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Aid translocation dna

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https://www.readbyqxmd.com/read/27859411/dna-demethylation-pathways-additional-players-and-regulators
#1
Matthias Bochtler, Agnieszka Kolano, Guo-Liang Xu
DNA demethylation can occur passively by "dilution" of methylation marks by DNA replication, or actively and independently of DNA replication. Direct conversion of 5-methylcytosine (5mC) to cytosine (C), as originally proposed, does not occur. Instead, active DNA methylation involves oxidation of the methylated base by ten-eleven translocations (TETs), or deamination of the methylated or a nearby base by activation induced deaminase (AID). The modified nucleotide, possibly together with surrounding nucleotides, is then replaced by the BER pathway...
November 16, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27372762/quantification-of-oxidized-5-methylcytosine-bases-and-tet-enzyme-activity
#2
M Y Liu, J E DeNizio, R M Kohli
In eukaryotic DNA, cytosine can be enzymatically modified to yield up to four epigenetic base variants. DNA methyltransferases convert cytosine to 5-methylcytosine (mC), which plays critical roles in gene regulation during development. Ten-eleven translocation (TET) enzymes can sequentially oxidize mC to three products: 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC). These oxidized bases have been found in numerous mammalian cell types, where they potentially carry out independent epigenetic functions and aid in DNA demethylation...
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27283771/aberrant-methylation-of-muc1-and-muc4-promoters-are-potential-prognostic-biomarkers-for-pancreatic-ductal-adenocarcinomas
#3
Seiya Yokoyama, Michiyo Higashi, Sho Kitamoto, Monika Oeldorf, Uwe Knippschild, Marko Kornmann, Kosei Maemura, Hiroshi Kurahara, Edwin Wiest, Tomofumi Hamada, Ikumi Kitazono, Yuko Goto, Takashi Tasaki, Tsubasa Hiraki, Kazuhito Hatanaka, Yuko Mataki, Hiroki Taguchi, Shinichi Hashimoto, Surinder K Batra, Akihide Tanimoto, Suguru Yonezawa, Michael A Hollingsworth
Pancreatic cancer is still a disease of high mortality despite availability of diagnostic techniques. Mucins (MUC) play crucial roles in carcinogenesis and tumor invasion in pancreatic neoplasms. MUC1 and MUC4 are high molecular weight transmembrane mucins. These are overexpressed in many carcinomas, and high expression of these molecules is a risk factor associated with poor prognosis. We evaluated the methylation status of MUC1 and MUC4 promoter regions in pancreatic tissue samples from 169 patients with various pancreatic lesions by the methylation specific electrophoresis (MSE) method...
July 5, 2016: Oncotarget
https://www.readbyqxmd.com/read/27220482/mechanisms-of-human-lymphoid-chromosomal-translocations
#4
Michael R Lieber
Analysis of chromosomal translocation sequence locations in human lymphomas has provided valuable clues about the mechanism of the translocations and when they occur. Biochemical analyses on the mechanisms of DNA breakage and rejoining permit formulation of detailed models of the human chromosomal translocation process in lymphoid neoplasms. Most human lymphomas are derived from B cells in which a DNA break at an oncogene is initiated by activation-induced deaminase (AID). The partner locus in many cases is located at one of the antigen receptor loci, and this break is generated by the recombination activating gene (RAG) complex or by AID...
May 25, 2016: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/27133766/recent-adaptations-of-fluorescence-techniques-for-the-determination-of-mechanistic-parameters-of-helicases-and-translocases
#5
Máté Gyimesi, Gábor M Harami, Zsuzsa S Kocsis, Mihály Kovács
Helicases and translocases are nucleic acid (NA)-based molecular motors that use the free energy liberated during the nucleoside triphosphate (NTP, usually ATP) hydrolysis cycle for unidirectional translocation along their NA (DNA, RNA or heteroduplex) substrates. Determination of the kinetic and thermodynamic parameters of their mechanoenzymatic cycle serves as a basis for the exploration of their physiological behavior and various cellular functions. Here we describe how recent adaptations of fluorescence-based solution kinetic methods can be used to determine practically all important mechanistic parameters of NA-based motor proteins...
October 1, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27095148/on-nanopore-dna-sequencing-by-signal-and-noise-analysis-of-ionic-current
#6
Chenyu Wen, Shuangshuang Zeng, Zhen Zhang, Klas Hjort, Ralph Scheicher, Shi-Li Zhang
DNA sequencing, i.e., the process of determining the succession of nucleotides on a DNA strand, has become a standard aid in biomedical research and is expected to revolutionize medicine. With the capability of handling single DNA molecules, nanopore technology holds high promises to become speedier in sequencing at lower cost than what are achievable with the commercially available optics- or semiconductor-based massively parallelized technologies. Despite tremendous progress made with biological and solid-state nanopores, high error rates and large uncertainties persist with the sequencing results...
May 27, 2016: Nanotechnology
https://www.readbyqxmd.com/read/27015368/the-retinoblastoma-protein-regulates-hypoxia-inducible-genetic-programs-tumor-cell-invasiveness-and-neuroendocrine-differentiation-in-prostate-cancer-cells
#7
Mark P Labrecque, Mandeep K Takhar, Rebecca Nason, Stephanie Santacruz, Kevin J Tam, Shabnam Massah, Anne Haegert, Robert H Bell, Manuel Altamirano-Dimas, Colin C Collins, Frank J S Lee, Gratien G Prefontaine, Michael E Cox, Timothy V Beischlag
Loss of tumor suppressor proteins, such as the retinoblastoma protein (Rb), results in tumor progression and metastasis. Metastasis is facilitated by low oxygen availability within the tumor that is detected by hypoxia inducible factors (HIFs). The HIF1 complex, HIF1α and dimerization partner the aryl hydrocarbon receptor nuclear translocator (ARNT), is the master regulator of the hypoxic response. Previously, we demonstrated that Rb represses the transcriptional response to hypoxia by virtue of its association with HIF1...
April 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/26873538/distinct-patterns-of-colocalization-of-the-ccnd1-and-cmyc-genes-with-their-potential-translocation-partner-igh-at-successive-stages-of-b-cell-differentiation
#8
Ilya Sklyar, Olga V Iarovaia, Alexey A Gavrilov, Andrey Pichugin, Diego Germini, Tatiana Tsfasman, Gersende Caron, Thierry Fest, Marc Lipinski, Sergey V Razin, Yegor S Vassetzky
The immunoglobulin heavy chain (IGH) locus is submitted to intra-chromosomal DNA breakages and rearrangements during normal B cell differentiation that create a risk for illegitimate inter-chromosomal translocations leading to a variety of B-cell malignancies. In most Burkitt's and Mantle Cell lymphomas, specific chromosomal translocations juxtapose the IGH locus with a CMYC or Cyclin D1 (CCND1) gene, respectively. 3D-fluorescence in situ hybridization was performed on normal peripheral B lymphocytes induced to mature in vitro from a naive state to the stage where they undergo somatic hypermutation (SHM) and class switch recombination (CSR)...
July 2016: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/26740101/combined-deletion-of-xrcc4-and-trp53-in-mouse-germinal-center-b-cells-leads-to-novel-b-cell-lymphomas-with-clonal-heterogeneity
#9
Zhangguo Chen, Mihret T Elos, Sawanee S Viboolsittiseri, Katherine Gowan, Sonia M Leach, Michael Rice, Maxwell D Eder, Kenneth Jones, Jing H Wang
BACKGROUND: Activated B lymphocytes harbor programmed DNA double-strand breaks (DSBs) initiated by activation-induced deaminase (AID) and repaired by non-homologous end-joining (NHEJ). While it has been proposed that these DSBs during secondary antibody gene diversification are the primary source of chromosomal translocations in germinal center (GC)-derived B cell lymphomas, this point has not been directly addressed due to the lack of proper mouse models. METHODS: In the current study, we establish a unique mouse model by specifically deleting a NHEJ gene, Xrcc4, and a cell cycle checkpoint gene, Trp53, in GC B cells, which results in the spontaneous development of B cell lymphomas that possess features of GC B cells...
January 7, 2016: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/26681117/activation-induced-deoxycytidine-deaminase-aid-co-transcriptional-scanning-at-single-molecule-resolution
#10
Gayan Senavirathne, Jeffrey G Bertram, Malgorzata Jaszczur, Kathy R Chaurasiya, Phuong Pham, Chi H Mak, Myron F Goodman, David Rueda
Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble...
December 18, 2015: Nature Communications
https://www.readbyqxmd.com/read/26385350/aid-associated-dna-repair-pathways-regulate-malignant-transformation-in-a-murine-model-of-bcl6-driven-diffuse-large-b-cell-lymphoma
#11
Xiwen Gu, Carmen J Booth, Zongzhi Liu, Matthew P Strout
Somatic hypermutation and class-switch recombination of the immunoglobulin (Ig) genes occur in germinal center (GC) B cells and are initiated through deamination of cytidine to uracil by activation-induced cytidine deaminase (AID). Resulting uracil-guanine mismatches are processed by uracil DNA glycosylase (UNG)-mediated base-excision repair and MSH2-mediated mismatch repair (MMR) to yield mutations and DNA strand lesions. Although off-target AID activity also contributes to oncogenic point mutations and chromosome translocations associated with GC and post-GC B-cell lymphomas, the role of downstream AID-associated DNA repair pathways in the pathogenesis of lymphoma is unknown...
January 7, 2016: Blood
https://www.readbyqxmd.com/read/26355458/cell-cycle-regulates-nuclear-stability-of-aid-and-determines-the-cellular-response-to-aid
#12
Quy Le, Nancy Maizels
AID (Activation Induced Deaminase) deaminates cytosines in DNA to initiate immunoglobulin gene diversification and to reprogram CpG methylation in early development. AID is potentially highly mutagenic, and it causes genomic instability evident as translocations in B cell malignancies. Here we show that AID is cell cycle regulated. By high content screening microscopy, we demonstrate that AID undergoes nuclear degradation more slowly in G1 phase than in S or G2-M phase, and that mutations that affect regulatory phosphorylation or catalytic activity can alter AID stability and abundance...
September 2015: PLoS Genetics
https://www.readbyqxmd.com/read/26308889/orientation-specific-joining-of-aid-initiated-dna-breaks-promotes-antibody-class-switching
#13
Junchao Dong, Rohit A Panchakshari, Tingting Zhang, Yu Zhang, Jiazhi Hu, Sabrina A Volpi, Robin M Meyers, Yu-Jui Ho, Zhou Du, Davide F Robbiani, Feilong Meng, Monica Gostissa, Michel C Nussenzweig, John P Manis, Frederick W Alt
During B-cell development, RAG endonuclease cleaves immunoglobulin heavy chain (IgH) V, D, and J gene segments and orchestrates their fusion as deletional events that assemble a V(D)J exon in the same transcriptional orientation as adjacent Cμ constant region exons. In mice, six additional sets of constant region exons (CHs) lie 100-200 kilobases downstream in the same transcriptional orientation as V(D)J and Cμ exons. Long repetitive switch (S) regions precede Cμ and downstream CHs. In mature B cells, class switch recombination (CSR) generates different antibody classes by replacing Cμ with a downstream CH (ref...
September 3, 2015: Nature
https://www.readbyqxmd.com/read/26276629/plasmodium-infection-promotes-genomic-instability-and-aid-dependent-b-cell-lymphoma
#14
Davide F Robbiani, Stephanie Deroubaix, Niklas Feldhahn, Thiago Y Oliveira, Elsa Callen, Qiao Wang, Mila Jankovic, Israel T Silva, Philipp C Rommel, David Bosque, Tom Eisenreich, André Nussenzweig, Michel C Nussenzweig
Chronic infection with Plasmodium falciparum was epidemiologically associated with endemic Burkitt's lymphoma, a mature B cell cancer characterized by chromosome translocation between the c-myc oncogene and Igh, over 50 years ago. Whether infection promotes B cell lymphoma, and if so by which mechanism, remains unknown. To investigate the relationship between parasitic disease and lymphomagenesis, we used Plasmodium chabaudi (Pc) to produce chronic malaria infection in mice. Pc induces prolonged expansion of germinal centers (GCs), unique compartments in which B cells undergo rapid clonal expansion and express activation-induced cytidine deaminase (AID), a DNA mutator...
August 13, 2015: Cell
https://www.readbyqxmd.com/read/26276627/somatic-rearrangement-in-b-cells-it-s-mostly-nuclear-physics
#15
REVIEW
Erez Lieberman Aiden, Rafael Casellas
We discuss how principles of nuclear architecture drive typical gene rearrangements in B lymphocytes, whereas translocation hot spots and recurrent lesions reflect the extent of AID-mediated DNA damage and selection.
August 13, 2015: Cell
https://www.readbyqxmd.com/read/26263206/nbs1-chip-seq-identifies-off-target-dna-double-strand-breaks-induced-by-aid-in-activated-splenic-b-cells
#16
Lyne Khair, Richard E Baker, Erin K Linehan, Carol E Schrader, Janet Stavnezer
Activation-induced cytidine deaminase (AID) is required for initiation of Ig class switch recombination (CSR) and somatic hypermutation (SHM) of antibody genes during immune responses. AID has also been shown to induce chromosomal translocations, mutations, and DNA double-strand breaks (DSBs) involving non-Ig genes in activated B cells. To determine what makes a DNA site a target for AID-induced DSBs, we identify off-target DSBs induced by AID by performing chromatin immunoprecipitation (ChIP) for Nbs1, a protein that binds DSBs, followed by deep sequencing (ChIP-Seq)...
August 2015: PLoS Genetics
https://www.readbyqxmd.com/read/26226003/misdelivery-at-the-nuclear-pore-complex-stopping-a-virus-dead-in-its-tracks
#17
REVIEW
Justin W Flatt, Urs F Greber
Many viruses deliver their genomes into the host cell's nucleus before they replicate. While onco-retroviruses and papillomaviruses tether their genomes to host chromatin upon mitotic breakdown of the nuclear envelope, lentiviruses, such as human immunodeficiency virus, adenoviruses, herpesviruses, parvoviruses, influenza viruses, hepatitis B virus, polyomaviruses, and baculoviruses deliver their genomes into the nucleus of post-mitotic cells. This poses the significant challenge of slipping a DNA or RNA genome past the nuclear pore complex (NPC) embedded in the nuclear envelope...
2015: Cells
https://www.readbyqxmd.com/read/26007657/two-mechanisms-coordinate-replication-termination-by-the-escherichia-coli-tus-ter-complex
#18
Manjula Pandey, Mohamed M Elshenawy, Slobodan Jergic, Masateru Takahashi, Nicholas E Dixon, Samir M Hamdan, Smita S Patel
The Escherichia coli replication terminator protein (Tus) binds to Ter sequences to block replication forks approaching from one direction. Here, we used single molecule and transient state kinetics to study responses of the heterologous phage T7 replisome to the Tus-Ter complex. The T7 replisome was arrested at the non-permissive end of Tus-Ter in a manner that is explained by a composite mousetrap and dynamic clamp model. An unpaired C(6) that forms a lock by binding into the cytosine binding pocket of Tus was most effective in arresting the replisome and mutation of C(6) removed the barrier...
July 13, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25917378/the-expression-patterns-of-dna-methylation-reprogramming-related-genes-are-associated-with-the-developmental-competence-of-cloned-embryos-after-zygotic-genome-activation-in-pigs
#19
Yanjun Huan, Hongmei Wang, Zhanfeng Wu, Jiguang Zhang, Zhonghua Liu, Hongbin He
DNA methylation reprogramming, regulated by DNA methylation and demethylation related genes, is essential for early embryo development; however, it is incomplete in cloned embryos, leading to poor cloning efficiency. Previous studies have shown that DNA methylation inhibitor, 5-aza-2'-deoxycytidine (5-aza-dC), could enhance the development of cloned embryos, thus, the genes regulating DNA methylation reprogramming should appropriately express in these embryos. To examine whether there is a correlation between embryo development and the expression patterns of DNA methylation reprogramming related genes, we investigated the developmental progress and transcription levels of candidate genes containing DNA methyltransferases (Dnmt1 and Dnmt3a), ten eleven translocation (Tet) dioxygenases (Tet1, Tet2 and Tet3) and base excision repair related genes including activation induced deamination (Aid), thymine DNA glycosylase (Tdg) and AP endonuclease 1 (Apex1) in porcine early embryos...
May 2015: Gene Expression Patterns: GEP
https://www.readbyqxmd.com/read/25897377/historical-abiotic-events-or-human-aided-dispersal-inferring-the-evolutionary-history-of-a-newly-discovered-galaxiid-fish
#20
Gamuchirai Chakona, Ernst R Swartz, Albert Chakona
Range expansion of obligate freshwater fishes in the Cape Floristic Region (CFR) of South Africa has mostly been attributed to river capture events and confluence of rivers following sea-level regression. The role of low drainage divides and interbasin water transfers has received less attention. This study analyzed mitochondrial and nuclear DNA sequences to assess the processes that could have influenced the phylogeographic patterns of a newly discovered lineage of Galaxias zebratus (hereafter Galaxias zebratus "Joubertina") that occurs across two currently isolated river systems close to the Joubertina area in the eastern CFR...
April 2015: Ecology and Evolution
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