrially important dairy species Lactococcus lactis The Cas9 expression vector pLABTarget was constructed, encoding the Streptocccus pyogenes Cas9 under control of a constitutive promoter, and allowing plug and play introduction of sgRNA sequences to target specific genetic loci. Introduction of a pepN -targeting derivative of pLABTarget into L...
February 16, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29452769/the-radiation-resistance-of-human-multipotent-mesenchymal-stromal-cells-is-independent-of-their-tissue-of-origin
#3
Alexander Rühle, Oliver Xia, Ramon Lopez Perez, Thuy Trinh, Wiltrud Richter, Anna Sarnowska, Patrick Wuchter, Jürgen Debus, Rainer Saffrich, Peter E Huber, Nils H Nicolay
PURPOSE: Human mesenchymal stromal cells (MSCs) may aid the regeneration of ionizing radiation (IR)-induced tissue damage. They can be harvested from different tissues for clinical purposes; however, the role of the tissue source on the radiation response of human MSCs remains unknown. METHODS AND MATERIALS: Human MSCs were isolated from adipose tissue, bone marrow, and umbilical cord, and cellular survival, proliferation, and apoptosis were measured after irradiation...
January 9, 2018: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/29452234/exploring-the-deleterious-snps-in-xrcc4-gene-using-computational-approach-and-studying-their-association-with-breast-cancer-in-the-population-of-west-india
#4
Preety Kadian Singh, Kinnari Mistry, C Haritha, D N Rank, Chaitanya Joshi
Non-homologous end joining (NHEJ) pathway has pivotal role in repair of double-strand DNA breaks that may lead to carcinogenesis. XRCC4 is one of the essential proteins of this pathway and single-nucleotide polymorphisms (SNPs) of this gene are reported to be associated with cancer risks. In our study, we first used computational approaches to predict the damaging variants of XRCC4 gene. Tools predicted rs79561451 (S110P) nsSNP as the most deleterious SNP. Along with this SNP, we analysed other two SNPs (rs3734091 and rs6869366) to study their association with breast cancer in population of West India...
February 13, 2018: Gene
https://www.readbyqxmd.com/read/29449511/crispr-cas12a-target-binding-unleashes-indiscriminate-single-stranded-dnase-activity
#5
Janice S Chen, Enbo Ma, Lucas B Harrington, Maria Da Costa, Xinran Tian, Joel M Palefsky, Jennifer A Doudna
CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind and cut DNA as components of bacterial adaptive immune systems. Like CRISPR-Cas9, Cas12a has been harnessed for genome editing based on its ability to generate targeted, double-stranded DNA (dsDNA) breaks. Here we show that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA (ssDNA) cleavage activity by Cas12a that completely degrades ssDNA molecules. We find that target-activated, non-specific ssDNase cleavage is also a property of other type V CRISPR-Cas12 enzymes...
February 15, 2018: Science
https://www.readbyqxmd.com/read/29448059/monte-carlo-simulation-of-the-relative-biological-effectiveness-and-dna-damage-from-a-400-mev-u-carbon-ion-beam-in-water
#6
Haifeng Ou, Bin Zhang, Shujun Zhao
A 400 MeV/u carbon ion beam incident on a water phantom was simulated with GATE/Geant4 to calculate the energy spectra of 12 C and its fragments at various depths. Based on the energy spectra, the DNA double strand break (DSB) yields from 12 C and its fragments were calculated with Monte Carlo Damage Simulation (MCDS) code. The relative biological effectiveness (RBE) distributions for 12 C and its fragments were calculated from the DSB yields. The DNA damages from each type of the particles and their contribution to the total DNA damages at various depths were calculated from the DSB yields and dose distributions...
January 31, 2018: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/29447390/pold3-is-required-for-genomic-stability-and-telomere-integrity-in-embryonic-stem-cells-and-meiosis
#7
Zhongcheng Zhou, Lingling Wang, Feixiang Ge, Peng Gong, Hua Wang, Feng Wang, Lingyi Chen, Lin Liu
Embryonic stem cells (ESCs) and meiosis are featured by relatively higher frequent homologous recombination associated with DNA double strand breaks (DSB) repair. Here, we show that Pold3 plays important roles in DSB repair, telomere maintenance and genomic stability of both ESCs and spermatocytes in mice. By attempting to generate Pold3 deficient mice using CRISPR/Cas9 or transcription activator-like effector nucleases, we show that complete loss of Pold3 (Pold3-/-) resulted in early embryonic lethality at E6...
February 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29447383/super-resolution-imaging-identifies-parp1-and-the-ku-complex-acting-as-dna-double-strand-break-sensors
#8
Guang Yang, Chao Liu, Shih-Hsun Chen, Muzaffer A Kassab, J Damon Hoff, Nils G Walter, Xiaochun Yu
DNA double-strand breaks (DSBs) are fatal DNA lesions and activate a rapid DNA damage response. However, the earliest stage of DSB sensing remains elusive. Here, we report that PARP1 and the Ku70/80 complex localize to DNA lesions considerably earlier than other DSB sensors. Using super-resolved fluorescent particle tracking, we further examine the relocation kinetics of PARP1 and the Ku70/80 complex to a single DSB, and find that PARP1 and the Ku70/80 complex are recruited to the DSB almost at the same time...
February 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29447381/dna-mismatch-repair-and-oligonucleotide-end-protection-promote-base-pair-substitution-distal-from-a-crispr-cas9-induced-dna-break
#9
Tim Harmsen, Sjoerd Klaasen, Henri van de Vrugt, Hein Te Riele
Single-stranded oligodeoxyribonucleotide (ssODN)-mediated repair of CRISPR/Cas9-induced DNA double-strand breaks (DSB) can effectively be used to introduce small genomic alterations in a defined locus. Here, we reveal DNA mismatch repair (MMR) activity is crucial for efficient nucleotide substitution distal from the Cas9-induced DNA break when the substitution is instructed by the 3' half of the ssODN. Furthermore, protecting the ssODN 3' end with phosphorothioate linkages enhances MMR-dependent gene editing events...
February 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29446719/dna-double-strand-breaks-repair-inhibitors-relevance-as-potential-new-anticancer-therapeutics
#10
Paulina Kopa, Anna Macieja, Grzegorz Galita, Zbigniew J Witczak, Tomasz Poplawski
DNA Double-strand breaks are considered one of the most lethal form of DNA damage. Many effective anticancer therapeutic approaches used chemical and physical methods to generate DNA double-strand breaks in the cancer cells. They include: IR and drugs which mimetic its action, topoisomerase poisons, some alkylating agents or drugs which affected DNA replication process. On the other hand, cancer cells are mostly characterized by highly effective systems of DNA damage repair. There are two main DNA repair pathways used to fix double-strand breaks: NHEJ and HRR...
February 13, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29445424/promoter-methylation-of-dna-damage-repair-ddr-genes-in-human-tumor-entities-rbbp8-ctip-is-almost-exclusively-methylated-in-bladder-cancer
#11
Jolein Mijnes, Jürgen Veeck, Nadine T Gaisa, Eduard Burghardt, Tim C de Ruijter, Sonja Gostek, Edgar Dahl, David Pfister, Sebastian C Schmid, Ruth Knüchel, Michael Rose
Background: Genome-wide studies identified pan-cancer genes and shared biological networks affected by epigenetic dysregulation among diverse tumor entities. Here, we systematically screened for hypermethylation of DNA damage repair (DDR) genes in a comprehensive candidate-approach and exemplarily identify and validate candidate DDR genes as targets of epigenetic inactivation unique to bladder cancer (BLCA), which may serve as non-invasive biomarkers. Methods: Genome-wide DNA methylation datasets (2755 CpG probes of n = 7819 tumor and n = 659 normal samples) of the TCGA network covering 32 tumor entities were analyzed in silico for 177 DDR genes...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29445421/evidence-for-a-pre-malignant-cell-line-in-a-skin-biopsy-from-a-patient-with-nijmegen-breakage-syndrome
#12
Raneem Habib, Heidemarie Neitzel, Aurelie Ernst, John K L Wong, Bozenna Goryluk-Kozakiewicz, Antje Gerlach, Ilja Demuth, Karl Sperling, Krystyna Chrzanowska
Background: Nijmegen breakage syndrome is an autosomal recessive disorder characterized by microcephaly, immunodeficiency, hypersensitivity to X-irradiation, and a high predisposition to cancer. Nibrin, the product of the NBN gene, is part of the MRE11/RAD50 (MRN) complex that is involved in the repair of DNA double strand breaks (DSBs), and plays a critical role in the processing of DSBs in immune gene rearrangements, telomere maintenance, and meiotic recombination. NBS skin fibroblasts grow slowly in culture and enter early into senescence...
2018: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29444896/regulation-of-hed1-and-rad54-binding-during-maturation-of-the-meiosis-specific-presynaptic-complex
#13
J Brooks Crickard, Kyle Kaniecki, YoungHo Kwon, Patrick Sung, Michael Lisby, Eric C Greene
Most eukaryotes have two Rad51/RecA family recombinases, Rad51, which promotes recombination during mitotic double-strand break (DSB) repair, and the meiosis-specific recombinase Dmc1. During meiosis, the strand exchange activity of Rad51 is downregulated through interactions with the meiosis-specific protein Hed1, which helps ensure that strand exchange is driven by Dmc1 instead of Rad51. Hed1 acts by preventing Rad51 from interacting with Rad54, a cofactor required for promoting strand exchange during homologous recombination...
February 14, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29444806/multiple-applications-of-a-transient-crispr-cas9-coupled-with-electroporation-trace-system-in-the-cryptococcus-neoformans-species-complex
#14
Yumeng Fan, Xiaorong Lin
Cryptococcus neoformans is a fungal pathogen that claims hundreds of thousands of lives annually. Targeted genetic manipulation through biolistic transformation in C. neoformans drove the investigation of this clinically important pathogen at the molecular level. Although costly and inefficient, biolistic transformation remains the major method for editing Cryptococcus genome as foreign DNAs introduced by other methods such as electroporation are predominantly not integrated into the genome. Although the majority of DNAs introduced by biolistic transformation are stably inherited, the transformation efficiency and the homologous integration rate (1~10%) are low...
February 14, 2018: Genetics
https://www.readbyqxmd.com/read/29444071/the-phd-finger-protein-spp1-has-distinct-functions-in-the-set1-and-the-meiotic-dsb-formation-complexes
#15
Céline Adam, Raphaël Guérois, Anna Citarella, Laura Verardi, Florine Adolphe, Claire Béneut, Vérane Sommermeyer, Claire Ramus, Jérôme Govin, Yohann Couté, Valérie Borde
Histone H3K4 methylation is a feature of meiotic recombination hotspots shared by many organisms including plants and mammals. Meiotic recombination is initiated by programmed double-strand break (DSB) formation that in budding yeast takes place in gene promoters and is promoted by histone H3K4 di/trimethylation. This histone modification is recognized by Spp1, a PHD-finger containing protein that belongs to the conserved histone H3K4 methyltransferase Set1 complex. During meiosis, Spp1 binds H3K4me3 and interacts with a DSB protein, Mer2, to promote DSB formation close to gene promoters...
February 14, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29443341/super-resolution-localization-microscopy-of-radiation-induced-histone-h2ax-phosphorylation-in-relation-to-h3k9-trimethylation-in-hela-cells
#16
Michael Hausmann, Emma Wagner, Jin-Ho Lee, Gerrit Schrock, Wladimir Schaufler, Matthias Krufczik, Franziska Papenfuß, Matthias Port, Felix Bestvater, Harry Scherthan
Ionizing radiation (IR)-induced damage confers functional and conformational changes to nuclear chromatin associated with DNA single and double strand breaks. This leads to the activation of complex DNA repair machineries that aim to preserve the integrity of the DNA molecule. Since hetero- and euchromatin are differentially accessible to DNA repair pathways, local chromatin re-arrangements and structural changes are among the consequences of an activated DNA damage response. Using super-resolution localization microscopy (SRLM), we investigated the X-ray-induced repositioning of γ-H2AX and histone H3K9me3 heterochromatin marks in the nuclei of HeLa cells...
February 14, 2018: Nanoscale
https://www.readbyqxmd.com/read/29441648/aggregatibacter-actinomycetemcomitans-infection-causes-dna-double-strand-breaks-in-host-cells
#17
Rie Teshima, Katsuhiro Hanada, Junko Akada, Kenji Kawano, Yoshio Yamaoka
Periodontal disease, an inflammatory disease, is caused by infection with periodontal pathogens. Long-term periodontal disease increases the risk of oral carcinogenesis. Similar to other peptic cancers, oral carcinogenesis also requires multiple genome instabilities; however, the risk factors related to the accumulation of genome instabilities are poorly understood. Here, we suggested that specific periodontal pathogens may increase the risk of genome instability. Accordingly, we screened several periodontal pathogens based on the ability to induce DNA double-strand breaks (DSBs) in host cells...
February 14, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/29441594/influence-of-extended-incubation-time-on-human-sperm-chromatin-condensation-sperm-dna-strand-breaks-and-their-effect-on-fertilisation-rate
#18
I Ahmed, S Abdelateef, M Laqqan, H Amor, M A Abdel-Lah, M E Hammadeh
The purpose of this study was to determine influence of extended incubation time on sperm chromatin condensation and DNA strand breaks and their effect on fertilisation rate. Forty couples undergoing ICSI therapy were included. Semen was prepared by PureSperm gradient centrifugation and divided into two parts. The first part (G1) was used immediately for ICSI, whereas the second part (G2) was kept in the incubator at 37°C, 5% and 90% Humidity for 5 hr, and thereafter, the capacitated spermatozoa were used for ICSI...
February 14, 2018: Andrologia
https://www.readbyqxmd.com/read/29441364/impaired-cohesion-and-homologous-recombination-during-replicative-aging-in-budding-yeast
#19
Sangita Pal, Spike D Postnikoff, Myrriah Chavez, Jessica K Tyler
The causal relationship between genomic instability and replicative aging is unclear. We reveal here that genomic instability at the budding yeast ribosomal DNA (rDNA) locus increases during aging, potentially due to the reduced cohesion that we uncovered during aging caused by the reduced abundance of multiple cohesin subunits, promoting increased global chromosomal instability. In agreement, cohesion is lost during aging at other chromosomal locations in addition to the rDNA, including centromeres. The genomic instability in old cells is exacerbated by a defect in DNA double-strand break (DSB) repair that we uncovered in old yeast...
February 2018: Science Advances
https://www.readbyqxmd.com/read/29440683/rpb9-deficient-cells-are-defective-in-dna-damage-response-and-require-histone-h3-acetylation-for-survival
#20
Henel Sein, Kristina Reinmets, Kadri Peil, Kersti Kristjuhan, Signe Värv, Arnold Kristjuhan
Rpb9 is a non-essential subunit of RNA polymerase II that is involved in DNA transcription and repair. In budding yeast, deletion of RPB9 causes several phenotypes such as slow growth and temperature sensitivity. We found that simultaneous mutation of multiple N-terminal lysines within histone H3 was lethal in rpb9Δ cells. Our results indicate that hypoacetylation of H3 leads to inefficient repair of DNA double-strand breaks, while activation of the DNA damage checkpoint regulators γH2A and Rad53 is suppressed in Rpb9-deficient cells...
February 13, 2018: Scientific Reports
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