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  1 / 133 MEDLINE  
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PMID:28137275
Autor:Kawasaki F; Beraldi D; Hardisty RE; McInroy GR; van Delft P; Balasubramanian S
Endereço:Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
Título:Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania.
Fonte:Genome Biol; 18(1):23, 2017 Jan 30.
ISSN:1474-760X
País de publicação:England
Idioma:eng
Resumo:BACKGROUND: 5-Hydroxymethyluracil (5hmU) is a thymine base modification found in the genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we develop a method for the genome-wide mapping of 5hmU-modified loci based on a chemical tagging strategy for the hydroxymethyl group. RESULTS: We apply the method to generate genome-wide maps of 5hmU in the parasitic protozoan Leishmania sp. In this genus, another thymine modification, 5-(ß-glucopyranosyl) hydroxymethyluracil (base J), plays a key role during transcription. To elucidate the relationship between 5hmU and base J, we also map base J loci by introducing a chemical tagging strategy for the glucopyranoside residue. Observed 5hmU peaks are highly consistent among technical replicates, confirming the robustness of the method. 5hmU is enriched in strand switch regions, telomeric regions, and intergenic regions. Over 90% of 5hmU-enriched loci overlapped with base J-enriched loci, which occurs mostly within strand switch regions. We also identify loci comprising 5hmU but not base J, which are enriched with motifs consisting of a stretch of thymine bases. CONCLUSIONS: By chemically detecting 5hmU we present a method to provide a genome-wide map of this modification, which will help address the emerging interest in the role of 5hmU. This method will also be applicable to other organisms bearing 5hmU.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, Protozoan); 0 (Glucosides); 4433-40-3 (5-hydroxymethyluracil); 53910-96-6 (5-((glucopyranosyloxy)methyl)uracil); 56HH86ZVCT (Uracil); 7LCS1FW4JV (Pentoxyl)


  2 / 133 MEDLINE  
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PMID:27029792
Autor:Smith KE; House CH; Dworkin JP; Callahan MP
Endereço:Department of Geosciences and Penn State Astrobiology Research Center, Pennsylvania State University, University Park, PA, 16802, USA.
Título:Spontaneous Oligomerization of Nucleotide Alternatives in Aqueous Solutions.
Fonte:Orig Life Evol Biosph; 47(1):3-11, 2017 Mar.
ISSN:1573-0875
País de publicação:Netherlands
Idioma:eng
Resumo:On early Earth, a primitive polymer that could spontaneously form from likely available precursors may have preceded both RNA and DNA as the first genetic material. Here, we report that heated aqueous solutions containing 5-hydroxymethyluracil (HMU) result in oligomers of uracil, heated solutions containing 5-hydroxymethylcytosine (HMC) result in oligomers of cytosine, and heated solutions containing both HMU and HMC result in mixed oligomers of uracil and cytosine. Oligomerization of hydroxymethylated pyrimidines, which may have been abundant on the primitive Earth, might have been important in the development of simple informational polymers.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:059QF0KO0R (Water); 1123-95-1 (5-hydroxymethylcytosine); 4433-40-3 (5-hydroxymethyluracil); 6R795CQT4H (5-Methylcytosine); 7LCS1FW4JV (Pentoxyl)


  3 / 133 MEDLINE  
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PMID:27146565
Autor:Seiler VK; Hützler WM; Bolte M
Endereço:Institut für Organische Chemie und Chemische Biologie, Goethe-Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany.
Título:Eight new crystal structures of 5-(hydroxymethyl)uracil, 5-carboxyuracil and 5-carboxy-2-thiouracil: insights into the hydrogen-bonded networks and the predominant conformations of the C5-bound residues.
Fonte:Acta Crystallogr C Struct Chem; 72(Pt 5):379-88, 2016 05 01.
ISSN:2053-2296
País de publicação:England
Idioma:eng
Resumo:In order to examine the preferred hydrogen-bonding pattern of various uracil derivatives, namely 5-(hydroxymethyl)uracil, 5-carboxyuracil and 5-carboxy-2-thiouracil, and for a conformational study, crystallization experiments yielded eight different structures: 5-(hydroxymethyl)uracil, C5H6N2O3, (I), 5-carboxyuracil-N,N-dimethylformamide (1/1), C5H4N2O4·C3H7NO, (II), 5-carboxyuracil-dimethyl sulfoxide (1/1), C5H4N2O4·C2H6OS, (III), 5-carboxyuracil-N,N-dimethylacetamide (1/1), C5H4N2O4·C4H9NO, (IV), 5-carboxy-2-thiouracil-N,N-dimethylformamide (1/1), C5H4N2O3S·C3H7NO, (V), 5-carboxy-2-thiouracil-dimethyl sulfoxide (1/1), C5H4N2O3S·C2H6OS, (VI), 5-carboxy-2-thiouracil-1,4-dioxane (2/3), 2C5H4N2O3S·3C6H12O3, (VII), and 5-carboxy-2-thiouracil, C10H8N4O6S2, (VIII). While the six solvated structures, i.e. (II)-(VII), contain intramolecular S(6) O-H...O hydrogen-bond motifs between the carboxy and carbonyl groups, the usually favoured R2(2)(8) pattern between two carboxy groups is formed in the solvent-free structure, i.e. (VIII). Further R2(2)(8) hydrogen-bond motifs involving either two N-H...O or two N-H...S hydrogen bonds were observed in three crystal structures, namely (I), (IV) and (VIII). In all eight structures, the residue at the ring 5-position shows a coplanar arrangement with respect to the pyrimidine ring which is in agreement with a search of the Cambridge Structural Database for six-membered cyclic compounds containing a carboxy group. The search confirmed that coplanarity between the carboxy group and the cyclic residue is strongly favoured.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:4433-40-3 (5-hydroxymethyluracil); 56HH86ZVCT (Uracil); 59X161SCYL (Thiouracil); 7LCS1FW4JV (Pentoxyl)


  4 / 133 MEDLINE  
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PMID:27036066
Autor:Olinski R; Starczak M; Gackowski D
Endereço:Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Karlowicza 24, Bydgoszcz 85-092, Poland. Electronic address: ryszardo@cm.umk.pl.
Título:Enigmatic 5-hydroxymethyluracil: Oxidatively modified base, epigenetic mark or both?
Fonte:Mutat Res Rev Mutat Res; 767:59-66, 2016 Jan-Mar.
ISSN:1388-2139
País de publicação:Netherlands
Idioma:eng
Resumo:The aim of this review is to describe the reactions which lead to generation of 5-hydroxymethyluracil, as well as the repair processes involved in its removal from DNA, and its level in various cells and urine. 5-hydroxymethyluracil may be formed during the course of the two processes: oxidation/hydroxylation of thymine with resultant formation of 5-hydroxymethyluracil paired with adenine (produced by reactive oxygen species), and reacting of reactive oxygen species with 5-methylcytosine forming 5-hydroxymethylcytosine, followed by its deamination to 5-hydroxymethyluracil mispaired with guanine. However, other, perhaps enzymatic, mechanism(s) may be involved in formation of 5-hydroxymethyluracil mispaired with guanine. Indeed, this mispair may be also formed as a result of deamination of 5-hydroxymethylcytosine, recently described "sixth" DNA base. It was demonstrated that 5-hydroxymethyluracil paired with adenine can be also generated by TET enzymes from thymine during mouse embryonic cell differentiation. Therefore, it is possible that 5-hydroxymethyluracil is epigenetic mark. The level of 5-hydroxymethyluracil in various somatic tissues is relatively stable and resembles that observed in lymphocytes, about 0.5/10(6) dN in human colon, colorectal cancer as well as various rat and porcine tissues. Experimental evidence suggests that SMUG1 and TDG are main enzymes involved in removal of 5-hydroxymethyluracil from DNA. 5-hydroxymethyluracil, in form of 5-hydroxymethyluridine, was also detected in rRNA, and together with SMUG1 may play a role in rRNA quality control. To summarize, 5-hydroxymethyluracil is with no doubt a product of both enzymatic and reactive oxygen species-induced reaction. This modification may probably serve as an epigenetic mark, providing additional layer of information encoded within the genome. However, the pool of 5-hydroxymethyluracil generated as a result of oxidative stress is also likely to disturb physiological epigenetic processes, and as such may be defined as a lesion. Altogether this suggests that 5-hydroxymethyluracil may be either a regulatory or erroneous compound.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; REVIEW
Nome de substância:0 (Reactive Oxygen Species); 4433-40-3 (5-hydroxymethyluracil); 6R795CQT4H (5-Methylcytosine); 7LCS1FW4JV (Pentoxyl); 9007-49-2 (DNA); QR26YLT7LT (Thymine)


  5 / 133 MEDLINE  
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PMID:26843430
Autor:Grin I; Ishchenko AA
Endereço:Laboratoire «Stabilité Génétique et Oncogenèse¼ CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, F-94805 Villejuif, France Gustave Roussy Cancer Campus, F-94805 Villejuif, France SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, Russia Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia.
Título:An interplay of the base excision repair and mismatch repair pathways in active DNA demethylation.
Fonte:Nucleic Acids Res; 44(8):3713-27, 2016 05 05.
ISSN:1362-4962
País de publicação:England
Idioma:eng
Resumo:Active DNA demethylation (ADDM) in mammals occurs via hydroxylation of 5-methylcytosine (5mC) by TET and/or deamination by AID/APOBEC family enzymes. The resulting 5mC derivatives are removed through the base excision repair (BER) pathway. At present, it is unclear how the cell manages to eliminate closely spaced 5mC residues whilst avoiding generation of toxic BER intermediates and whether alternative DNA repair pathways participate in ADDM. It has been shown that non-canonical DNA mismatch repair (ncMMR) can remove both alkylated and oxidized nucleotides from DNA. Here, a phagemid DNA containing oxidative base lesions and methylated sites are used to examine the involvement of various DNA repair pathways in ADDM in murine and human cell-free extracts. We demonstrate that, in addition to short-patch BER, 5-hydroxymethyluracil and uracil mispaired with guanine can be processed by ncMMR and long-patch BER with concomitant removal of distant 5mC residues. Furthermore, the presence of multiple mispairs in the same MMR nick/mismatch recognition region together with BER-mediated nick formation promotes proficient ncMMR resulting in the reactivation of an epigenetically silenced reporter gene in murine cells. These findings suggest cooperation between BER and ncMMR in the removal of multiple mismatches that might occur in mammalian cells during ADDM.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
Nome de substância:4433-40-3 (5-hydroxymethyluracil); 56HH86ZVCT (Uracil); 6R795CQT4H (5-Methylcytosine); 7LCS1FW4JV (Pentoxyl); 9007-49-2 (DNA); EC 3.6.1.3 (Msh2 protein, mouse); EC 3.6.1.3 (MutS Homolog 2 Protein)


  6 / 133 MEDLINE  
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PMID:26578595
Autor:Carson S; Wilson J; Aksimentiev A; Weigele PR; Wanunu M
Endereço:Department of Physics, Northeastern University, Boston, MA, USA.
Título:Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA.
Fonte:Nucleic Acids Res; 44(5):2085-92, 2016 Mar 18.
ISSN:1362-4962
País de publicação:England
Idioma:eng
Resumo:Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and molecular dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified molecules. Molecular dynamics simulations suggest that 5-hydroxymethyluracil alters the flexibility and hydrophilicity of the DNA molecules, which may account for the differences observed in our nanopore translocation experiments. The altered physico-chemical properties of DNA produced by the thymine modifications may have implications for recognition and processing of such modifications by regulatory DNA-binding proteins.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
Nome de substância:0 (DNA-Binding Proteins); 4433-40-3 (5-hydroxymethyluracil); 7LCS1FW4JV (Pentoxyl); 9007-49-2 (DNA); QR26YLT7LT (Thymine)


  7 / 133 MEDLINE  
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PMID:26815240
Autor:Bullard W; Cliffe L; Wang P; Wang Y; Sabatini R
Endereço:From the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States.
Título:Base J glucosyltransferase does not regulate the sequence specificity of J synthesis in trypanosomatid telomeric DNA.
Fonte:Mol Biochem Parasitol; 204(2):77-80, 2015 Dec.
ISSN:1872-9428
País de publicação:Netherlands
Idioma:eng
Resumo:Telomeric DNA of trypanosomatids possesses a modified thymine base, called base J, that is synthesized in a two-step process; the base is hydroxylated by a thymidine hydroxylase forming hydroxymethyluracil (hmU) and a glucose moiety is then attached by the J-associated glucosyltransferase (JGT). To examine the importance of JGT in modifiying specific thymine in DNA, we used a Leishmania episome system to demonstrate that the telomeric repeat (GGGTTA) stimulates J synthesis in vivo while mutant telomeric sequences (GGGTTT, GGGATT, and GGGAAA) do not. Utilizing an in vitro GT assay we find that JGT can glycosylate hmU within any sequence with no significant change in Km or kcat, even mutant telomeric sequences that are unable to be J-modified in vivo. The data suggests that JGT possesses no DNA sequence specificity in vitro, lending support to the hypothesis that the specificity of base J synthesis is not at the level of the JGT reaction.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
Nome de substância:0 (DNA, Protozoan); 0 (Protozoan Proteins); 4433-40-3 (5-hydroxymethyluracil); 7LCS1FW4JV (Pentoxyl); EC 2.4.1.- (Glucosyltransferases); QR26YLT7LT (Thymine)


  8 / 133 MEDLINE  
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PMID:26660343
Autor:Gackowski D; Zarakowska E; Starczak M; Modrzejewska M; Olinski R
Endereço:Department of Clinical Biochemistry, Nicolaus Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland.
Título:Tissue-Specific Differences in DNA Modifications (5-Hydroxymethylcytosine, 5-Formylcytosine, 5-Carboxylcytosine and 5-Hydroxymethyluracil) and Their Interrelationships.
Fonte:PLoS One; 10(12):e0144859, 2015.
ISSN:1932-6203
País de publicação:United States
Idioma:eng
Resumo:BACKGROUND: Replication-independent active/enzymatic demethylation may be an important process in the functioning of somatic cells. The most plausible mechanisms of active 5-methylcytosine demethylation, leading to activation of previously silenced genes, involve ten-eleven translocation (TET) proteins that participate in oxidation of 5-methylcytosine to 5-hydroxymethylcytosine which can be further oxidized to 5-formylcytosine and 5-carboxylcytosine. Recently, 5-hydroxymethylcytosine was demonstrated to be a relatively stable modification, and the previously observed substantial differences in the level of this modification in various murine tissues were shown to depend mostly on cell proliferation rate. Some experimental evidence supports the hypothesis that 5-hydroxymethyluracil may be also generated by TET enzymes and has epigenetic functions. RESULTS: Using an isotope-dilution automated online two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry, we have analyzed, for the first time, all the products of active DNA demethylation pathway: 5-methyl-2'-deoxycytidine, 5-hydroxymethyl-2'-deoxycytidine, 5-formyl-2'-deoxycytidine and 5-carboxyl-2'-deoxycytidine, as well as 5-hydroxymethyl-2'-deoxyuridine, in DNA isolated from various rat and porcine tissues. A strong significant inverse linear correlation was found between the proliferation rate of cells and the global level of 5-hydroxymethyl-2'-deoxycytidine in both porcine (R2 = 0.88) and rat tissues (R2 = 0.83); no such relationship was observed for 5-formyl-2'-deoxycytidine and 5-carboxyl-2'-deoxycytidine. Moreover, a substrate-product correlation was demonstrated for the two consecutive steps of iterative oxidation pathway: between 5-hydroxymethyl-2'-deoxycytidine and its product 5-formyl-2'-deoxycytidine, as well as between 5-formyl-2'-deoxycytidine and 5-carboxyl-2'-deoxycytidine (R2 = 0.60 and R2 = 0.71, respectively). CONCLUSIONS: Good correlations within the substrate-product sets of iterative oxidation pathway may suggest that a part of 5-formyl-2'-deoxycytidine and/or 5-carboxyl-2'-deoxycytidine can be directly linked to a small portion of 5-hydroxymethyl-2'-deoxycytidine which defines the active demethylation process.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
Nome de substância:0 (5-carboxylcytosine); 0 (5-formylcytosine); 1123-95-1 (5-hydroxymethylcytosine); 4433-40-3 (5-hydroxymethyluracil); 6R795CQT4H (5-Methylcytosine); 7LCS1FW4JV (Pentoxyl); 8J337D1HZY (Cytosine); 9007-49-2 (DNA); EC 1.- (TET1 protein, rat); EC 1.13.11.- (Dioxygenases)


  9 / 133 MEDLINE  
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PMID:26429971
Autor:Li W; Zhang T; Ding J
Endereço:National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.
Título:Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi.
Fonte:Nucleic Acids Res; 43(20):10026-38, 2015 Nov 16.
ISSN:1362-4962
País de publicação:England
Idioma:eng
Resumo:TET proteins play a vital role in active DNA demethylation in mammals and thus have important functions in many essential cellular processes. The chemistry for the conversion of 5mC to 5hmC, 5fC and 5caC catalysed by TET proteins is similar to that of T to 5hmU, 5fU and 5caU catalysed by thymine-7-hydroxylase (T7H) in the nucleotide anabolism in fungi. Here, we report the crystal structures and biochemical properties of Neurospora crassa T7H. T7H can bind the substrates only in the presence of cosubstrate, and binding of different substrates does not induce notable conformational changes. T7H exhibits comparable binding affinity for T and 5hmU, but 3-fold lower affinity for 5fU. Residues Phe292, Tyr217 and Arg190 play critical roles in substrate binding and catalysis, and the interactions of the C5 modification group of substrates with the cosubstrate and enzyme contribute to the slightly varied binding affinity and activity towards different substrates. After the catalysis, the products are released and new cosubstrate and substrate are reloaded to conduct the next oxidation reaction. Our data reveal the molecular basis for substrate specificity and catalytic mechanism of T7H and provide new insights into the molecular mechanism of substrate recognition and catalysis of TET proteins.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
Nome de substância:0 (Fungal Proteins); 0 (Ketoglutaric Acids); 1195-08-0 (5-formyluracil); 4433-40-3 (5-hydroxymethyluracil); 56HH86ZVCT (Uracil); 7LCS1FW4JV (Pentoxyl); 8ID597Z82X (alpha-ketoglutaric acid); EC 1.- (Mixed Function Oxygenases); EC 1.14.11.6 (thymine, 2-oxoglutarate dioxygenase); QR26YLT7LT (Thymine)


  10 / 133 MEDLINE  
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PMID:26358812
Autor:Malik SS; Coey CT; Varney KM; Pozharski E; Drohat AC
Endereço:Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
Título:Thymine DNA glycosylase exhibits negligible affinity for nucleobases that it removes from DNA.
Fonte:Nucleic Acids Res; 43(19):9541-52, 2015 Oct 30.
ISSN:1362-4962
País de publicação:England
Idioma:eng
Resumo:Thymine DNA Glycosylase (TDG) performs essential functions in maintaining genetic integrity and epigenetic regulation. Initiating base excision repair, TDG removes thymine from mutagenic G ·: T mispairs caused by 5-methylcytosine (mC) deamination and other lesions including uracil (U) and 5-hydroxymethyluracil (hmU). In DNA demethylation, TDG excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), which are generated from mC by Tet (ten-eleven translocation) enzymes. Using improved crystallization conditions, we solved high-resolution (up to 1.45 Å) structures of TDG enzyme-product complexes generated from substrates including G·U, G·T, G·hmU, G·fC and G·caC. The structures reveal many new features, including key water-mediated enzyme-substrate interactions. Together with nuclear magnetic resonance experiments, the structures demonstrate that TDG releases the excised base from its tight product complex with abasic DNA, contrary to previous reports. Moreover, DNA-free TDG exhibits no significant binding to free nucleobases (U, T, hmU), indicating a Kd >> 10 mM. The structures reveal a solvent-filled channel to the active site, which might facilitate dissociation of the excised base and enable caC excision, which involves solvent-mediated acid catalysis. Dissociation of the excised base allows TDG to bind the beta rather than the alpha anomer of the abasic sugar, which might stabilize the enzyme-product complex.
Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
Nome de substância:4433-40-3 (5-hydroxymethyluracil); 56HH86ZVCT (Uracil); 7LCS1FW4JV (Pentoxyl); 9007-49-2 (DNA); EC 3.2.2.- (Thymine DNA Glycosylase); QR26YLT7LT (Thymine)



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