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https://www.readbyqxmd.com/read/28730334/mir-181a-2-downregulates-the-e3-ubiquitin-ligase-cul4a-transcript-and-promotes-cell-proliferation
#1
Venkateshwarlu Bandi, Sudhakar Baluchamy
MiR-181a-2 plays a major role in cell proliferation both positively and negatively depending on tissue type by targeting several regulators 3'UTR regions. We have predicted several targets for miR-181a-2 through computational approaches and characterized one its interesting target, CUL4A, an E3 ubiquitin ligase. CUL4A regulates diverse functions in the cells including DNA repair, DNA replication, cell cycle, genomic stability through polyubiquitination of target proteins. Deregulation of both miR-181a-2 and CUL4A are reported in many cancerous cells, but the functional link between them is unknown...
August 2017: Medical Oncology
https://www.readbyqxmd.com/read/28720507/formation-and-degradation-of-nitrogen-mustard-induced-mgmt-dna-crosslinking-in-16hbe-cells
#2
Jin Cheng, Feng Ye, Guorong Dan, Yuanpeng Zhao, Jiqing Zhao, Zhongmin Zou
N-methyl-2,2-di(chloroethyl)amine (HN2) is a kind of bifunctional alkyltating agent, which can react with nucleophilic groups in DNA and/or protein to form HN2-bridged crosslinking of target molecules, such as DNA-protein crosslinkings (DPC). O(6)-methylguanine-DNA methyltransferase (MGMT) is a DNA damage repair enzyme which solely repairs alkyl adduct on DNA directly. However, MGMT was detected to act as a protein cross-linked with DNA via alkylation in presence of HN2, and unexpectedly turned into a DNA damage enhancer in the form of MGMT-DNA cross-link (mDPC)...
July 15, 2017: Toxicology
https://www.readbyqxmd.com/read/28713409/phylogenetic-resolution-in-juglans-based-on-complete-chloroplast-genomes-and-nuclear-dna-sequences
#3
Wenpan Dong, Chao Xu, Wenqing Li, Xiaoman Xie, Yizeng Lu, Yanlei Liu, Xiaobai Jin, Zhili Suo
Walnuts (Juglans of the Juglandaceae) are well-known economically important resource plants for the edible nuts, high-quality wood, and medicinal use, with a distribution from tropical to temperate zones and from Asia to Europe and Americas. There are about 21 species in Juglans. Classification of Juglans at section level is problematic, because the phylogenetic position of Juglans cinerea is disputable. Lacking morphological and DNA markers severely inhibited the development of related researches. In this study, the complete chloroplast genomes and two nuclear DNA regions (the internal transcribed spacer and ubiquitin ligase gene) of 10 representative taxa of Juglans were used for comparative genomic analyses in order to deepen the understanding on the application value of genetic information for inferring the phylogenetic relationship of the genus...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28710763/zebra-tail-amplification-accelerated-detection-of-apoptotic-blunt-ended-dna-breaks-by-in-situ-ligation
#4
Vladimir V Didenko
In situ ligation (ISL) is a simple and specific technique for apoptosis labeling in tissue sections. In its most economical version ISL uses ordinary PCR-labeled DNA fragments as probes. In tissue sections these makeshift probes are ligated to apoptotic DNA breaks by T4 DNA ligase. The approach can selectively label 5'PO4 DNA breaks with blunt ends, and is the histological equivalent of electrophoretic apoptotic ladder detection. The main drawback of this technique is its low speed, as it requires 18 h-incubation for efficient labeling...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28708824/tex19-1-promotes-spo11-dependent-meiotic-recombination-in-mouse-spermatocytes
#5
James H Crichton, Christopher J Playfoot, Marie MacLennan, David Read, Howard J Cooke, Ian R Adams
Meiosis relies on the SPO11 endonuclease to generate the recombinogenic DNA double strand breaks (DSBs) required for homologous chromosome synapsis and segregation. The number of meiotic DSBs needs to be sufficient to allow chromosomes to search for and find their homologs, but not excessive to the point of causing genome instability. Here we report that the mammal-specific gene Tex19.1 promotes Spo11-dependent recombination in mouse spermatocytes. We show that the chromosome asynapsis previously reported in Tex19...
July 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28707666/-identification-of-proteins-associated-with-transcription-factors-hoxa9-and-e2a-pbx1-by-tandem-affinity-purification
#6
E A Shestakova, M Boutin, S Bourassa, E Bonneil, J J Bijl
Chimeric transcription factor E2A-PBX1 induces the development of acute lymphoblastic B-cell leukemia in children. Using a transgenic mouse model, we previously demonstrated that homeobox (HOX) gene HOXA9 genetically interact with E2A-PBX1 gene in the development of B-cell leukemia in mice. HOXA9 itself is a potent oncogene resulting in myeloid leukemia when overexpressed, which is strongly accelerated by its collaborator Meis1. HOX, PBX1 and MEIS1 proteins have been shown to form hetero dimeric or trimeric complexes in different combinations...
May 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28700629/escherichia-coli-dna-ligase-b-may-mitigate-damage-from-oxidative-stress
#7
Truston J Bodine, Michael A Evangelista, Huan Ting Chang, Christopher A Ayoub, Buck S Samuel, Richard Sucgang, Lynn Zechiedrich
Escherichia coli encodes two DNA ligases, ligase A, which is essential under normal laboratory growth conditions, and ligase B, which is not. Here we report potential functions of ligase B. We found that across the entire Enterobacteriaceae family, ligase B is highly conserved in both amino acid identity and synteny with genes associated with oxidative stress. Deletion of ligB sensitized E. coli to specific DNA damaging agents and antibiotics resulted in a weak mutator phenotype, and decreased biofilm formation...
2017: PloS One
https://www.readbyqxmd.com/read/28700342/neurl4-regulates-the-transcriptional-activity-of-tumor-suppressor-protein-p53-by-modulating-its-oligomerization
#8
Monica Cubillos-Rojas, Taiane Schneider, Ramon Bartrons, Francesc Ventura, Jose Luis Rosa
p53 is a transcription factor that regulates important cellular processes related to tumor suppression, including induction of senescence, apoptosis, and DNA repair as well as the inhibition of angiogenesis and cell migration. Therefore, it is critical to understand the molecular mechanism that regulates it. p53 tetramerization is a key step in its activation process and the regulation of this oligomerization, an important control point. The E3 ubiquitin ligase HERC2 controls the p53 transcriptional activity by regulation of its oligomerization state...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28698355/tissue-specific-control-of-the-endocycle-by-the-anaphase-promoting-complex-cyclosome-inhibitors-uvi4-and-del1
#9
Jefri Heyman, Stefanie Polyn, Thomas Eekhout, Lieven De Veylder
The endocycle represents a modified mitotic cell cycle that in plants is often coupled to cell enlargement and differentiation. Endocycle onset is controlled by activity of the Anaphase Promoting Complex/Cyclosome (APC/C), a multi-subunit E3 ubiquitin ligase targeting cell cycle factors for destruction. CELL CYCLE SWITCH 52 (CCS52) proteins represent rate-limiting activator subunits of the APC/C. In Arabidopsis thaliana (Arabidopsis), mutations in either CCS52A1 or CCS52A2 activators result in a delayed endocycle onset, whereas their overexpression triggers increased DNA ploidy levels...
July 11, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28696258/effects-of-dna-end-configuration-on-xrcc4-dna-ligase-iv-and-its-stimulation-of-artemis-activity
#10
Christina A Gerodimos, Howard H Y Chang, Go Watanabe, Michael R Lieber
In humans, nonhomologous DNA end-joining (NHEJ) is the major pathway by which DNA double-strand breaks are repaired. Recognition of each broken DNA end by the DNA repair protein Ku is the first step in NHEJ, followed by the iterative binding of nucleases, DNA polymerases, and the XRCC4:DNA ligase IV (X4:LIV) complex in an order influenced by the configuration of the two DNA ends at the break site. The endonuclease Artemis improves joining efficiency by functioning in a complex with DNA-dependent protein kinase, catalytic subunit (DNA-PKcs) that carries out endonucleolytic cleavage of 5' and 3' overhangs...
July 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28695890/dual-loss-of-human-polq-and-lig4-abolishes-random-integration
#11
Shinta Saito, Ryo Maeda, Noritaka Adachi
Homologous recombination-mediated gene targeting has greatly contributed to genetic analysis in a wide range of species, but is highly inefficient in human cells because of overwhelmingly frequent random integration events, whose molecular mechanism remains elusive. Here we show that DNA polymerase θ, despite its minor role in chromosomal DNA repair, substantially contributes to random integration, and that cells lacking both DNA polymerase θ and DNA ligase IV, which is essential for non-homologous end joining (NHEJ), exhibit 100% efficiency of spontaneous gene targeting by virtue of undetectable levels of random integration...
July 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28692049/mdm2-selectively-suppresses-dna-damage-arising-from-inhibition-of-topoisomerase-ii-independent-of-p53
#12
J C Senturk, S Bohlman, J J Manfredi
Mdm2 is often overexpressed in tumors that retain wild-type TP53 but may affect therapeutic response independently of p53. Herein is shown that tumor cells with MDM2 amplification are selectively resistant to treatment with topoisomerase II poisons but not other DNA damaging agents. Tumor cells that overexpress Mdm2 have reduced DNA double-strand breaks in response to doxorubicin or etoposide. This latter result is not due to altered drug uptake. The selective attenuation of DNA damage in response to these agents is dependent on both Mdm2 levels and an intact ubiquitin ligase function...
July 10, 2017: Oncogene
https://www.readbyqxmd.com/read/28691929/biallelic-mutations-in-the-ubiquitin-ligase-rfwd3-cause-fanconi-anemia
#13
Kerstin Knies, Shojiro Inano, María J Ramírez, Masamichi Ishiai, Jordi Surrallés, Minoru Takata, Detlev Schindler
The WD40-containing E3 ubiquitin ligase RFWD3 has been recently linked to the repair of DNA damage by homologous recombination (HR). Here we have shown that an RFWD3 mutation within the WD40 domain is connected to the genetic disease Fanconi anemia (FA). An individual presented with congenital abnormalities characteristic of FA. Cells from the patient carrying the compound heterozygous mutations c.205_206dupCC and c.1916T>A in RFWD3 showed increased sensitivity to DNA interstrand cross-linking agents in terms of increased chromosomal breakage, reduced survival, and cell cycle arrest in G2 phase...
July 10, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28679532/the-non-homologous-end-joining-factor-nej1-inhibits-resection-mediated-by-dna2-sgs1-at-dna-double-strand-breaks
#14
Kyle S Sorenson, Brandi L Mahaney, Susan P Lees-Miller, Jennifer A Cobb
Double strand breaks (DSBs) represent highly deleterious DNA damage and need to be accurately repaired. Homology directed repair (HDR) and non-homologous end-joining (NHEJ) are the two major DSB repair pathways that are highly conserved from yeast to mammals. The choice between these pathways is largely based on 5' to 3' DNA resection, and NHEJ proceeds only if resection has not initiated. In yeast, yKu70/80 (Ku) rapidly localizes to the break, protecting DNA ends from nuclease accessibility and recruits additional NHEJ factors, including Nej1 and Lif1...
July 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28679464/linoleic-la-and-linolenic-ala-acid-concentrations-in-follicular-fluid-of-prepubertal-goats-and-their-effect-on-oocyte-in-vitro-maturation-and-embryo-development
#15
Montserrat Roura, María G Catalá, Sandra Soto-Heras, Sondes Hammami, Dolors Izquierdo, Ali Fouladi-Nashta, Maria-Teresa Paramio
In this study we assessed the concentration of linoleic acid (LA) and linolenic acid (ALA) in follicular fluid of prepubertal goats according to follicle size (<3mm or ≥3mm) by gas chromatography and tested the addition of different LA and ALA (LA:ALA) concentration ratios (50:50, 100:50 and 200:50µM) to the IVM medium on embryo development, mitochondrial activity, ATP concentration and relative gene expression (RPL19, ribosomal protein L19; SLC2A1, facilitated glucose transporter 1; ATF4, activating transcription factor 4; GPX1, glutathione peroxidase 1; HSPA5, heat-shock protein family A 70 kDa; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; DNMT1, DNA methyltransferase 1; GCLC, glutamate-cysteine ligase catalytic subunit; SOD1, superoxide dismutase 1)...
July 6, 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28666352/a-phosphorylation-and-ubiquitylation-circuitry-driving-atr-activation-and-homologous-recombination
#16
Jean-Christophe Dubois, Maïlyn Yates, Antoine Gaudreau-Lapierre, Geneviève Clément, Laurent Cappadocia, Luc Gaudreau, Lee Zou, Alexandre Maréchal
RPA-coated single-stranded DNA (RPA-ssDNA), a nucleoprotein structure induced by DNA damage, promotes ATR activation and homologous recombination (HR). RPA is hyper-phosphorylated and ubiquitylated after DNA damage. The ubiquitylation of RPA by PRP19 and RFWD3 facilitates ATR activation and HR, but how it is stimulated by DNA damage is still unclear. Here, we show that RFWD3 binds RPA constitutively, whereas PRP19 recognizes RPA after DNA damage. The recruitment of PRP19 by RPA depends on PIKK-mediated RPA phosphorylation and a positively charged pocket in PRP19...
June 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28657724/engineering-of-bacteriophage-t4-genome-using-crispr-cas9
#17
Pan Tao, Xiaorong Wu, Wei-Chun Tang, Jingen Zhu, V B Rao
Bacteriophages likely constitute the largest biomass on Earth. However, very few phage genomes have been well-characterized, the tailed phage T4 genome being one of them. Even in T4, much of the genome remained uncharacterized. The classical genetic strategies are tedious, compounded by genome modifications such as cytosine hydroxylmethylation and glucosylation which makes T4 DNA resistant to most restriction endonucleases. Here, using the type-II CRISPR-Cas9 system, we report the editing of both modified (ghm-Cytosine) and unmodified (Cytosine) T4 genomes...
June 28, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28657121/differential-ube2c-and-hoxa1-expression-in-spitz-nevus-and-melanoma
#18
Stefan Kraft, Johanna B Moore, Alona Muzikansky, Kenneth L Scott, Lyn M Duncan
BACKGROUND: Recent molecular advances suggest that Spitz nevi and other spitzoid neoplasms are biologically distinct from melanoma and conventional nevi. The ubiquitin ligase UBE2C and the homeobox transcription factor HOXA1 are candidate oncogenes in melanoma. METHODS: Using RNA expression analysis and immunohistochemistry, we evaluated these biomarkers in Spitz nevi (n = 20) melanoma (n = 20), and by immunohistochemistry in conventional nevi (n = 20)...
June 28, 2017: Journal of Cutaneous Pathology
https://www.readbyqxmd.com/read/28657072/development-of-a-crispr-cas9-system-for-efficient-genome-editing-of-candida-lusitaniae
#19
Emily L Norton, Racquel K Sherwood, Richard J Bennett
Candida lusitaniae is a member of the Candida clade that includes a diverse group of fungal species relevant to both human health and biotechnology. This species exhibits a full sexual cycle to undergo interconversion between haploid and diploid forms. C. lusitaniae is also an emerging opportunistic pathogen that can cause serious bloodstream infections in the clinic and yet has often proven to be refractory to facile genetic manipulations. In this work, we develop a clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (Cas9) system to enable genome editing of C...
May 2017: MSphere
https://www.readbyqxmd.com/read/28655200/highly-efficient-preparation-of-single-stranded-dna-rings-by-t4-ligase-at-abnormally-low-mg-ii-concentration
#20
Ran An, Qi Li, Yiqiao Fan, Jing Li, Xiaoming Pan, Makoto Komiyama, Xingguo Liang
Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buffer for ligase reactions. This strategy is based on our unexpected finding that, in diluted T4 buffers, intermolecular polymerization of DNA fragments is greatly suppressed with respect to their intramolecular cyclization...
June 26, 2017: Nucleic Acids Research
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