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Non canonical DNA

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https://www.readbyqxmd.com/read/28077297/exosomes-key-mediators-of-metastasis-and-pre-metastatic-niche-formation
#1
REVIEW
Richard J Lobb, Luize G Lima, Andreas Möller
While tumour cells are classically known to communicate via direct cell-to-cell contact and the secretion of soluble protein-based factors such as cytokines and growth factors, alternative novel mechanisms that promote tumour progression have recently emerged. Now, new critical components of the secretome thought to be involved in tumour progression are exosomes, small vesicles of endocytic origin that carry a variety of bioactive molecules, including proteins, lipids, RNA, as well as DNA molecules. Cancer cell-derived exosomes have been shown to participate in crucial steps of metastatic spread of a primary tumour, ranging from oncogenic reprogramming of malignant cells to formation of pre-metastatic niches...
January 8, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28072566/guard-the-guardian-a-crl4-ligase-stands-watch-over-histone-production
#2
Fabienne Lampert, Mia M L Brodersen, Matthias Peter
Histones are evolutionarily conserved proteins that together with DNA constitute eukaryotic chromatin in a defined stoichiometry. Core histones are dynamic scaffolding proteins that undergo a myriad of post-translational modifications, which selectively engage chromosome condensation, replication, transcription and DNA damage repair. Cullin4-RING ubiquitin E3 ligases are known to hold pivotal roles in a wide spectrum of chromatin biology ranging from chromatin remodeling and transcriptional repression, to sensing of cytotoxic DNA lesions...
January 10, 2017: Nucleus
https://www.readbyqxmd.com/read/28067787/effects-of-replication-and-transcription-on-dna-structure-related-genetic-instability
#3
REVIEW
Guliang Wang, Karen M Vasquez
Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e...
January 5, 2017: Genes
https://www.readbyqxmd.com/read/28056815/comparative-genomics-of-host-adaptive-traits-in-xanthomonas-translucens-pv-graminis
#4
Lena Hersemann, Daniel Wibberg, Jochen Blom, Alexander Goesmann, Franco Widmer, Frank-Jörg Vorhölter, Roland Kölliker
BACKGROUND: Xanthomonas translucens pathovars differ in their individual host ranges among Poaceae. As the causal agent of bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.), X. translucens pv. graminis (Xtg) is one of the most important bacterial pathogens in temperate grassland regions. The genomes of six Xtg strains from Switzerland, Norway, and New Zealand were sequenced in order to gain insight into conserved genomic traits from organisms covering a wide geographical range...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28045181/mercury-ii-mediated-base-pairs-in-dna-unexpected-behavior-in-metal-ion-binding-and-duplex-stability-induced-by-2-deoxyuridine-5-substituents
#5
Xiurong Guo, Sachin A Ingale, Haozhe Yang, Yang He, Frank Seela
The stability of the mercury ion mediated dU-Hg(II)-dU pair depends on substituents introduced at the 5-position of the pyrimidine moiety. To this end, a series of oligonucleotides were synthesized with dU modification in central position. Common and new phosphoramidites were utilized. Hybridization experiments provided 12-mer duplexes with non-canonical "dU-dU" pairs. In most cases Hg(2+) stabilizes duplexes by metal ion mediated base pair formation identified by higher duplex melting. Among the three types of dU derivatives incorporated in duplex DNA those with small aliphatic side chains have only a minor impact on the stability of the mercury-mediated base pair, while those with a triple bond in the side chain show hysteresis during duplex heating and cooling cycle implying triple bond interaction with mercury ions...
January 3, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28035693/identification-of-a-u-zn-cu-responsive-global-regulatory-two-component-system-in-caulobacter-crescentus
#6
Dan M Park, K Wesley Overton, Megan J Liou, Yongqin Jiao
Despite the well-known toxicity of uranium (U) to bacteria, little is known about how cells sense and respond to U. The recent finding of a U-specific stress response in Caulobacter crescentus has provided a foundation for studying the mechanisms of U- perception in bacteria. To gain insight into this process, we used a forward genetic screen to identify the regulatory components governing expression of the urcA promoter (PurcA ) that is strongly induced by U. This approach unearthed a previously uncharacterized two-component system, named UzcRS, which is responsible for U-dependent activation of PurcA ...
December 30, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/28025497/mechanisms-governing-ddk-regulation-of-the-initiation-of-dna-replication
#7
REVIEW
Larasati, Bernard P Duncker
The budding yeast Dbf4-dependent kinase (DDK) complex-comprised of cell division cycle (Cdc7) kinase and its regulatory subunit dumbbell former 4 (Dbf4)-is required to trigger the initiation of DNA replication through the phosphorylation of multiple minichromosome maintenance complex subunits 2-7 (Mcm2-7). DDK is also a target of the radiation sensitive 53 (Rad53) checkpoint kinase in response to replication stress. Numerous investigations have determined mechanistic details, including the regions of Mcm2, Mcm4, and Mcm6 phosphorylated by DDK, and a number of DDK docking sites...
December 22, 2016: Genes
https://www.readbyqxmd.com/read/28007578/nmr-based-model-of-human-telomeric-repeat-g-quadruplex-in-complex-with-2-4-6-triarylpyridine-family-ligand
#8
Abdelaziz Kerkour, Jean-Louis Mergny, Gilmar F Salgado
G-quadruplexes (G4) are one of the several different forms of non-canonical DNA structures that can occur in our genome. Their existence is thought to be implicated in important biological functions such as positive and negative transcription regulation or telomeric extension. The human telomeric sequence G4 formed by repetitive nucleotide sequences (T2AG3) at each chromosome end is an important example of intramolecular G4. Knowing the atomic details for different families of ligands targeting G-quadruplex structures hypothetically found in the telomeric repeat it is an important step for rational drug design...
December 19, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28000665/a-somatic-pirna-pathway-in-the-drosophila-fat-body-ensures-metabolic-homeostasis-and-normal-lifespan
#9
Brian C Jones, Jason G Wood, Chengyi Chang, Austin D Tam, Michael J Franklin, Emily R Siegel, Stephen L Helfand
In gonadal tissues, the Piwi-interacting (piRNA) pathway preserves genomic integrity by employing 23-29 nucleotide (nt) small RNAs complexed with argonaute proteins to suppress parasitic mobile sequences of DNA called transposable elements (TEs). Although recent evidence suggests that the piRNA pathway may be present in select somatic cells outside the gonads, the role of a non-gonadal somatic piRNA pathway is not well characterized. Here we report a functional somatic piRNA pathway in the adult Drosophila fat body including the presence of the piRNA effector protein Piwi and canonical 23-29 nt long TE-mapping piRNAs...
December 21, 2016: Nature Communications
https://www.readbyqxmd.com/read/27973397/p53-as-a-regulator-of-lipid-metabolism-in-cancer
#10
REVIEW
Alejandro Parrales, Tomoo Iwakuma
Enhanced proliferation and survival are common features of cancer cells. Cancer cells are metabolically reprogrammed which aids in their survival in nutrient-poor environments. Indeed, changes in metabolism of glucose and glutamine are essential for tumor progression. Thus, metabolic reprogramming is now well accepted as a hallmark of cancer. Recent findings suggest that reprogramming of lipid metabolism also occurs in cancer cells, since lipids are used for biosynthesis of membranes, post-translational modifications, second messengers for signal transduction, and as a source of energy during nutrient deprivation...
December 10, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27958335/non-canonical-integration-events-in-pichia-pastoris-encountered-during-standard-transformation-analysed-with-genome-sequencing
#11
Jan-Philipp Schwarzhans, Daniel Wibberg, Anika Winkler, Tobias Luttermann, Jörn Kalinowski, Karl Friehs
The non-conventional yeast Pichia pastoris is a popular host for recombinant protein production in scientific research and industry. Typically, the expression cassette is integrated into the genome via homologous recombination. Due to unknown integration events, a large clonal variability is often encountered consisting of clones with different productivities as well as aberrant morphological or growth characteristics. In this study, we analysed several clones with abnormal colony morphology and discovered unpredicted integration events via whole genome sequencing...
December 13, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27941819/corrigendum-non-canonical-rna-directed-dna-methylation
#12
Diego Cuerda-Gil, R Keith Slotkin
No abstract text is available yet for this article.
December 12, 2016: Nature Plants
https://www.readbyqxmd.com/read/27939291/structures-of-the-karyopherins-kap121p-and-kap60p-bound-to-the-nuclear-pore-targeting-domain-of-the-sumo-protease-ulp1p
#13
Hidemi Hirano, Junya Kobayashi, Yoshiyuki Matsuura
The budding yeast small ubiquitin-like modifier (SUMO) protease Ulp1p catalyzes both the processing of newly synthesized SUMO to its mature form and the deconjugation of SUMO from target proteins, thereby regulating a wide range of cellular processes including cell division, DNA repair, DNA replication, transcription, and mRNA quality control. Ulp1p is localized primarily at the nuclear pore complex (NPC) through interactions involving the karyopherins Kap121p and Kap95p-Kap60p heterodimer and a subset of nuclear pore-associated proteins...
December 6, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27933115/effects-of-trimethylamine-n-oxide-and-urea-on-dna-duplex-and-g-quadruplex
#14
Yu-Mi Ueda, Yu-Ki Zouzumi, Atsushi Maruyama, Shu-Ichi Nakano, Naoki Sugimoto, Daisuke Miyoshi
We systematically investigated effects of molecular crowding with trimethylamine N-oxide (TMAO) as a zwitterionic and protective osmolyte and urea as a nonionic denaturing osmolyte on conformation and thermodynamics of the canonical DNA duplex and the non-canonical DNA G-quadruplex. It was found that TMAO and urea stabilized and destabilized, respectively, the G-quadruplex. On the other hand, these osmolytes generally destabilize the duplex; however, it was observed that osmolytes having the trimethylamine group stabilized the duplex at the lower concentrations because of a direct binding to a groove of the duplex...
2016: Science and Technology of Advanced Materials
https://www.readbyqxmd.com/read/27923713/when-transcription-goes-on-holliday-double-holliday-junctions-block-rna-polymerase-ii-transcription-in-vitro
#15
Anne Pipathsouk, Boris P Belotserkovskii, Philip C Hanawalt
Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJ), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact...
December 3, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27915381/regulation-of-non-homologous-end-joining-via-post-translational-modifications-of-components-of-the-ligation-step
#16
REVIEW
Kristína Durdíková, Miroslav Chovanec
DNA double-strand breaks are the most serious type of DNA damage and non-homologous end joining (NHEJ) is an important pathway for their repair. In Saccharomyces cerevisiae, three complexes mediate the canonical NHEJ pathway, Ku (Ku70/Ku80), MRX (Mre11/Rad50/Xrs2) and DNA ligase IV (Dnl4/Lif1). Mammalian NHEJ is more complex, primarily as a consequence of the fact that more factors are involved in the process, and also because higher chromatin organization and more complex regulatory networks exist in mammals...
December 3, 2016: Current Genetics
https://www.readbyqxmd.com/read/27915287/light-induced-oxidation-of-the-telomeric-g4-dna-in-complex-with-zn-ii-tetracarboxymethyl-porphyrin
#17
Artemy D Beniaminov, Roman A Novikov, Olga K Mamaeva, Vladimir A Mitkevich, Igor P Smirnov, Mikhail A Livshits, Anna K Shchyolkina, Dmitry N Kaluzhny
Structure-specific ligands are convenient tools for the recognition, targeting or probing of non-canonical DNA structures. Porphyrin derivatives exhibit a preference for interaction with G-quadruplex (G4) structures over canonical duplex DNA and are able to cause photoinducible damage to nucleic acids. Here, we show that Zn(II) 5,10,15,20-tetrakis(N-carboxymethyl-4-pyridinium)porphyrin ( ZNP1: ) interacts with different conformations of the telomeric sequence d(TAGGG(TTAGGG)3) at submicromolar concentrations without any detectible disturbance of the particular fold...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27911399/tools-to-study-the-role-of-architectural-protein-hmgb1-in-the-processing-of-helix-distorting-site-specific-dna-interstrand-crosslinks
#18
Anirban Mukherjee, Karen M Vasquez
High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, such as transcription, DNA replication, and DNA repair. HMGB1 binds to structurally distorted DNA with higher affinity than to canonical B-DNA. For example, we found that HMGB1 binds to DNA interstrand crosslinks (ICLs), which covalently link the two strands of the DNA, cause distortion of the helix, and if left unrepaired can cause cell death. Due to their cytotoxic potential, several ICL-inducing agents are currently used as chemotherapeutic agents in the clinic...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27902403/the-non-canonical-tomato-yellow-leaf-curl-virus-recombinant-that-displaced-its-parental-viruses-in-southern-morocco-exhibits-a-high-selective-advantage-in-experimental-conditions
#19
Zineb Belabess, Michel Peterschmitt, Martine Granier, Abdessalem Tahiri, Abdelali Blenzar, Cica Urbino
Recombination events are frequently inferred from the increasing number of sequenced viral genomes, but their impact on natural viral populations has rarely been evidenced. TYLCV-IS76 is a recombinant (Begomovirus,Geminiviridae) between the Israel strain of tomato yellow leaf curl virus (TYLCV-IL) and the Spanish strain of tomato yellow leaf curl Sardinia virus (TYLCSV-ES) that was generated most probably in the late 1990s in southern Morocco (Souss). Its emergence in the 2000s coincided with the increasing use of resistant tomato cultivars bearing the Ty-1 gene, and led eventually to the entire displacement of both parental viruses in the Souss...
December 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27898568/whole-exome-sequencing-to-identify-novel-biological-pathways-associated-with-infertility-after-pelvic-inflammatory-disease
#20
Brandie D Taylor, Xiaojing Zheng, Toni Darville, Wujuan Zhong, Kranti Konganti, Olayinka Abiodun-Ojo, Roberta B Ness, Catherine M O'Connell, Catherine L Haggerty
BACKGROUND: Ideal management of sexually transmitted infections (STI) may require risk markers for pathology or vaccine development. Previously, we identified common genetic variants associated with chlamydial pelvic inflammatory disease (PID) and reduced fecundity. As this explains only a proportion of the long-term morbidity risk, we used whole-exome sequencing to identify biological pathways that may be associated with STI-related infertility. METHODS: We obtained stored DNA from 43 non-Hispanic black women with PID from the PID Evaluation and Clinical Health Study...
January 2017: Sexually Transmitted Diseases
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