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Protein dna interaction

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https://www.readbyqxmd.com/read/28092692/smile-seq-identifies-binding-motifs-of-single-and-dimeric-transcription-factors
#1
Alina Isakova, Romain Groux, Michael Imbeault, Pernille Rainer, Daniel Alpern, Riccardo Dainese, Giovanna Ambrosini, Didier Trono, Philipp Bucher, Bart Deplancke
Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq). SMiLE-seq is neither limited by DNA bait length nor biased toward strong affinity binders; it probes the DNA-binding properties of TFs over a wide affinity range in a fast and cost-effective fashion. We validated SMiLE-seq by analyzing 58 full-length human, mouse, and Drosophila TFs from distinct structural classes...
January 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/28092679/genome-wide-analysis-of-p53-regulated-transcription-in-myc-driven-lymphomas
#2
C Tonelli, M J Morelli, A Sabò, A Verrecchia, L Rotta, T Capra, S Bianchi, S Campaner, B Amati
The tumour suppressor p53 is a transcription factor that controls cellular stress responses. Here, we dissected the transcriptional programmes triggered upon restoration of p53 in Myc-driven lymphomas, based on the integrated analysis of p53 genomic occupancy and gene regulation. p53 binding sites were identified at promoters and enhancers, both characterized by the pre-existence of active chromatin marks. Only a small fraction of these sites showed the 20 base-pair p53 consensus motif, suggesting that p53 recruitment to genomic DNA was primarily mediated through protein-protein interactions in a chromatin context...
January 16, 2017: Oncogene
https://www.readbyqxmd.com/read/28092440/molecular-interactions-between-graphene-and-biological-molecules
#3
Xingquan Zou, Shuai Wei, Joshua Jasensky, Minyu Xiao, Qiuming Wang, Charles L Brooks, Zhan Chen
Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e...
January 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28092380/chromatin-immunoprecipitation-in-microfluidic-droplets-towards-fast-and-cheap-analyses
#4
Bruno Teste, Jerome Champ, Arturo Londono-Vallejo, Stéphanie Descroix, Laurent Malaquin, Jean-Louis Viovy, Irena Draskovic, Guillaume Mottet
Genetic organization is governed by the interaction of DNA with histone proteins, and differential modifications of these proteins is a fundamental mechanism of gene regulation. Histone modifications are primarily studied through chromatin immunoprecipitation (ChIP) assays, however conventional ChIP procedures are time consuming, laborious and require a large number of cells. Here we report for the first time the development of ChIP in droplets based on a microfluidic platform combining nanoliter droplets, magnetic beads (MB) and magnetic tweezers (MT)...
January 16, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28089251/mutations-in-mapkbp1-cause-juvenile-or-late-onset-cilia-independent-nephronophthisis
#5
Maxence S Macia, Jan Halbritter, Marion Delous, Cecilie Bredrup, Arthur Gutter, Emilie Filhol, Anne E C Mellgren, Sabine Leh, Albane Bizet, Daniela A Braun, Heon Y Gee, Flora Silbermann, Charline Henry, Pauline Krug, Christine Bole-Feysot, Patrick Nitschké, Dominique Joly, Philippe Nicoud, André Paget, Heidi Haugland, Damien Brackmann, Nayir Ahmet, Richard Sandford, Nurcan Cengiz, Per M Knappskog, Helge Boman, Bolan Linghu, Fan Yang, Edward J Oakeley, Pierre Saint Mézard, Andreas W Sailer, Stefan Johansson, Eyvind Rødahl, Sophie Saunier, Friedhelm Hildebrandt, Alexandre Benmerah
Nephronophthisis (NPH), an autosomal-recessive tubulointerstitial nephritis, is the most common cause of hereditary end-stage renal disease in the first three decades of life. Since most NPH gene products (NPHP) function at the primary cilium, NPH is classified as a ciliopathy. We identified mutations in a candidate gene in eight individuals from five families presenting late-onset NPH with massive renal fibrosis. This gene encodes MAPKBP1, a poorly characterized scaffolding protein for JNK signaling. Immunofluorescence analyses showed that MAPKBP1 is not present at the primary cilium and that fibroblasts from affected individuals did not display ciliogenesis defects, indicating that MAPKBP1 may represent a new family of NPHP not involved in cilia-associated functions...
January 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28088582/ripk1-protects-hepatocytes-from-kupffer-cells-mediated-tnf-induced-apoptosis-in-mouse-models-of-pamp-induced-hepatitis
#6
Aveline Filliol, Claire Piquet-Pellorce, Céline Raguénès-Nicol, Sarah Dion, Muhammad Farooq, Catherine Lucas-Clerc, Peter Vandenabeele, Mathieu J M Bertrand, Jacques Le Seyec, Michel Samson
BACKGROUND & AIMS: The severity of liver diseases is exacerbated by the death of hepatocytes, which can be induced by the sensing of Pathogen Associated Molecular Patterns (PAMPs) derived from the gut microbiota. The molecular mechanisms regulating these cell death pathways are poorly documented. In this study, we investigated the role of the Receptor Interacting Protein Kinase 1 (RIPK1), a protein known to regulate cell fate decisions, in the death of hepatocytes using two in vivo models of PAMP-induced hepatitis...
January 11, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28088539/the-dna-damage-response-of-c-elegans-affected-by-gravity-sensing-and-radiosensitivity-during-the-shenzhou-8-spaceflight
#7
Ying Gao, Dan Xu, Lei Zhao, Yeqing Sun
Space radiation and microgravity are recognized as primary and inevitable risk factors for humans traveling in space, but the reports regarding their synergistic effects remain inconclusive and vary across studies due to differences in the environmental conditions and intrinsic biological sensitivity. Thus, we studied the synergistic effects on transcriptional changes in the global genome and DNA damage response (DDR) by using dys-1 mutant and ced-1 mutant of C. elegans, which respectively presented microgravity-insensitivity and radiosensitivity when exposure to spaceflight condition (SF) and space radiation (SR)...
January 7, 2017: Mutation Research
https://www.readbyqxmd.com/read/28088481/saxs-structural-studies-of-dps-from-deinococcus-radiodurans-highlights-the-conformation-of-the-mobile-n-terminal-extensions
#8
Sandra P Santos, Maxime G Cuypers, Adam Round, Stephanie Finet, Theyencheri Narayanan, Edward P Mitchell, Célia V Romão
The radiation resistant bacterium Deinococcus radiodurans contains two DNA binding proteins from starved cells (Dps): Dps1 (DR2263) and Dps2 (DRB0092). These are suggested to play a role in DNA interaction, manganese and iron storage. The proteins assemble as a conserved dodecameric structure with structurally uncharacterized N-terminal extensions. In the case of DrDps1 these extensions have been proposed to be involved in DNA interactions, while in DrDps2 their function has yet to be established. The reported data reveals the relative position of the N-terminal extensions to the dodecameric sphere in solution for both Dps...
January 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28088146/photoinduced-c-i-bond-homolysis-of-5-iodouracil-a-singlet-predissociation-pathway
#9
Xiaojuan Dai, Di Song, Kunhui Liu, Hongmei Su
5-Iodouracil (5-IU) can be integrated into DNA and acts as a UV sensitive chromophore suitable for probing DNA structure and DNA-protein interactions based on the photochemical reactions of 5-IU. Here, we perform joint studies of time-resolved Fourier transform infrared (TR-FTIR) spectroscopy and ab initio calculations to examine the state-specific photochemical reaction mechanisms of the 5-IU. The fact that uracil (U) is observed in TR-FTIR spectra after 266 nm irradiation of 5-IU in acetonitrile and ascribed to the product of hydrogen abstraction by the uracil-5-yl radical (U·) provides experimental evidence for the C-I bond homolysis of 5-IU...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088012/new-4-4-chlorophenyl-2-2-6-2%C3%A2-terpyridine-ruthenium-ii-complexes-synthesis-characterization-interaction-with-dna-bsa-and-cytotoxicity-studies
#10
Milan M Milutinović, Ana Rilak, Ioannis Bratsos, Olivera Klisurić, Milan Vraneš, Nevenka Gligorijević, Siniša Radulović, Živadin D Bugarčić
In this study, we have developed a series of new monofunctional Ru(II) complexes of the general formula mer-[Ru(Cl-Ph-tpy)(N-N)Cl]Cl in which Cl-Ph-tpy is 4'-(4-chlorophenyl)-2,2':6',2″-terpyridine, N-N is a bidentate chelating ligand (1,2-diaminoethane (en, 1), 1,2-diaminocyclohexane (dach, 2) or 2,2'-bipyridine (bpy, 3)). All complexes were fully characterized by elemental analysis and spectroscopic techniques (IR, UV-Vis, 1D and 2D NMR). Their chemical behavior in aqueous solution was studied by UV-Vis and NMR spectroscopy showing that all compounds are relatively labile leading to the formation of the corresponding aqua species 1aq-3aq...
October 14, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28087739/tnf-signaling-through-rip1-kinase-enhances-sn38-induced-death-in-colon-adenocarcinoma
#11
Lucia Cabal-Hierro, Peter J O'Dwyer
: Elucidation of tumor necrosis factor (TNF)-directed mechanisms for cell death induction and maintenance of tumor growth has revealed a role for receptor-interacting protein kinases 1 and 3 (RIPK1/RIP1 and RIPK3/RIP3), components of the necrosome complex, as determinants of cell fate. Here the participation of TNF signaling was analyzed with regard to the cytotoxic action of different DNA damaging agents in a panel of colon cancer cells. While most of these cell lines were insensitive to TNF, combination with these drugs increased sensitivity by inducing cell death and DNA damage, especially in the case of the topoisomerase inhibitor SN38...
January 13, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28087731/increased-nbcn1-expression-na-hco3-co-transport-and-intracellular-ph-in-human-vascular-smooth-muscle-cells-with-a-risk-allele-for-hypertension
#12
Fu Liang Ng, Ebbe Boedtkjer, Katarzyna Witkowska, Meixia Ren, Ruoxin Zhang, Arthur Tucker, Christian Aalkjær, Mark J Caulfield, Shu Ye
Genome-wide association studies have revealed an association between variation at the SLC4A7 locus and blood pressure. SLC4A7 encodes the electroneutral Na(+)/HCO3 co-transporter NBCn1 which regulates intracellular pH (pHi). We conducted a functional study of variants at this locus in primary cultures of vascular smooth muscle and endothelial cells. In both cell types, we found genotype-dependent differences for rs13082711 in DNA-nuclear protein interactions, where the risk allele is associated with increased SLC4A7 expression level, NBCn1 availability and function as reflected in elevated steady-state pHi and accelerated recovery from intracellular acidosis...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28087710/targeting-argonaute-to-chromatin
#13
Jered M Wendte, Craig S Pikaard
In many eukaryotes, siRNAs bound to Argonaute proteins guide chromatin-modifying enzymes to complementary loci, resulting in transcriptional gene silencing. Multiple lines of evidence indicate that siRNAs base-pair with longer RNAs produced at target loci, but the possibility that siRNAs base-pair directly with DNA remains an attractive hypothesis. In a recent study, Shimada et al. (pp. 2571-2580) conducted experiments that address these alternative hypotheses, yielding additional evidence that fission yeast siRNA-Argonaute silencing complexes are recruited to target loci exclusively via interactions with nascent transcripts...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28081440/a-knockout-screen-of-apiap2-genes-reveals-networks-of-interacting-transcriptional-regulators-controlling-the-plasmodium-life-cycle
#14
Katarzyna Modrzynska, Claudia Pfander, Lia Chappell, Lu Yu, Catherine Suarez, Kirsten Dundas, Ana Rita Gomes, David Goulding, Julian C Rayner, Jyoti Choudhary, Oliver Billker
A family of apicomplexa-specific proteins containing AP2 DNA-binding domains (ApiAP2s) was identified in malaria parasites. This family includes sequence-specific transcription factors that are key regulators of development. However, functions for the majority of ApiAP2 genes remain unknown. Here, a systematic knockout screen in Plasmodium berghei identified ten ApiAP2 genes that were essential for mosquito transmission: four were critical for the formation of infectious ookinetes, and three were required for sporogony...
January 11, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28081275/role-of-xrcc1-gene-polymorphisms-in-non-small-cell-lung-cancer-cisplatin-based-chemotherapy-and-their-effect-on-clinical-and-pathological-characteristics
#15
H F Liu, J S Liu, J H Deng, R R Wu
Non-small cell lung cancer (NSCLC) is the most common cancer globally. The XRCC1 protein interacts with ligase and poly(ADP-ribose) polymerase to repair cisplatin-induced DNA damage. The authors of previous studies have reported XRCC1 Arg399Gln, Arg280His, and Arg194Trp polymorphisms and advanced NSCLC prognosis, but the results are inconclusive. We investigated the association between clinical outcome and XRCC1 Arg399Gln, Arg280His, and Arg194Trp polymorphisms in advanced NSCLC patients treated with cisplatin...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28081154/sensitization-of-radioresistant-prostate-cancer-cells-by-resveratrol-isolated-from-arachis-hypogaea-stems
#16
Yu-An Chen, Hsiu-Man Lien, Min-Chuan Kao, U-Ging Lo, Li-Chiung Lin, Chun-Jung Lin, Sheau-Jiun Chang, Chia-Chang Chen, Jer-Tsong Hsieh, Ho Lin, Chih-Hsin Tang, Chih-Ho Lai
Resveratrol (RV, 3,4',5-trihydroxystilbene) is naturally produced by a wide variety of plants including grapes and peanuts (Arachis hypogaea). However, the yield of RV from peanut stem and its potential radiosensitizing effects in prostate cancer (PCa) have not been well investigated. In this study, we characterized RV in peanut stem extract (PSE) for the first time and showed that both RV and PSE dose-dependently induced cell death in DOC-2/DAB2 interactive protein (DAB2IP)-deficient PCa cells with the radioresistant phenotype...
2017: PloS One
https://www.readbyqxmd.com/read/28079882/stability-of-the-cancer-target-ddias-is-regulated-by-the-chip-hsp70-pathway-in-lung-cancer-cells
#17
Kyoung-Jae Won, Joo-Young Im, Bo-Kyung Kim, Hyun Seung Ban, Young-Jin Jung, Kyeong Eun Jung, Misun Won
DNA damage-induced apoptosis suppressor (DDIAS) rescues lung cancer cells from apoptosis in response to DNA damage. DDIAS is transcriptionally activated by NFATc1 and EGF-mediated ERK5/MEF2B, leading to cisplatin resistance and cell invasion. Therefore, DDIAS is suggested as a therapeutic target for lung cancer. Here, we report that DDIAS stability is regulated by E3 U-box ubiquitin ligase carboxyl terminus of HSP70-interacting protein (CHIP)-mediated proteasomal degradation. We first isolated CHIP as an interacting partner of DDIAS by yeast two-hybrid screening...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28079019/an-efficient-targeted-nuclease-strategy-for-high-resolution-mapping-of-dna-binding-sites
#18
Peter J Skene, Steven Henikoff
We describe Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. Unlike Chromatin Immunoprecipitation (ChIP), which fragments and solubilizes total chromatin, CUT&RUN is performed in situ, allowing for both quantitative high-resolution chromatin mapping and probing of the local chromatin environment. When applied to yeast and human nuclei, CUT&RUN yielded precise transcription factor profiles while avoiding cross-linking and solubilization issues...
January 12, 2017: ELife
https://www.readbyqxmd.com/read/28078793/insights-into-nuclear-dynamics-using-live-cell-imaging-approaches
#19
REVIEW
Rachel B Bigley, Alexander Y Payumo, Jeffrey M Alexander, Guo N Huang
The nucleus contains the genetic blueprint of the cell and myriad interactions within this subcellular structure are required for gene regulation. In the current scientific era, characterization of these gene regulatory networks through biochemical techniques coupled with systems-wide 'omic' approaches has become commonplace. However, these strategies are limited because they represent a mere snapshot of the cellular state. To obtain a holistic understanding of nuclear dynamics, relevant molecules must be studied in their native contexts in living systems...
January 12, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28078722/ssb-and-the-recg-dna-helicase-an-intimate-association-to-rescue-a-stalled-replication-fork
#20
REVIEW
Piero R Bianco, Yuri L Lyubchenko
In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy...
January 12, 2017: Protein Science: a Publication of the Protein Society
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