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https://www.readbyqxmd.com/read/29340219/a-novel-hybrid-promoter-are-htert-for-cancer-gene-therapy
#1
S V Kalinichenko, M V Shepelev, P N Vikhreva, I V Korobko
describe a novel hybrid tumor-specific promoter, ARE-hTERT, composed of the human TERT gene promoter (hTERT) and the antioxidant response element (ARE) from the human GCLM gene promoter. The hybrid promoter retains the tumor specificity of the basal hTERT promoter but is characterized by an enhanced transcriptional activity in cancer cells with abnormal activation of the Nrf2 transcription factor and upon induction of oxidative stress. In the in vitro enzyme-prodrug cancer gene therapy scheme, ARE-hTERT promoter-driven expression of CD : UPRT (yeast cytosine deaminase : uracil phosphoribosyltransferase) chimeric protein induced a more pronounced death of cancer cells either upon treatment with 5-fluorouracil (5FC) alone or when 5FC was combined with chemotherapeutic drugs as compared to the hTERT promoter...
October 2017: Acta Naturae
https://www.readbyqxmd.com/read/29233176/uncoordinated-expression-of-dna-methylation-related-enzymes-in-human-cancer
#2
Jiao Liu, Xiuliang Cui, Jinhua Jiang, Dan Cao, Yufei He, Hongyang Wang
BACKGROUND: In addition to the important roles played by 5-methylcytosine (5mC), emerging evidence suggests that 5mC derivatives, such as 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), also exhibit regulatory functions in physiological and pathological processes. Four cytosine modifications (5mC, 5hmC, 5fC and 5caC) are produced and erased by a cyclic enzymatic cascade mediated by DNA methyltransferases (DNMTs), ten-eleven translocation (TET) family enzymes and thymine DNA glycosylase (TDG)...
December 12, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29224139/antibody-based-detection-of-global-nuclear-dna-methylation-in-cells-tissue-sections-and-mammalian-embryos
#3
Nathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, Sari Pennings
Immunostaining is widely used in cell biology for the in situ detection of proteins in fixed cells. The method is based on the specificity of antibodies for recognizing and binding to a selected target, combined with immunolabeling techniques for microscopic imaging. Antibodies with high specificities for modified nucleotides have also been widely developed, and among those, antibodies that recognize modified cytosine: 5-methylcytosine (5mC), and more recently, its derivates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29163896/fluorogenic-labeling-and-single-base-resolution-analysis-of-5-formylcytosine-in-dna
#4
Chaoxing Liu, Yafen Wang, Wei Yang, Fan Wu, Weiwu Zeng, Zonggui Chen, Jinguo Huang, Guangrong Zou, Xiong Zhang, Shaoru Wang, Xiaocheng Weng, Zhiguo Wu, Yu Zhou, Xiang Zhou
5-Formylcytosine (5fC), which plays an important role in epigenetic functions, has received widespread attention in many related fields. Here, we demonstrate a new design for both the fluorogenic switch-on detection and single-base resolution analysis of 5fC through selectively reacting a reagent with 5fC to yield an intramolecular cyclization nucleobase. The generated product, bearing a similar benzothiazole-iminocoumarin scaffold, is highly fluorescent and enables us to qualitatively and quantitatively detect 5fC moieties in γ-irradiated calf thymus DNA...
November 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29158345/stable-oxidative-cytosine-modifications-accumulate-in-cardiac-mesenchymal-cells-from-type2-diabetes-patients-rescue-by-alpha-ketoglutarate-and-tet-tdg-functional-reactivation
#5
Francesco Spallotta, Chiara Cencioni, Sandra Atlante, Davide Garella, Mattia Cocco, Mattia Mori, Raffaella Mastrocola, Carsten Künne, Stefan Günther, Simona Nanni, Valerio Azzimato, Sven Zukunft, Angela Kornberger, Duran Sueruen, Frank Schnutgen, Harald von Melchner, Antonella Di Stilo, Manuela Aragno, Maarten Braspenning, Wim Van Criekinge, Miles J De Blasio, Rebecca H Ritchie, Germana Zaccagnini, Fabio Martelli, Antonella Farsetti, Ingrid Fleming, Thomas Braun, Andres Beiras-Fernandez, Bruno Botta, Massimo Collino, Massimo Bertinaria, Andreas M Zeiher, Carlo Gaetano
Rationale: Human cardiac mesenchymal cells (CMSCs) are a therapeutically-relevant primary cell population. Diabetes compromises CMSC function as consequence of metabolic alterations and incorporation of stable epigenetic changes. Objective: To investigate the role of α-ketoglutarate (αKG) in the epi-metabolic control of DNA demethylation in CMSCs. Methods and Results: Quantitative global analysis, methylated and hydroxymethylated DNA sequencing and gene specific GC methylation detection revealed an accumulation of 5mC, 5hmC and 5fC in the genomic DNA of human CMSCs isolated from diabetic (D) donors (D-CMSCs)...
November 20, 2017: Circulation Research
https://www.readbyqxmd.com/read/29091409/cucurbit-7-uril-driven-host-guest-chemistry-for-reversible-intervention-of-5-formylcytosine-targeted-biochemical-reactions
#6
Shao-Ru Wang, Yan-Yan Song, Lai Wei, Chao-Xing Liu, Bo-Shi Fu, Jia-Qi Wang, Xi-Ran Yang, Yi-Nong Liu, Si-Min Liu, Tian Tian, Xiang Zhou
5-Formylcytosine (5fC) is identified as one of the key players in active DNA demethylation and also as an epigenetic mark in mammals, thus representing a novel attractive target to chemical intervention. The current study represents an attempt to develop a reversible 5fC-targeted intervention tool. A supramolecular aldehyde reactive probe was therefore introduced for selective conversion of the 5fC to 5fC-AD nucleotide. Using various methods, we demonstrate that cucurbit[7]uril (CB7) selectively targets the 5fC-AD nucleotide in DNA, however, the binding of CB7 to 5fC-AD does not affect the hydrogen bonding properties of natural nucleobases in duplex DNA...
November 9, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29028987/in-silico-structural-modelling-of-multiple-epigenetic-marks-on-dna
#7
Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M Deane, Peter Minary
Summary: There are four known epigenetic cytosine modifications in mammals: 5mC, 5hmC, 5fC and 5caC. The biological effects of 5mC are well understood but the roles of the remaining modifications remain elusive. Experimental and computational studies suggest that a single epigenetic mark has little structural effect but six of them can radically change the structure of DNA to a new form, F-DNA. Investigating the collective effect of multiple epigenetic marks requires the ability to interrogate all possible combinations of epigenetic states (e...
September 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28930980/immunostaining-for-dna-modifications-computational-analysis-of-confocal-images
#8
Ashley H Ramsawhook, Lara C Lewis, Maria Eleftheriou, Abdulkadir Abakir, Paulina Durczak, Robert Markus, Seema Rajani, Nicholas R F Hannan, Beth Coyle, Alexey Ruzov
For several decades, 5-methylcytosine (5mC) has been thought to be the only DNA modification with a functional significance in metazoans. The discovery of enzymatic oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) as well as detection of N6-methyladenine (6mA) in the DNA of multicellular organisms provided additional degrees of complexity to the epigenetic research. According to a growing body of experimental evidence, these novel DNA modifications may play specific roles in different cellular and developmental processes...
September 7, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28898504/reversible-dna-protein-cross-linking-at-epigenetic-dna-marks
#9
Shaofei Ji, Hongzhao Shao, Qiyuan Han, Christopher L Seiler, Natalia Y Tretyakova
5-Formylcytosine (5fC) is an endogenous DNA modification frequently found within regulatory elements of mammalian genes. Although 5fC is an oxidation product of 5-methylcytosine (5mC), the two epigenetic marks show distinct genome-wide distributions and protein affinities, suggesting that they perform different functions in epigenetic signaling. A unique feature of 5fC is the presence of a potentially reactive aldehyde group in its structure. Herein, we show that 5fC bases in DNA readily form Schiff-base conjugates with Lys side chains of nuclear proteins in vitro and in vivo...
September 12, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28827588/nei-like-1-neil1-excises-5-carboxylcytosine-directly-and-stimulates-tdg-mediated-5-formyl-and-5-carboxylcytosine-excision
#10
Anton Slyvka, Karolina Mierzejewska, Matthias Bochtler
Thymine DNA glycosylase (TDG) and Nei-like 1 (NEIL1) have both been implicated in the base excision repair step of active DNA demethylation. The robust glycosylase activity of TDG on DNA substrates containing 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC) is universally accepted, but the mode of action of NEIL1 is still debated. Based on genetic experiments, it has been suggested that NEIL1 acts redundantly with TDG and excises 5fC and 5caC directly. However, this result has been disputed, and it was suggested instead that NEIL1 is recruited by the monofunctional TDG for the 2'-deoxyribose excision step...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28769976/new-insights-into-5hmc-dna-modification-generation-distribution-and-function
#11
REVIEW
Dong-Qiao Shi, Iftikhar Ali, Jun Tang, Wei-Cai Yang
Dynamic DNA modifications, such as methylation/demethylation on cytosine, are major epigenetic mechanisms to modulate gene expression in both eukaryotes and prokaryotes. In addition to the common methylation on the 5th position of the pyrimidine ring of cytosine (5mC), other types of modifications at the same position, such as 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC), are also important. Recently, 5hmC, a product of 5mC demethylation by the Ten-Eleven Translocation family proteins, was shown to regulate many cellular and developmental processes, including the pluripotency of embryonic stem cells, neuron development, and tumorigenesis in mammals...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28742335/5-formylcytosine-yields-dna-protein-cross-links-in-nucleosome-core-particles
#12
Fengchao Li, Yingqian Zhang, Jing Bai, Marc M Greenberg, Zhen Xi, Chuanzheng Zhou
In situ generation of 5-formylcytosine (5fC) in nucleosome core particles (NCPs) reveals that 5fC leads to essential DNA-protein cross-links (DPCs). Mechanistic studies using chemical models and mutated histones demonstrate that DPCs form reversibly between the formyl function of 5fC and primary amines on histones. These results suggest that DPC formation from 5fC in chromatin occurs in addition to its role in DNA demethylation.
August 9, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28680034/high-dose-fluconazole-in-combination-with-amphotericin-b-is-more-efficient-than-monotherapy-in-murine-model-of-cryptococcosis
#13
Julliana Ribeiro Alves Santos, Noelly Queiroz Ribeiro, Rafael Wesley Bastos, Rodrigo Assunção Holanda, Letícia Chagas Silva, Estela Rezende Queiroz, Daniel Assis Santos
Cryptococcus spp., the causative agents of cryptococcosis, are responsible for deaths of hundreds of thousands of people every year worldwide. The drawbacks of available therapeutic options are aggravated by the increased resistance of yeast to the drugs, resulting in inefficient therapy. Also, the antifungal 5FC is not available in many countries. Therefore, a combination of antifungal drugs may be an interesting option, but in vitro and theoretical data point to the possible antagonism between the main antifungals used to treat cryptococcosis, i...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28668047/substituents-effect-in-electron-attachment-to-epigenetic-modifications-of-cytosine
#14
Fernanda B Nunes, Márcio H F Bettega, Sergio d'Almeida Sanchez
Epigenetic modifications of cytosine have been found to influence differently in many processes in biological systems. In order to investigate the differences in electron attachment to different epigenetic modifications of cytosine, we reported the A″ component of the integral cross section of electron scattering by cytosine (C) and its epigenetic modifications 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Our results were obtained with the Schwinger multichannel method with pseudopotentials in the static-exchange (SE) and static-exchange plus polarization (SEP) approximations...
June 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28647531/a-rapid-mass-spectrometric-method-for-the-measurement-of-catalytic-activity-of-ten-eleven-translocation-enzymes
#15
Babu Sudhamalla, Debasis Dey, Megan Breski, Kabirul Islam
Enzymatic methylation at carbon five on cytosine (5mC) in DNA is a hallmark of mammalian epigenetic programming and is critical to gene regulation during early embryonic development. It has recently been shown that dynamic erasure of 5mC by three members of the ten-eleven translocation (TET) family plays a key role in cellular differentiation. TET enzymes belong to Fe (II)- and 2-ketoglutarate (2KG) dependent dioxygenases that successively oxidize 5mC to 5-hydroxymethyl cytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5CaC), thus providing a chemical basis for the removal of 5mC which once was thought to be a permanent mark in mammalian genome...
October 1, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28555658/tet-mediated-active-dna-demethylation-mechanism-function-and-beyond
#16
REVIEW
Xiaoji Wu, Yi Zhang
In mammals, DNA methylation in the form of 5-methylcytosine (5mC) can be actively reversed to unmodified cytosine (C) through TET dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), followed by replication-dependent dilution or thymine DNA glycosylase (TDG)-dependent base excision repair. In the past few years, biochemical and structural studies have revealed mechanistic insights into how TET and TDG mediate active DNA demethylation...
September 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28538185/regulation-of-active-dna-demethylation-through-rar-mediated-recruitment-of-a-tet-tdg-complex
#17
Haider M Hassan, Bart Kolendowski, Majdina Isovic, Kerstin Bose, Helen J Dranse, Arthur V Sampaio, T Michael Underhill, Joseph Torchia
Retinoic acid (RA) plays important roles in development, growth, and homeostasis through regulation of the nuclear receptors for RA (RARs). Herein, we identify Hypermethylated in Cancer 1 (Hic1) as an RA-inducible gene. HIC1 encodes a tumor suppressor, which is often silenced by promoter hypermethylation in cancer. Treatment of cells with an RAR agonist causes a rapid recruitment of an RAR/RXR complex consisting of TDG, the lysine acetyltransferase CBP, and TET 1/2 to the Hic1 promoter. Complex binding coincides with a transient accumulation of 5fC/5caC and concomitant upregulation of Hic1 expression, both of which are TDG dependent...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28360182/simultaneous-mapping-of-active-dna-demethylation-and-sister-chromatid-exchange-in-single-cells
#18
Xiaoji Wu, Azusa Inoue, Tsukasa Suzuki, Yi Zhang
To understand mammalian active DNA demethylation, various methods have been developed to map the genomic distribution of the demethylation intermediates 5-formylcysotine (5fC) and 5-carboxylcytosine (5caC). However, the majority of these methods requires a large number of cells to begin with. In this study, we describe low-input methylase-assisted bisulfite sequencing (liMAB-seq ) and single-cell MAB-seq (scMAB-seq), capable of profiling 5fC and 5caC at genome scale using ∼100 cells and single cells, respectively...
March 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28348165/combinatorial-dna-methylation-codes-at-repetitive-elements
#19
Christophe Papin, Abdulkhaleg Ibrahim, Stéphanie Le Gras, Amandine Velt, Isabelle Stoll, Bernard Jost, Hervé Menoni, Christian Bronner, Stefan Dimitrov, Ali Hamiche
DNA methylation is an essential epigenetic modification, present in both unique DNA sequences and repetitive elements, but its exact function in repetitive elements remains obscure. Here, we describe the genome-wide comparative analysis of the 5mC, 5hmC, 5fC, and 5caC profiles of repetitive elements in mouse embryonic fibroblasts and mouse embryonic stem cells. We provide evidence for distinct and highly specific DNA methylation/oxidation patterns of the repetitive elements in both cell types, which mainly affect CA repeats and evolutionarily conserved mouse-specific transposable elements including IAP-LTRs, SINEs B1m/B2m, and L1Md-LINEs...
June 2017: Genome Research
https://www.readbyqxmd.com/read/28343982/single-cell-5-formylcytosine-landscapes-of-mammalian-early-embryos-and-escs-at-single-base-resolution
#20
Chenxu Zhu, Yun Gao, Hongshan Guo, Bo Xia, Jinghui Song, Xinglong Wu, Hu Zeng, Kehkooi Kee, Fuchou Tang, Chengqi Yi
Active DNA demethylation in mammals involves ten-eleven translocation (TET) family protein-mediated oxidation of 5-methylcytosine (5mC). However, base-resolution landscapes of 5-formylcytosine (5fC) (an oxidized derivative of 5mC) at the single-cell level remain unexplored. Here, we present "CLEVER-seq" (chemical-labeling-enabled C-to-T conversion sequencing), which is a single-cell, single-base resolution 5fC-sequencing technology, based on biocompatible, selective chemical labeling of 5fC and subsequent C-to-T conversion during amplification and sequencing...
May 4, 2017: Cell Stem Cell
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