5-Methylcytosine: A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.Deamination: The removal of an amino group (NH2) from a chemical compound.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Thymine DNA Glycosylase: An enzyme that removes THYMINE and URACIL bases mispaired with GUANINE through hydrolysis of their N-glycosidic bond. These mispaired nucleotides generally occur through the hydrolytic DEAMINATION of 5-METHYLCYTOSINE to thymine.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)DNA (Cytosine-5-)-Methyltransferase: An enzyme that catalyzes the transfer of a methyl group from S-ADENOSYLMETHIONINE to the 5-position of CYTOSINE residues in DNA.Sulfites: Inorganic salts of sulfurous acid.ThymineDNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Osmium: Osmium. A very hard, gray, toxic, and nearly infusible metal element, atomic number 76, atomic weight 190.2, symbol Os. (From Dorland, 28th ed)DNA Glycosylases: A family of DNA repair enzymes that recognize damaged nucleotide bases and remove them by hydrolyzing the N-glycosidic bond that attaches them to the sugar backbone of the DNA molecule. The process called BASE EXCISION REPAIR can be completed by a DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA.DNA-Cytosine Methylases: Methylases that are specific for CYTOSINE residues found on DNA.Pentoxyl: 5-Hydroxymethyl-6-methyl- 2,4-(1H,3H)-pyrimidinedione. Uracil derivative used in combination with toxic antibiotics to lessen their toxicity; also to stimulate leukopoiesis and immunity. Synonyms: pentoksil; hydroxymethylmethyluracil.Dioxygenases: Non-heme iron-containing enzymes that incorporate two atoms of OXYGEN into the substrate. They are important in biosynthesis of FLAVONOIDS; GIBBERELLINS; and HYOSCYAMINE; and for degradation of AROMATIC HYDROCARBONS.Adenine: A purine base and a fundamental unit of ADENINE NUCLEOTIDES.N-Glycosyl Hydrolases: A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Dinucleoside Phosphates: A group of compounds which consist of a nucleotide molecule to which an additional nucleoside is attached through the phosphate molecule(s). The nucleotide can contain any number of phosphates.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.DNA Modification Methylases: Enzymes that are part of the restriction-modification systems. They are responsible for producing a species-characteristic methylation pattern, on either adenine or cytosine residues, in a specific short base sequence in the host cell's own DNA. This methylated sequence will occur many times in the host-cell DNA and remain intact for the lifetime of the cell. Any DNA from another species which gains entry into a living cell and lacks the characteristic methylation pattern will be recognized by the restriction endonucleases of similar specificity and destroyed by cleavage. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms.Methyltransferases: A subclass of enzymes of the transferase class that catalyze the transfer of a methyl group from one compound to another. (Dorland, 28th ed) EC 2.1.1.Nanopores: Small holes of nanometer dimensions in a membrane, that can be used as single molecule detectors. The pores can be biological or synthetic.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Deoxycytidine Monophosphate: Deoxycytidine (dihydrogen phosphate). A deoxycytosine nucleotide containing one phosphate group esterified to the deoxyribose moiety in the 2'-,3'- or 5- positions.Azacitidine: A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent.UracilDeoxyribonuclease (Pyrimidine Dimer): An enzyme which catalyzes an endonucleolytic cleavage near PYRIMIDINE DIMERS to produce a 5'-phosphate product. The enzyme acts on the damaged DNA strand, from the 5' side of the damaged site.Epigenomics: The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.Endodeoxyribonucleases: A group of enzymes catalyzing the endonucleolytic cleavage of DNA. They include members of EC 3.1.21.-, EC 3.1.22.-, EC 3.1.23.- (DNA RESTRICTION ENZYMES), EC 3.1.24.- (DNA RESTRICTION ENZYMES), and EC 3.1.25.-.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.GuanineDeoxyribonuclease HpaII: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequences C/CGG and GGC/C at the slash. HpaII is from Haemophilus parainfluenzae. Several isoschizomers have been identified. EC 3.1.21.-.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Gardner Syndrome: A variant of ADENOMATOUS POLYPOSIS COLI caused by mutation in the APC gene (GENES, APC) on CHROMOSOME 5. It is characterized by not only the presence of multiple colonic polyposis but also extracolonic ADENOMATOUS POLYPS in the UPPER GASTROINTESTINAL TRACT; the EYE; the SKIN; the SKULL; and the FACIAL BONES; as well as malignancy in organs other than the GI tract.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Cytidine: A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.Base Pair Mismatch: The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).Photochemical Processes: Chemical reactions effected by light.Oxidation-Reduction: A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Zygote: The fertilized OVUM resulting from the fusion of a male and a female gamete.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Enzyme-Linked Immunosorbent Assay: An immunoassay utilizing an antibody labeled with an enzyme marker such as horseradish peroxidase. While either the enzyme or the antibody is bound to an immunosorbent substrate, they both retain their biologic activity; the change in enzyme activity as a result of the enzyme-antibody-antigen reaction is proportional to the concentration of the antigen and can be measured spectrophotometrically or with the naked eye. Many variations of the method have been developed.Reagent Kits, Diagnostic: Commercially prepared reagent sets, with accessory devices, containing all of the major components and literature necessary to perform one or more designated diagnostic tests or procedures. They may be for laboratory or personal use.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Embryonic Stem Cells: Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.

Base pairing of anhydrohexitol nucleosides with 2,6-diaminopurine, 5-methylcytosine and uracil asbase moiety. (1/489)

Hexitol nucleic acids (HNAs) with modified bases (5-methylcytosine, 2,6-diaminopurine or uracil) were synthesized. The introduction of the 5-methylcytosine base demonstrates that N -benzoylated 5-methylcytosyl-hexitol occurs as the imino tautomer. The base pairing systems (G:CMe, U:D, T:D and U:A) obey Watson-Crick rules. Substituting hT for hU, hCMefor hC and hD for hA generally leads to increased duplex stability. In a single case, replacement of hC by hCMedid not result in duplex stabilization. This sequence-specific effect could be explained by the geometry of the model duplex used for carrying out the thermal stability study. Generally, polypurine HNA sequences give more stable duplexes with their RNA complement than polypyrimidine HNA sequences. This observation supports the hypothesis that, besides changes in stacking pattern, the difference in conformational stress between purine and pyrimidine nucleosides may contribute to duplex stability. Introduction of hCMeand hD in HNA sequences further increases the potential of HNA to function as a steric blocking agent.  (+info)

Relationship between amount of esterase and gene copy number in insecticide-resistant Myzus persicae (Sulzer). (2/489)

Overproduction of the insecticide-degrading esterases, E4 and FE4, in peach-potato aphids, Myzus persicae (Sulzer), depends on both gene amplification and transcriptional control, the latter being associated with changes in DNA methylation. The structure and function of the aphid esterase genes have been studied but the determination of their copy number has proved difficult, a common problem with gene amplification. We have now used a combination of pulsed-field gel electrophoresis and quantitative competitive PCR to determine relative esterase gene copy numbers in aphid clones with different levels of insecticide resistance (R1, R2 and R3). There are approx. 4-fold increases between susceptible, R1, R2 and R3 aphids, reaching a maximum of approx. 80 times more genes in R3; this gives proportionate increases in esterase protein relative to susceptible aphids. Thus there is no overexpression of the amplified genes, in contrast with what was thought previously. For E4 genes, the loss of 5-methylcytosine is correlated with a loss of expression, greatly decreasing the amount of enzyme relative to the copy number.  (+info)

DNA methylation is a reversible biological signal. (3/489)

The pattern of DNA methylation plays an important role in regulating different genome functions. To test the hypothesis that DNA methylation is a reversible biochemical process, we purified a DNA demethylase from human cells that catalyzes the cleavage of a methyl residue from 5-methyl cytosine and its release as methanol. We show that similar to DNA methyltransferase, DNA demethylase shows CpG dinucleotide specificity, can demethylate mdCpdG sites in different sequence contexts, and demethylates both fully methylated and hemimethylated DNA. Thus, contrary to the commonly accepted model, DNA methylation is a reversible signal, similar to other physiological biochemical modifications.  (+info)

Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. (4/489)

CpG island methylation has been linked to tumor suppressor gene inactivation in neoplasia and may serve as a useful marker to clone novel cancer-related genes. We have developed a novel PCR-based method, methylated CpG island amplification (MCA), which is useful for both methylation analysis and cloning differentially methylated genes. Using restriction enzymes that have differential sensitivity to 5-methyl-cytosine, followed by adaptor ligation and PCR amplification, methylated CpG rich sequences can be preferentially amplified. In a model experiment using a probe from exon 1 of the p16 gene, signal was detected from MCA products of a colorectal cancer cell line but not in normal colon mucosa. To identify novel CpG islands differentially methylated in colorectal cancer, we have applied MCA coupled with representational difference analysis to the colon cancer cell line Caco2 as a tester and normal colon mucosa as a driver. Using this strategy, we isolated 33 differentially methylated DNA sequences, including fragments identical to several known genes (PAX6, Versican, alpha-tubulin, CSX, OPT, and rRNA gene). The association of hypermethylation of the clones obtained and transcriptional suppression in colorectal cancer was confirmed by examining the Versican gene, which we found to be silenced in methylated cell lines and reactivated by the methylation inhibitor 5-aza-2'-deoxycytidine. We therefore propose that MCA is a useful technique to study methylation and to isolate CpG islands differentially methylated in cancer.  (+info)

Growth phase-dependent regulation of Vsr endonuclease may contribute to 5-methylcytosine mutational hot spots in Escherichia coli. (5/489)

Using rabbit polyclonal antibodies, we have shown that the Dcm cytosine methylase of Escherichia coli is maintained at a constant level during cell growth, while Vsr endonuclease levels are growth phase dependent. Decreased production of Vsr relative to Dcm during the log phase may contribute substantially to the mutability of 5-methylcytosine.  (+info)

Impact of C5-cytosine methylation on the solution structure of d(GAAAACGTTTTC)2. An NMR and molecular modelling investigation. (6/489)

The solution structures of d(GAAAACGTTTTC)2 and of its methylated derivative d(GAAAAMe5CGTTTTC)2 have been determined by NMR and molecular modelling in order to examine the impact of cytosine methylation on the central CpG conformation. Detailed 1H NMR and 31P NMR investigation of the two oligomers includes quantitative NOESY, 2D homonuclear Hartmann-Hahn spectroscopy, double-quantum-filtered COSY and heteronuclear 1H-31P correlation. Back-calculations of NOESY spectra and simulations of double-quantum-filtered COSY patterns were performed to gain accurate information on interproton distances and sugar phase angles. Molecular models under experimental constraints were generated by energy minimization by means of the molecular mechanics program JUMNA. The MORASS software was used to iteratively refine the structures obtained. After methylation, the oligomer still has a B-DNA conformation. However, there are differences in the structural parameters and the thermal stability as compared to the unmethylated molecule. Careful structural analysis shows that after methylation CpG departs from the usual conformation observed in other ACGT tetramers with different surroundings. Subtle displacements of bases, sugars and backbone imposed by the steric interaction of the two methyl groups inside the major groove are accompanied by severe pinching of the minor groove at the C-G residues.  (+info)

The role of the Escherichia coli mug protein in the removal of uracil and 3,N(4)-ethenocytosine from DNA. (7/489)

The human thymine-DNA glycosylase has a sequence homolog in Escherichia coli that is described to excise uracils from U.G mismatches (Gallinari, P., and Jiricny, J. (1996) Nature 383, 735-738) and is named mismatched uracil glycosylase (Mug). It has also been described to remove 3,N(4)-ethenocytosine (epsilonC) from epsilonC.G mismatches (Saparbaev, M., and Laval, J. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 8508-8513). We used a mug mutant to clarify the role of this protein in DNA repair and mutation avoidance. We find that inactivation of mug has no effect on C to T or 5-methylcytosine to T mutations in E. coli and that this contrasts with the effect of ung defect on C to T mutations and of vsr defect on 5-methylcytosine to T mutations. Even under conditions where it is overproduced in cells, Mug has little effect on the frequency of C to T mutations. Because uracil-DNA glycosylase (Ung) and Vsr are known to repair U.G and T.G mismatches, respectively, we conclude that Mug does not repair U.G or T.G mismatches in vivo. A defect in mug also has little effect on forward mutations, suggesting that Mug does not play a role in avoiding mutations due to endogenous damage to DNA in growing E. coli. Cell-free extracts from mug(+) ung cells show very little ability to remove uracil from DNA, but can excise epsilonC. The latter activity is missing in extracts from mug cells, suggesting that Mug may be the only enzyme in E. coli that can remove this mutagenic adduct. Thus, the principal role of Mug in E. coli may be to help repair damage to DNA caused by exogenous chemical agents such as chloroacetaldehyde.  (+info)

5-Methylcytosine distribution and genome organization in triticale before and after treatment with 5-azacytidine. (8/489)

Triticale (2n=6x=42) is a hybrid plant including rye (R) and wheat (A and B) genomes. Using genomic in situ hybridization with rye DNA as a probe, we found the chromosomes of the R genome were not intermixed with the wheat chromosomes in 85% of nuclei. After treatment of seedlings with low doses of the drug 5-azacytidine (5-AC), leading to hypomethylation of the DNA, the chromosomes became intermixed in 60% of nuclei; the next generation showed intermediate organization. These results correlate with previous data showing that expression of R-genome rRNA genes, normally suppressed, is activated by 5-AC treatment and remains partially activated in the next generation. The distribution of 5-methylcytosine (5-mC) was studied using an antibody to 5-mC. Methylation was detected along the lengths of all chromosomes; there were some chromosome regions with enhanced and reduced methylation, but these were not located at consistent positions, nor were there differences between R and wheat genome chromosomes. After 5-AC treatment, lower levels of methylation were detected. After 5-AC treatment, in situ hybridization with rye genomic DNA sometimes showed micronuclei of rye origin and multiple translocations between wheat and rye chromosomes. Genomic DNA was analysed using methylation-sensitive restriction enzymes and, as probes, two rDNA sequences, two tandemly organised DNA sequences from rye (pSc200 and pSc250), and copia and the gypsy group retrotransposon fragments from rye and wheat. DNA extracted immediately after 5-AC treatment was cut more by methylation-sensitive restriction enzymes than DNA from untreated seedlings. Each probe gave a characteristic restriction fragment pattern, but rye- and wheat-origin probes behaved similarly, indicating that hypomethylation was induced in both genomes. In DNA samples from leaves taken 13-41 days after treatment, RFLP (Restriction Fragment Length Polymorphism) patterns were indistinguishable from controls and 5-AC treatments with all probes. Surprising differences in hybridization patterns were seen between DNA from root tips and leaves with the copia-fragment probes.  (+info)

Recent studies suggest that DNA demethylation can be achieved through ten-eleven translocation (Tet) family of DNA deoxygenates mediated oxidation followed by thymine DNA glycosylase (TDG) mediated excision and repair, but it is unclear to what extent such active demethylation processes take place. Here, we generated genome-wide distribution maps of 5-methylcytosine(5mC),5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5- carboxylcytosine (5caC) in wild-type and Tdg-deficient mouse embryonic stem cells. We observe that the steady state 5fC and 5caC are preferentially detected at repetitive sequences in wild-type cells. Depletion of TDG causes marked accumulation of 5fC and 5caC at a large number of distal gene regulatory elements and transcriptionally repressed/poised gene promoters, suggesting that Tet/TDG- dependent dynamic cycling of 5mC oxidation states may be involved in regulating the function of these regions. Thus, comprehensive mapping of 5mC oxidation and BER pathway activity ...
T4 β-glucosyltransferase catalyzes glucose addition to 5-hydroxymethylcytosine but not 5-methylcytosine, allowing differentiation of these types of DNA methylation.
DNA methylation is established by DNA methyltransferases (DNMTs) and is a key epigenetic mark. Ten Eleven Translocation (TET) proteins are enzymes that oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidization products (oxi-mCs), which indirectly promote DNA demethylation. Here, we provide an overview of the effect of TET proteins and altered DNA modification status in T and B cell development and function. We summarize current advances in our understanding of the role of TET proteins and 5hmC in T and B cells in both physiological and pathological contexts. We describe how TET proteins and 5hmC regulate DNA modification, chromatin accessibility, gene expression and transcriptional networks, and discuss potential underlying mechanisms and open questions in the field.
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Ten-Eleven Translocation (TET) proteins play an important role in regulating DNA methylation fidelity and their inactivation contributes to the DNA hypermethylation phenotype in cancer; they are Fe²+- and 2-oxoglutarate-dependent dioxygenases that successively oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) and these oxidized methylcytosines are important intermediates in the process of 5mC demethylation.. TET proteins convert 5mC to 5hmC in vitro, but it is difficult to explore the process of DNA demethylation and their effects on endogenous hypermethylated genes in cells. In this study, we tried to develop a system that accumulates TET oxidase activity at hypermethylated promoters. To accomplish this, we constructed a fusion protein-producing vector consisting of methyl-CpG binding domain (MBD) and TET1 catalytic domain (TET1 CD) and asked whether this fusion protein (MBD-TET1 CD) could lead to DNA demethylation and gene ...
Active DNA demethylation in mammals. (a) The action of AID on 5-methylcytosine residues (white circles) in DNA (thick black line) gives rise to deaminated 5-met
The DNA demethylation pathway has been discovered to play a significant role in DNA epigenetics. This pathway removes the methyl group from cytosine, which is involved in the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC) by ten-eleven translocation (TET) proteins. Then, 5-hmC can be iteratively oxidized to generate 5-formylcytosine (5-foC) and 5-carboxylcytosine (5-caC). However, 5-hmC, 5-foC, and 5-caC are hardly detected due to their low content. In this study, we have developed a LC-HRMS method coupled with derivatization to accurately and simultaneously quantify 5-mC levels, along with its oxidation products in genomic DNA ...
Chemical modifications of proteins and nucleic acids can have significant effects on gene expression. Dr. He presented a technique to investigate the presence of the modified base 5-hydroxymethylcytosine (5-hmC) on genome wide scale. Tet methylcytosine dioxygenase (TET) oxidizes 5-methylcytosine (5-meC) to 5-hmC and further to 5-formylcytosine and 5-carboxylcytosine (He et al., 2011; Ito et al., 2011; Tahiliani et al., 2009). Yet both 5-meC and 5-hmC are protected from C to U conversion upon bisulfite treatment making it impossible to distinguish both DNA modifications with traditional bisulfite sequencing. This limitation can be overcome by TET-assisted bisulfite sequencing (TAB-Seq) (Yu et al., 2012).. Method: The bacteriophage T4 β-glucosyltransferase selectively glycosylates the hydroxyl group of 5-hmC. Utilization of glucose with an azide group (N3) allowed further modification such as addition of a biotin molecule (by simple click chemistry) which facilitates enrichment. Glycosylated, and ...
5-Methylcytosine (MeC) is an endogenous modification of DNA that plays a crucial role in DNA-protein interactions, chromatin structure, epigenetic regulation, and DNA repair. MeC is produced via enzymatic methylation of the C-5 position of cytosine by DNA-methyltransferases (DNMT) which use S-adenosylmethionine (SA Nucleic Acid Modifications
|p|5-Methylcytosine (m|sup|5|/sup|C) is a well-characterized DNA modification, and is also predominantly reported in abundant non-coding RNAs in bo...
Transcription factor binding and high resolution crystallographic studies (1.3 Å) of Dickerson-Drew duplexes with cytosine, methylcytosine and hydroxymethylcytosine bases provide evidence that C-5 cytosine modifications could regulate transcription by context dependent effects on DNA transcription factor int
DNA methylation is broadly recognized as the most stable epigenetic modification. Its distribution pattern in parental cells is faithfully transmitted to daughter cells during mitosis. Recent discoveries of the TET-mediated DNA oxidative demethylation greatly expanded our understanding about the plasticity and dynamics of this modification. TET family enzymes (TET1, TET2 and TET3) could successively oxidize 5-methylcytosine (5mC) to 5-hydroxymethycytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), which may lead to eventual demethylation. In the genome, different oxidized products occupy overlapping, but largely distinct, genomic regions, and only a subset of 5hmC is further oxidized, which leads to eventual demethylation. However, how the distributions and the fates of oxidative derivatives of 5mC are determined in cells remains elusive. Researchers from Prof. ZHU Bings group in the Institute of Biophysics (IBP) of the Chinese Academy of Sciences and their collaborators set ...
Methyl-CpG-binding domain protein 2 (MBD2) is a member of the MBD protein family and has been shown to catalyze demethylation by direclty removing methyl groups from 5-methylcytosine residues in DNA. Chromatin...
Lucy A. Godley, The University of Chicago. Dr. Godleys work was stimulated by the difficulty of predicting how Acute Myeloid Leukemia patients would respond to hypomethylating agents, and whether baseline epigenetics could lend important information for treatment strategies. Godley studied covalent cytosine modifications using high-density methyaltion arrays and 5-hydroxymethylcytosine (5hmC) affinity sequencing in normal and leukemic hematopoietic stem cell development. Her group also examined baseline cytosine modifications between African and European populations, showing ~36,000 distinct CpG modifications between the two groups.. Dr. Godley emphasized the importance of 5hmC, the late-blooming cousin of 5-methylcytosine (5mC) that has eluded experimenters until recently. While 5hmC and 5mC have distinct functionality (5hmC is thought to play a role as an intermediate between 5mC and unmodified C, but also may have its own transcriptional regulatory role), current bisulfite-based ...
Tumors exhibit oncogenic epigenetic alterations including global hypomethylation and local promoter hypermethylation that can repress the transcription of tumor suppressor genes and promote cancer cell growth. Oxygen-dependent tet methylcytosine dioxygenase (TET) family proteins catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), resulting in DNA demethylation. 5hmC is frequently lost in cancer, but in the majority of tumors, the underlying mechanism is unclear. Thienpont and colleagues observed that hypoxia induced 5hmC loss in a majority of tested human and murine cell lines, resulting from reduced activity, but not reduced expression, of TETs. DNA-immunoprecipitation sequencing (DIP-seq) revealed global loss of 5hmC in response to hypoxia, predominantly at gene promoters, many of which had concomitant gain of 5mC, and RNA-seq confirmed that expression of these genes was repressed. Data from The Cancer Genome Atlas showed increased promoter hypermethylation in ...
Values are the averages of 3 experiments, and the level of 18S rRNA is employed as an interior control. (D) Indicate levels of DNA methylation in diverse cytosine context at the exogenous RD29A promoter in WT and the rpt2a-two mutant. Frequencies of methylcytosine at CG, CHG and CHH websites are indicated. Twenty clones are sequenced for each sample.CI-1011 (E) Mean ranges of DNA methylation in various cytosine contexts at the endogenous RD29A promoter in WT and the rpt2a-two mutant.For germination of Arabidopsis thaliana (ecotype Columbia-) wild type and mutants, seeds have been floor-sterilized and put on Murashige and Skoog (MS) medium supplemented with two% sucrose (Germination inducible medium: GIM). Soon after cold remedy for two times to synchronize germination, seeds were transferred to 22uC and fifty% relative humidity beneath a sixteen/8 h gentle/dim cycle (this time position suggests days following sowing: DAS). The seeds of the met1-1 mutant had been supplied by Dr. Robert A. ...
5-Hydroxymethylcytosine Remodeling Precedes Lineage Specification during Differentiation of Human CD4+ T Cells Researchers report early and widespread 5-methylcytosine/5-hydroxymethylcytosine remodeling during human CD4+ T cell differentiation ex vivo at genes and cell-specific enhancers with known T cell function. [Cell Rep] Full Article , Graphical Abstract , Press Release IκB Kinase ε Is an NFATc1 Kinase that Inhibits T Cell Immune Response IKKε is an IκB kinase (IKK)-related kinase, and the function of IKKε remains obscure in T cells, despite its abundant expression. Scientists report that IKKε inhibits nuclear factor of activated T cells (NFAT) activation and T cell responses by promoting NFATc1 phosphorylation. [Cell Rep] Full Article , Graphical Abstract A Human Trypanosome Suppresses CD8+ T Cell Priming by Dendritic Cells through the Induction of Immune Regulatory CD4+ Foxp3+ T Cells Using an in vivo assay that eliminated multiple variables associated with antigen processing and ...
We report how the mammalian 5-methylcytosine (5mC) oxidase Tet3 exists as 3 main isoforms and characterized the full-length isoform containing an N-terminal CXXC domain (Tet3FL). stopping neurodegenerative diseases. Launch 5 (5mC) is certainly a customized cytosine bottom implicated in gene control and is definitely thought to be the only modified base naturally present in mammalian DNA (Klose and Bird 2006 Only lately 5 (5hmC) in addition has been discovered (Kriaucionis and Heintz 2009 Tahiliani et al. 2009 5 is certainly formed enzymatically with the Tet category of 5mC oxidases (Tahiliani et al. 2009 Ito et al. 2010 and is currently regarded as a stable element of the epigenetic code (Koh and Rao 2013 Pfeifer et al. 2013 Wu and Zhang 2014 Additionally 5 continues to be seen as an intermediate bottom in developmentally managed DNA demethylation reactions. Both proposed features of 5hmC arent necessarily mutually distinctive (Hahn et al. 2014 Degrees of 5hmC are especially saturated in ...
In eukaryotic DNA, methylation most commonly occurs as 5-methylcytosine. This is often in blocks of heterochromatin or in CpG islands surrounding genes (http://www.methdb.de) and is recognized as playing a fundamental role in regulating gene expression. In the case of mRNA, a number of modifications are possible, such as C-to-U editing in some chloroplast and mitochondrial transcripts (Shikanai, 2006) or A-to-I deamination, found in some animal RNAs (Zhang and Carmichael, 2001). Methylation of the N6 position of the adenosine base has been observed in many RNA species, including tRNA, rRNA, and small nuclear RNA (snRNA) (Bjork et al., 1987; Maden, 1990; Shimba et al., 1995; Gu et al., 1996; Agris et al., 2007; Piekna-Przybylska et al., 2008), but the functional importance of its occurrence in mRNA has remained unclear since its discovery ,30 years ago (Desrosiers et al., 1974; Perry and Kelley, 1974).. N6-Methyladenosine (m6A) is found in the mRNA of some viruses (Beemon and Keith, 1977; Aloni ...
Gene target information for TET1P1 - tet methylcytosine dioxygenase 1 pseudogene 1 (human). Find diseases associated with this biological target and compounds tested against it in bioassay experiments.
M.EcoKII methylates the first A at the palindromic site ATGCAT (as well as the corresponding A on the opposite strand), see (Kossykh VG (2004) J. Bact 186: 2061-2067 PMID 15028690) Note that this article has been retracted; the retraction appears to center on textual plagarism, not experimental results. The homology to AvaIII is real. I think I believe it. tk 20:28, 9 December 2005 (EST). Rich Roberts reports: "We have tried ourselves to detect activity with this gene product and cannot detect any methyltransferase activity. In our case we used antibodies able to detect N6-methyladenine or N4 methylcytosine in DNA. The ones we have are very sensitive and should have been able to detect 5-methyl groups in the whole E. coli chromosome. Nothing was detected in an over-expressing strain ...
M.EcoKII methylates the first A at the palindromic site ATGCAT (as well as the corresponding A on the opposite strand), see (Kossykh VG (2004) J. Bact 186: 2061-2067 PMID 15028690) Note that this article has been retracted; the retraction appears to center on textual plagarism, not experimental results. The homology to AvaIII is real. I think I believe it. tk 20:28, 9 December 2005 (EST). Rich Roberts reports: "We have tried ourselves to detect activity with this gene product and cannot detect any methyltransferase activity. In our case we used antibodies able to detect N6-methyladenine or N4 methylcytosine in DNA. The ones we have are very sensitive and should have been able to detect 5-methyl groups in the whole E. coli chromosome. Nothing was detected in an over-expressing strain ...
Complexes of β-cylodextrin with five nucleotides of adenine (A), thymine (T) guanine (G), cytosine (C), and 5-methylcytosine have been investigated using Hatree-Fock (HF) and density functional theory (DFT) calculations of different quality. [...]
Hydroxymethyl Collector Kit is designed for the detection and enrichment of 5-hydroxymethylcytosine (5-hmC) DNA for whole-genome or gene specific hydroxymethylation analyis.
Bisulfite sequencing (also known as bisulphite sequencing) is the use of bisulfite treatment of DNA to determine its pattern of methylation. DNA methylation was the first discovered epigenetic mark, and remains the most studied. In animals it predominantly involves the addition of a methyl group to the carbon-5 position of cytosine residues of the dinucleotide CpG, and is implicated in repression of transcriptional activity. Treatment of DNA with bisulfite converts cytosine residues to uracil, but leaves 5-methylcytosine residues unaffected. Therefore, DNA that has been treated with bisulfite retains only methylated cytosines. Thus, bisulfite treatment introduces specific changes in the DNA sequence that depend on the methylation status of individual cytosine residues, yielding single-nucleotide resolution information about the methylation status of a segment of DNA. Various analyses can be performed on the altered sequence to retrieve this information. The objective of this analysis is ...
It is widely accepted that cAMP regulates gene transcription principally by activating the protein kinase A (PKA)-targeted transcription factors. Here, we show that cAMP enhances the generation of 5-hydroxymethylcytosine (5hmC) in multiple cell types. 5hmC is converted from 5-methylcytosine (5mC) by Tet methylcytosine dioxygenases, for which Fe(II) is an essential cofactor. The promotion of 5hmC was mediated by a prompt increase of the intracellular labile Fe(II) pool (LIP). cAMP enhanced the acidification of endosomes for Fe(II) release to the LIP likely through RapGEF2. The effect of cAMP on Fe(II) and 5hmC was confirmed by adenylate cyclase activators, phosphodiesterase inhibitors, and most notably by stimulation of G protein-coupled receptors (GPCR). The transcriptomic changes caused by cAMP occurred in concert with 5hmC elevation in differentially transcribed genes. Collectively, these data show a previously unrecognized regulation of gene transcription by GPCR-cAMP signaling through ...
The presence of 6-methyladenine and 5-methylcytosine at Dam (GATC) and Dcm (CCA/TGG) sites in DNA of mycobacterial species was investigated using isoschizomer restriction enzymes. In all species examined, Dam and Dcm recognition sequences were not methylated indicating the absence of these methyltransferases. On the other hand, high performance liquid chromatographic analysis of genomic DNA from Mycobacterium smegmatis and Mycobacterium tuberculosis showed significant levels of 6-methyladenine and 5-methylcytosine suggesting the presence of DNA methyltransferases other than Dam and Dcm. Occurrence of methylation was also established by a sensitive genetic assay. ...
The Ten-Eleven Translocation (TET) enzymes comprise a family of three dioxygenases TET 1-3, that depend on iron (II) and 2-oxoglutarate, as cofactors for activity. They convert the methylcytosine into other cytosine derivatives by hydroxylation. The TET enzymes catalyze the sequential oxidations of 5-mC to 5-hydroxymethylcytosine (5-hmC) and to 5-formylcytosine (5-fC and 5-carboxycytosine (5-caC), and also the direct conversion to 5-fC and 5-caC from 5-mC. 5-fC and 5-caC could be converted back to cytosine by thymine DNA glycosylase (TDG) in base excision repair, rendering the cytosine completely unmethylated. ...
Methylation at 5-cytosine (5-mC) is a fundamental epigenetic DNA modification associated recently with cardiac disease. In contrast, the role of 5-hydroxymethylcytosine (5-hmC) - 5-mCs oxidation product - is unknown in the context of the heart. Here, we assess the hydroxymethylome in embryonic, neonatal, adult and hypertrophic mouse cardiomyocytes, showing that dynamic modulation of hydroxymethylated DNA is associated with specific transcriptional networks during heart development and failure. DNA hydroxymethylation marks gene bodies of highly expressed genes and distal regulatory regions with enhanced activity. Pathological hypertrophy is characterized by a partial shift towards a fetal-like distribution pattern. We further demonstrate a regulatory function of TET2 and provide evidence that the expression of key cardiac genes, such as Myh7 is modulated by TET2-mediated 5-hmC deposition on the gene body and at enhancers in cardiac cells. We thus provide the first genome-wide analysis of 5-hmC in the
Leu Ala Phe Pro Val Asp Thr Asn Val Gly Arg Ile Ala Val 1300 1305 1310Arg Met Gly Trp Val Pro Leu Gln Pro Leu Pro Glu Ser Leu Gln Leu 1315 1320 1325His Leu Leu Glu Leu Tyr Pro Val Leu Glu Ser Ile Gln Lys Phe Leu 1330 1335 1340Trp Pro Arg Leu Cys Lys Leu Asp Gln Arg Thr Leu Tyr Glu Leu His1345 1350 1355 1360Tyr Gln Leu Ile Thr Phe Gly Lys Val Phe Cys Thr Lys Ser Arg Pro 1365 1370 1375Asn Cys Asn Ala Cys Pro Met Arg Gly Glu Cys Arg His Phe Ala Ser 1380 1385 1390Ala Tyr Ala Ser Ala Arg Leu Ala Leu Pro Ala Pro Glu Glu Arg Ser 1395 1400 1405Leu Thr Ser Ala Thr Ile Pro Val Pro Pro Glu Ser Phe Pro Pro Val 1410 1415 1420Ala Ile Pro Met Ile Glu Leu Pro Leu Pro Leu Glu Lys Ser Leu Ala1425 1430 1435 1440Ser Gly Ala Pro Ser Asn Arg Glu Asn Cys Glu Pro Ile Ile Glu Glu 1445 1450 1455Pro Ala Ser Pro Gly Gln Glu Cys Thr Glu Ile Thr Glu Ser Asp Ile 1460 1465 1470Glu Asp Ala Tyr Tyr Asn Glu Asp Pro Asp Glu Ile Pro Thr Ile Lys 1475 1480 1485Leu Asn Ile Glu Gln Phe Gly Met Thr Leu Arg Glu His Met Glu Arg 1490 1495 ...
Total P16 methylation (P16M), including P16 hydroxymethylation (P16H) and true-P16M, correlates with malignant transformation of oral epithelial dysplasia (OED). Both true-P16M and P16H are early events in carcinogenesis. The aim of this study is to prospectively determine if discrimination of true-P16M from P16H is necessary for prediction of cancer development from OEDs. Patients (n = 265) with mild or moderate OED were recruited into the double blind two-center cohort. Total-P16M and P16H were analyzed using the 115-bp MethyLight, TET-assisted bisulfite (TAB) methylation-specific PCR (MSP), and TAB-sequencing. Total-P16M-positive and P16H-negative samples were defined as true-P16M-positive. Progression of OEDs was monitored for a minimum 24 months follow-up period. P16H was detected in 23 of 73 (31.5%) total-P16M-positive OEDs. Follow-up information was obtained from 247 patients with an ultimate compliance rate of 93.2%. OED-derived squamous cell carcinomas were observed in 13.0% (32/247) patients
Data Availability StatementNot applicable. DNA and RNA methylation, histone modification, noncoding RNA modification and chromatin CALCR rearrangement. In epigenetic modification, DNA methylation and histone modification have been well studied. For example, 5-methylcytosine methylation in DNA has affected gene expression in many tumours. Significant advances have been achieved in recent years in the study of methylated drugs, such as demethylation drugs Decitabine and Azacitidine and histone deacetylase inhibitor Sedamine, which provides additional strategies for treatment of clinical diseases [2, 3]. In addition to DNA and histone methylation, another level of epigenetic regulation, namely, RNA methylation, has become a hot topic in biosciences over the past decade. Common RNA methylation sites include 5-methylcytosine (m5C), 7-methylguanosine (m7G), m1G, m2G, m6G, N1-methyladenosine (m1A) and m6A. m5C modification promotes splicing and translation [4]. m1G, m2G and m1A modifications at the ...
5-hmC (5-Hydroxymethylcytosine), DNA pyrimidine nitrogen base (CAS 1123-95-1). Join researchers using our high quality biochemicals.
Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes. We have carried out an unbiased global analysis of m5C in total and nuclear poly(A) RNA of mouse embryonic stem cells and murine brain. We show that there are intriguing differences in these samples and cell compartments with respect to the degree of methylation, functional classification of methylated transcripts, and position bias within the transcript. Specifically, we observe a pronounced accumulation of m5C sites in the vicinity of the translational start codon, depletion in coding sequences,
Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes. We have carried out an unbiased global analysis of m5C in total and nuclear poly(A) RNA of mouse embryonic stem cells and murine brain. We show that there are intriguing differences in these samples and cell compartments with respect to the degree of methylation, functional classification of methylated transcripts, and position bias within the transcript. Specifically, we observe a pronounced accumulation of m5C sites in the vicinity of the translational start codon, depletion in coding sequences,
Alterations in DNA methylation may cause disturbances in regulation of gene expression, including drug metabolism and distribution. Moreover, many cancers, including breast cancer, are characterized by DNA hypomethylation and a decreased 5-hydroxymethylcytosine level. The abnormal cell growth...
Distortions in the DNA sequence, such as damage or mispairs, are specifically recognized and processed by DNA repair enzymes. Many repair proteins and, in particular, glycosylases flip the target base out of the DNA helix into the enzymes active site. Our molecular dynamics simulations of DNA with intact and damaged (oxidized) methyl-cytosine show that the probability of being flipped is similar for damaged and intact methyl-cytosine. However, the accessibility of the different 5-methyl groups allows direct discrimination of the oxidized forms. Hydrogen-bonded patterns that vary between methyl-cytosine forms carrying a carbonyl oxygen atom are likely to be detected by the repair enzymes and may thus help target site recognition.
Cytosine methylation serves as a critical epigenetic mark by modifying DNA-protein interactions that influence transcriptional states and cellular identity. 5-m...
Measuring the 5-methylcytosine (5-mC) base in DNA allows researchers to investigate the role DNA methylation plays in various biological processes.
Açıklanan kolay ve yoğunluk bağımsız zenginleştirme için bir biyotin bağlayıcının aktarmak tıkırtı kimya ve ardından, 5-HMC için bir...
The rabbit Anti-5-hmC Polyclonal Antibody can robustly distinguish between hydroxymethylated DNA and methylated or unmodified DNA with limited to no cross-reactivity. The antibody has been validated in ELISA and immunoprecipitation-based enrichment assays, and is suitable for use in further applications including immun
Cell differentiation, reprogramming and malignant transformation are major events characterized by remarkable changes in the epigenome and involve remodeling of...
描述的是一个两步骤的标记过程中使用的β-葡糖基转移酶(β-GT)来传输的叠氮化物5-HMC-葡萄糖,然后通过点击化学生物素链接器为容易和密度独立富集转移。这种高效的和具体的标记方法使富集5 - ...
Anti-Methylcytosine dioxygenase TET1 Antibody is a Rabbit Polyclonal Antibody for detection of Methylcytosine dioxygenase TET1 also known as tet oncogene 1 & has been validated in WB, ChIP-seq. Find MSDS or SDS, a COA, data sheets and more information.
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16S rRNA (cytosine1402-N4)-methyltransferaseS-adenosyl-L-methionine + cytosine1402 in 16S rRNA = S-adenosyl-L-homocysteine + N4-methylcytosine1402 in 16S rRNA ...
by Dr. Mercola [1]. There are continual advances in science (as well as always some controversy), but new research supporting vitamin Cs potential in preventing the advancement of several forms of cancer is some of the most promising and remarkable thats emerged in a while.. More specifically, vitamin C may stop leukemia stem cells from multiplying, which could prevent certain forms of blood cancer from advancing, the journal Cell reveals, [1] along with pancreatic, colon, liver and ovarian cancers, according to several other notable medical journals and scientific reports.. An enzyme known as Tet methylcytosine dioxygenase 2 (TET2) has the ability to make stem cells "morph" into mature, normal blood cells that will eventually expire like normal cells. Stem cells, the study explains, are "undifferentiated cells that have not yet gained a specific identity and function." [2]. This ability helps patients with some blood cancers, including acute and chronic leukemia, because their stem cells ...
Introduction Diffuse intrinsic pontine glioma (DIPG) is a malignant pediatric brain tumor associated with dismal outcome. Recent high-throughput molecular studies have shown a high frequency of mutations in histone-encoding genes (H3F3A and HIST1B) and distinctive epigenetic alterations in these tumors. Epigenetic alterations described in DIPG include global DNA hypomethylation. In addition to the generally repressive methylcytosine DNA alteration, 5-hydroxymethylation of cytosine (5hmC) is recognized as an epigenetic mark associated with active chromatin. We hypothesized that in addition to alterations in DNA methylation, that there would be changes in 5hmC. To test this hypothesis, we performed immunohistochemical studies to compare epigenetic alterations in DIPG to extrapontine adult and pediatric glioblastoma (GBM) and normal brain. A total of 124 tumors were scored for histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 9 trimethylation (H3K9me3) and 104 for 5hmC
Colon cancer is one of the most frequent solid tumor and simultaneous diagnosis of primary colon cancer and liver metastases occurs in about one fourth of cases. The current knowledge on epigenetic signatures, especially those related to hydroxymethylation in primary cancer tissue, synchronous metastasis and blood circulating cells is lacking. This study aimed to investigate both methylcytosine (mCyt) and hydroxymethylcytosine (hmCyt) status in the DNA of individual patients from colon cancer tissue, synchronous liver metastases, and in cancer-free colon and liver tissues and leukocytes. Patients undergoing curative surgery (n=16) were enrolled and their laboratory and clinical history data collected. The contents of mCyt and hmCyt were determined by a liquid chromatography/mass spectrometry (LC/MS/MS) method in DNA extracted from primary colon cancer, synchronous hepatic metastatic tissues and homologous cancer-free tissues, i.e., colon and liver tissues as well as leukocytes. The mCyt and hmCyt
One of the hallmark events that occur during pre‐implantation embryonic development is genome‐wide demethylation. DNA methylation of CpG dinucleotides (5mC) in mammalian cells is associated with gene silencing. The maintenance methyltransferase DNMT1 is responsible for copying these patterns during DNA replication and DNMT3a and DNMT3b set up de novo DNA methylation during development (reviewed by Bagci and Fisher [29]). DNA demethylation can occur via active and passive mechanisms. Passive replication‐dependent loss of DNA methylation is achieved by downregulation of DNMT1 or NP95 or their exclusion from the nucleus resulting in the dilution of global DNA methylation during subsequent cell proliferation [30]. Active DNA demethylation is regulated by TET (Tet1‐3) enzymes that catalyze the conversion of 5‐methylcytosine to 5‐hydroxymethylcytosine (5hmC). 5hmC can subsequently be actively demethylated by its oxidation into 5‐formylcytosine (5fC) and 5‐carboxymethylcytosine (5caC) ...
It was from this compound that DNA methylation was discovered as it was the first molecule found to contain 5-methylcytosine. ... Johnson, Treat B.; Coghill, Robert D. (1925). "The discovery of 5-methyl-cytosine in tuberculinic acid, the nucleic acid of the ... Wyatt GR (1950). "Occurrence of 5-methylcytosine in nucleic acids". Nature. 166 (4214): 237-238. doi:10.1038/166237b0. PMID ...
Second, 5-aza-C is introduced to the cells so that it could be incorporated into nascent RNA in place of cytosine. Normally, ... For 5-aza-C, due to a nitrogen substitution in the C5 position of cytosine, the RNA methytransferase enzyme remains covalently ... 31(5): 459-464. Sakurai, M.; et al. (2014). "A biochemical landscape of A-to-I RNA editing in the human brain transcriptome". ... The chimeric oligonucleotide serves as a guide to allow RNase H to cleave the RNA strand precisely at the 5'-end of the ...
5 (1): 55-60. PMID 1825074.. *^ a b c Robertson, John A. (August 2003). "The $1000 Genome: Ethical and Legal Issues in Whole ... 307 (5): 461. doi:10.1001/jama.2012.68. PMC 3868436 . PMID 22298675.. *^ Hughes, Virginia. "It's Time To Stop Obsessing About ... 5 (1): 16-18. doi:10.1038/nmeth1156. PMID 18165802.. *^ Kalb, Gilbert; Moxley, Robert (1992). Massively Parallel, Optical, and ... 5 (23): 2638-49. doi:10.1002/smll.200900976. PMID 19904762.. *^ Schadt EE, Turner S, Kasarskis A (2010). "A window into third- ...
5-Aza-2'-deoxycytidine (decitabine) is a nucleoside analog that inhibits DNMTs by trapping them in a covalent complex on DNA by ... 90 (5): 785-790. doi:10.2307/3761319. JSTOR 3761319. Si-Yang, Liu; Jian-Qing, Lin; Hong-Long, Wu; Cheng-Cheng, Wang; Shu-Jia, ... Spontaneous deamination of 5-methylcytosine converts it to thymine. This results in a T:G mismatch. Repair mechanisms then ... 31 (5): 274-280. doi:10.1016/j.tig.2015.03.002. Maunakea, Alika K.; Nagarajan, Raman P.; Bilenky, Mikhail; Ballinger, Tracy J ...
This can occur in vitro through the use of bisulfite, which deaminates cytosine, but not 5-methylcytosine. This property has ... See Base excision repair.] Spontaneous deamination of 5-methylcytosine results in thymine and ammonia. This is the most common ... A DNA polymerase may perform this replacement via nick translation, a terminal excision reaction by its 5'-->3' exonuclease ...
90 (5): 785-790. doi:10.2307/3761319. JSTOR 3761319.. *^ Liu SY, Lin JQ, Wu HL, Wang CC, Huang SJ, Luo YF, Sun JH, Zhou JX, Yan ... 366 (6453): 362-5. doi:10.1038/366362a0. PMID 8247133.. *^ Borgel J, Guibert S, Li Y, Chiba H, Schübeler D, Sasaki H, Forné T, ... 480 (7378): 490-5. doi:10.1038/nature11086. PMID 22170606.. *^ Suzuki MM, Kerr AR, De Sousa D, Bird A (May 2007). "CpG ... doi:10.1016/s0168-9525(97)01181-5. PMID 9260521.. *^ Lev Maor G, Yearim A, Ast G (May 2015). "The alternative role of DNA ...
5-methylcytosine (5-mC) also commonly occurs in various RNA molecules. Recent data strongly suggest that m6A and 5-mC RNA ... This 5-O-methylation affects the flavonoid´s water solubility. Examples are 5-O-methylgenistein, 5-O-methylmyricetin or 5-O- ... Methionine synthase regenerates methionine (Met) from homocysteine (Hcy). The overall reaction transforms 5- ... Walsh, Christopher (2006). "Chapter 5 - Protein Methylation" (PDF). Posttranslational modification of proteins: expanding ...
In DNA, the most common modified base is 5-methylcytosine (m5C). In RNA, there are many modified bases, including those ... BIOL2060: Translation "Role of 5' mRNA and 5' U snRNA cap structures in regulation of gene expression" - Research - Retrieved ...
It was proposed that the CpG deficiency is due to an increased vulnerability of methylcytosines to spontaneously deaminate to ... 57 (5): 1394-400. doi:10.1073/pnas.57.5.1394. PMC 224485 . PMID 5231746. stevens M, Cheng J, Li D, Xi M, Hong C, Maire C, Ligon ... 145 (5): 773-786. doi:10.1016/j.cell.2011.04.024. PMID 21620139. Saxonov S, Berg P, Brutlag DL (2006). "A genome-wide analysis ... CpG should not be confused with GpC, the latter meaning that a guanine is followed by a cytosine in the 5' → 3' direction of a ...
0-671-22540-5. .. *. Olby RC (1994). The path to the double helix: the discovery of DNA. New York: Dover Publications. ISBN 0- ... Archived from the original on 5 February 2007.. *^ a b Ghosh A, Bansal M (April 2003). "A glossary of DNA structures from A to ... 978-0-8090-8947-5. .. *. Stent GS, Watson J (1980). The Double Helix: A Personal Account of the Discovery of the Structure of ... 7 (5): 337-48. doi:10.1038/nrg1838. PMID 16619049.. *^ O'Driscoll M, Jeggo PA (January 2006). "The role of double-strand break ...
6 (5): 435-40. Bibcode:2014NatCh...6..435B. doi:10.1038/nchem.1893. PMID 24755596. Royal Society of Chemistry, 2013. Corday- ... 3 (5): B37. PMID 17582897. Balasubramanian, S (2013). "An interview with Shankar Balasubramanian". Trends in Biochemical ... Booth, M. J.; Marsico, G.; Bachman, M.; Beraldi, D.; Balasubramanian, S. (2014). "Quantitative sequencing of 5-formylcytosine ... 5-hydroxymethylcytosine and 5-methylcytosine. 1998 Glaxo Wellcome Award for Innovative Organic Chemistry 2002 Corday-Morgan ...
... methylcytosine, giving a map of the true methylation status in the DNA sample. Levels of 5‑hydroxymethylcytosine can also be ... PloS one.2010;5(1):e8888. Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Jin, P., Ren, B., He, C. Tet-assisted bisulfite ... 29 (13): E65-5. doi:10.1093/nar/29.13.e65. PMC 55789 . PMID 11433041. Ehrich M, Zoll S, Sur S, van den Boom D (2007). "A new ... 30 (5): e21. doi:10.1093/nar/30.5.e21. PMC 101257 . PMID 11861926. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, ...
78 (2): 151-5. doi:10.1007/bf00278187. PMID 3338800. Howard JH, Frolov A, Tzeng CW, Stewart A, Midzak A, Majmundar A, Godwin A ... 9 (2): 393-5. doi:10.3892/or.9.2.393. PMID 11836615. Jost JP, Thiry S, Siegmann M (2002). "Estradiol receptor potentiates, in ... Deamination of cytosine (C) to uracil (U) and 5-methylcytosine (5mC) to thymine (T) generates G:U and G:T mismatches, ... doi:10.1016/S0304-3835(02)00043-5. PMID 12430186. Screaton RA, Kiessling S, Sansom OJ, Millar CB, Maddison K, Bird A, Clarke AR ...
10 (5): 535-9. doi:10.3892/ijmm.10.5.535. PMID 12373287. Reason AJ, Morris HR, Panico M, Marais R, Treisman RH, Haltiwanger RS ... 270 (32): 18961-5. doi:10.1074/jbc.270.32.18961. PMID 7642555. Murphy JE, Hanover JA, Froehlich M, DuBois G, Keen JH (Aug 1994 ... 324 (5929): 930-5. doi:10.1126/science.1170116. PMC 2715015 . PMID 19372391. Konrad RJ, Kudlow JE (Nov 2002). "The role of O- ... Matoba R, Okubo K, Hori N, Fukushima A, Matsubara K (Sep 1994). "The addition of 5'-coding information to a 3'-directed cDNA ...
5-Methylcytosine is more prone to transition than unmethylated cytosine, due to spontaneous deamination. This mechanism is ...
324 (5929): 930-5. doi:10.1126/science.1170116. PMC 2715015 . PMID 19372391. Protein O-GlcNAc transferase at the US National ... Studies show that O-GlcNAc transferase interacts directly with the Ten eleven translocation 2 (TET2) enzyme, which converts 5- ... methylcytosine to 5-hydroxymethylcytosine and regulates gene transcription. Additionally, increasing levels of OGT for O- ... "Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1". Science. ...
As soon as the TSA treatment was stopped, on day 4 the deacetylation was observed and the acetylation recovered on Day-5. The ... Global 5-methylcytosine levels have been measured prior to differentiation and after in vitro differentiation. The global ... H3K4 trimethylation coincides with the time of highest Brachyury gene expression since it only had gene expression on day 5. ... The morphological examination of the third group,' 5 nM TSA' showed the intermediate effect between the control and 10nM-TSA ...
4 (5): 452-6. doi:10.1038/ni920. PMID 12692548. Meng FL, Du Z, Federation A, Hu J, Wang Q, Kieffer-Kwon KR, Meyers RM, Amor C, ... 28 (5): 630-8. doi:10.1016/j.immuni.2008.04.002. PMC 2713656 . PMID 18455451. Teng G, Hakimpour P, Landgraf P, Rice A, Tuschl T ... AICDA can deaminate 5-methylcytosine, which can then be replaced with cytosine by base excision repair. AID is believed to ... 28 (5): 621-9. doi:10.1016/j.immuni.2008.03.015. PMC 2430982 . PMID 18450484. Fairfax KA, Gantier MP, Mackay F, Williams BR, ...
30 (5): e21. doi:10.1093/nar/30.5.e21. PMC 101257 . PMID 11861926. Dai Z, Weichenhan D, Wu YZ, et al. (October 2002). "An AscI ... 5 (2): 155-8. doi:10.4161/cc.5.2.2367. PMID 16397413. Zhang X, Yazaki J, Sundaresan A, et al. (September 2006). "Genome-wide ... Also, the size of the fragment affects the binding of 5-methyl-cytidine (5mC) antibody because the antibody needs more than ... A fraction of the input DNA obtained after the sonication step above is labeled with cyanine-5 (Cy5; red) deoxy-cytosine- ...
71 (5): 865-73. doi:10.1016/0092-8674(92)90561-P. PMID 1423634. Chuang LS, Ian HI, Koh TW, Ng HH, Xu G, Li BF (September 1997 ... 302 (1): 5-18. doi:10.1002/jez.b.20002. PMID 14760651. Alvarez-Buylla ER, Chaos A, Aldana M, Benítez M, Cortes-Poza Y, Espinosa ... 5-Methylcytosine performs much like a regular cytosine, pairing with a guanine in double-stranded DNA. However, some areas of ... Retrieved 5 May 2014. "Epigenetic cell memory". Cmol.nbi.dk. Retrieved 26 July 2012. Dodd IB, Micheelsen MA, Sneppen K, Thon G ...
He, together with R.D. Coghill, was the first to discover the existence of 5-Methylcytosine in nature, from tuberculinic acid, ... Nichols Medalists of the American Chemical Society Johnson TB, Coghill RD (1925). "The discovery of 5-methyl-cytosine in ...
Frommer's protocol yielded a clear positive display of methylcytosine residues. The PCR products of bisulphite reactions could ... A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl ...
89 (5): 1827-1831. doi:10.1073/pnas.89.5.1827. ISSN 0027-8424. PMC 48546 . PMID 1542678. Clark, S J; Harrison, J; Paul, C L; ... "A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands". ...
6 (5): 1183-1193. doi:10.1016/S1097-2765(00)00115-5. Pascal, John M.; O'Brien, Patrick J.; Tomkinson, Alan E.; Ellenberger, Tom ... Ligases are versatile and ubiquitous enzymes that join the 3' hydroxyl and 5' phosphate ends to form a phosphodiester bond, ... Some sources of mismatched base pairs include replication errors and deamination of 5-methylcytosine DNA to form thymine. MMR ...
Removal of methylated bases (either by direct removal of methylcytosine, or through cytosine deamination followed by removal of ... Ito, S; Li, S; Dai, Q; Wu, SC; Collins, SB; Swenberg, JA; He, C; Zhang, Y (21 July 2011). "Tet Proteins Can Convert 5- ... Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine". Science. 333 (6047): 1300-1303. doi:10.1126/science.1210597. PMC ... Guo, JU; Su, Y; Zhong, C; Ming, GL; Song, H (2011-04-29). "Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA ...
302 (1): 5-18. PMID 14760651. doi:10.1002/jez.b.20002.. *^ Alvarez-Buylla ER, Chaos A, Aldana M, Benítez M, Cortes-Poza Y, ... 5: 5055. PMC 4190663 . PMID 25268848. doi:10.1038/ncomms6055.. *^ Chahwan R, Wontakal SN, Roa S (March 2011). "The ... ISBN 1-904455-25-5.. [page needed]. *^ Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF (January 2009). "RNA regulation ... 41 (2): 240-5. PMID 19151718. doi:10.1038/ng.286.. *^ O'Connor, Anahad (11 March 2008). "The Claim: Identical Twins Have ...
In 5-methylcytosine, a methyl group is attached to the 5th atom in the 6-atom ring (counting counterclockwise from the NH ... In plants, 5-methylcytosine occurs at CpG, CpHpG and CpHpH sequences (where H = A, C or T). In fungi and animals, 5- ... methylcytosine predominantly occurs at CpG dinucleotides. Most eukaryotes methylate only a small percentage of these sites, but ... 5-Methylcytosine is a methylated form of the DNA base cytosine that may be involved in the regulation of gene transcription. ...
In addition to 5-meC paired to guanine, DME and ROS1 also removed thymine from a T·G mismatch located in either CpG or non-CpG ... 5). A DNA duplex with a single 7,8-dihydro-8-oxoguanine (8-OG) paired to cytosine located at the same position as the 5-meC·G ... 5-meC,. 5-methylcytosine;. 8-OG,. 7,8-dihydro-8-oxoguanine;. TDG,. thymine DNA glycosylase;. MBD,. methyl-CpG binding protein; ... 5, lane 4) or ROS1 (Fig. 5, lane 5). As expected, the complex for AtOGG1 (molecular mass = 44 kDa) migrated faster than those ...
5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3.. Brooks SC1, Fischer RL, Huh JH, ... 5-Methylcytosine Recognition by Arabidopsis thaliana DNA Glycosylases DEMETER and DML3. Biochemistry. 2014 Apr 22;53(15):2525- ... 5-Methylcytosine Recognition by Arabidopsis thaliana DNA Glycosylases DEMETER and DML3. Biochemistry. 2014 Apr 22;53(15):2525- ... 5-Methylcytosine Recognition by Arabidopsis thaliana DNA Glycosylases DEMETER and DML3. Biochemistry. 2014 Apr 22;53(15):2525- ...
Urine 5-methylcytosine Quantification Kit (Colorimetric) Epigenetic Kits datasheet (ab156903). Abcam offers quality products ... The urinary 5-mC level can be altered by a change of the bodies turnover of methylated DNA/RNA or alteration of cellular DNA/ ... Urinary excretion of 5-mC including both 5-methyl-2-deoxycytidine and 5-methylcytidine is an indication of a whole body ... A number of studies have indicated that 5-mC excreted in urine has the potential to act as a cancer biomarker, with an ...
5-MethylCytosine ELISA Kits available through Novus Biologicals. Browse our 5-MethylCytosine ELISA Kits all backed by our ...
A 5-mC Dot Blot Assay Quantifying the DNA Methylation Level of Chondrocyte Dedifferentiation In Vitro, Targeted DNA ... 5 methylcytosine include An Alternative Culture Method to Maintain Hypomethylation of Mouse Embryonic Stem Cells Using MEK ... Selective Capture of 5-hydroxymethylcytosine from Genomic DNA, Detection of Modified Forms of Cytosine Using Sensitive ... High Sensitivity 5-hydroxymethylcytosine Detection in Balb/C Brain Tissue, Determination of DNA Methylation of Imprinted ...
The bisulfite method is a highly sensitive approach to 5-methylcytosine mapping that utilizes the capability of the polymerase ... A bisulfite method of 5-methylcytosine mapping that minimizes template degradation Anal Biochem. 1995 Mar 20;226(1):161-6. doi ... The bisulfite method is a highly sensitive approach to 5-methylcytosine mapping that utilizes the capability of the polymerase ...
Restriction of 5-methyl and 5-hydroxymethylcytosines at the specific DNA sequence C(me)CGG. UniProt ...
Mouse monoclonal 5-methylcytosine (5-mC) antibody [5MC-CD]. Validated in SB, Flow Cyt, ICC/IF. Cited in 18 publication(s). ... It is not 5-methyl Cytosine as part of a CpG dinucleotide. I hope this information has been of help. If you require any further ... Anti-5-methylcytosine (5-mC) antibody [5MC-CD] (FITC) (ab179898) *Anti-5-methylcytosine (5-mC) antibody [5MC-CD] - Azide free ( ... Hi John (Anti 5-mC query) The antigen retrieval that was performed was 15 mins in the pressure cooker in citrate buffer pH 6 ...
5Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK.. *. 6School of Clinical Medicine, University of Cambridge, ... 5-Methylcytosine can be converted to 5-hydroxymethylcytosine (5hmC) in mammalian DNA by the ten-eleven translocation (TET) ... Selective chemical oxidation of 5hmC to 5-formylcytosine (5fC) enables bisulfite conversion of 5fC to uracil. We demonstrate ... Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution ...
5, D and E). Again, the difference is likely due to the presence of Tet2 and Tet3, which are both expressed in ES cells. ... The faint dCMP spot in each lane is derived from end-labeling of the C at the 5′ end of each strand of the substrate. (B) The ... 5 hmC is present in ES cell DNA, and its abundance decreases upon differentiation or Tet1 depletion. (A) (Left) TLC showing ... 5-methylcytosine (5mC) is a minor base in mammalian DNA: It constitutes ~1% of all DNA bases and is found almost exclusively as ...
5-Methylcytosine (MeC) is an endogenous modification of DNA that plays a crucial role in DNA-protein interactions, chromatin ... MeC is produced via enzymatic methylation of the C-5 position of cytosine by DNA-methyltransferases (DNMT) which use S- ... 5-Methylcytosine (MeC) is an endogenous modification of DNA that plays a crucial role in DNA-protein interactions, chromatin ... Can 5-methylcytosine analogues with extended alkyl side chains guide DNA methylation? D. Kotandeniya, C. L. Seiler, J. ...
The levels of 5-MeC and DNMT1 were assessed based on their immunoreactivities and then divided into low and high levels. In ... Results showed that 5-MeC levels were positively associated with DNMT1 levels in UC (p = 0.0288). Both 5-MeC and DNMT1 were low ... Low 5-MeC levels in stage I invasive UC were not significantly different from those of non-invasive tumors (p = 0.8478). Low ... The percentage of low 5-MeC levels was higher in invasive UC (65/110; 59%) than in normal urothelia (2/23; 13%) and non- ...
However, the bisulfite (BS) reaction commonly used with the 450K array cannot distinguish between 5-methylcytosine (5mC) and 5- ...
5-Methylcytosine content of nuclear DNA during chemical hepatocarcinogenesis and in carcinomas which result.. Lapeyre JN, ...
The post-transcriptional modification 5-methylcytosine (m5C) occurs in a wide range of coding and non-coding RNAs. We describe ... However, all m5C sites were confirmed by RIP using a monoclonal antibody raised against m5C (m5C-RIP) (Figure 1B) [45]. m5C-RIP ... a) Bisulfite sequencing, (b) m5C-RIP, (c) Aza-IP and (d) miCLIP can all be used to detect m5C sites. The asterisk in (a) ... A comparison of m 5 C target sites identified by three transcriptome-wide approaches (Additional file1) [[18, 23, 24]]. The ...
We observed that 5-Aza-CdR treatment demethylated these specific sites. Based on this sequence data, specific primers for the ... Demethylation by 5-aza-2-deoxycytidine of specific 5-methylcytosine sites in the promoter region of the retinoic acid receptor ... 5-Aza-CdR). In this report we have identified, by sequencing of bisulfite-modified DNA of DLD-1 colon tumor cells, the specific ... we observed that RARbeta expression could be activated by the hypomethylating action of 5-aza-2-deoxycytidine ( ...
T4 β-glucosyltransferase catalyzes glucose addition to 5-hydroxymethylcytosine but not 5-methylcytosine, allowing ... Detection of 5-hydroxymethylcytosine when coupled with digestion with a restriction enzyme that is sensitive to β-glucosyl-5- ... 5-hydroxymethylcytosine (5-hmC) is an epigenetic modification (methylated cytosine) that is thought to be a derivative of 5- ... methylcytosine (5-mC). T4 β-glucosyltransferase catalyzes the transfer of glucose from uridine diphosphoglucose (UDP-Glucose) ...
Supplementary Figure 5 - Uracil-DNA glycosylase (UDG) hydrolysis assay. *Supplementary Figure 6 - AICDA CRISPR1 and CRISPR2 ... The EGFR T790M Mutation Is Acquired through AICDA-Mediated Deamination of 5-Methylcytosine following TKI Treatment in Lung ... The EGFR T790M Mutation Is Acquired through AICDA-Mediated Deamination of 5-Methylcytosine following TKI Treatment in Lung ... The EGFR T790M Mutation Is Acquired through AICDA-Mediated Deamination of 5-Methylcytosine following TKI Treatment in Lung ...
5-Hydroxymethylcytosine was found enriched at LINE-1 prior to a decrease in both 5-hydroxymethylcytosine and 5-methylcytosine. ... Hydroquinone increases 5-hydroxymethylcytosine formation through ten eleven translocation 1 (TET1) 5-methylcytosine dioxygenase ... Hydroquinone also caused an increase in Ten Eleven Translocation 1 activity and global levels of 5-hydroxymethylcytosine. ... Home » » Hydroquinone increases 5-hydroxymethylcytosine formation through ten eleven translocation 1 (TET1) 5-methylcytosine ...
Brown, T C; Jiricny, J (1987). A specific mismatch repair event protects mammalian cells from loss of 5-methylcytosine. Cell, ... 5-Methylcytosine spontaneously deaminates to form thymine, thus generating G/T mispairs in DNA. We investigated the way in ... 5-Methylcytosine spontaneously deaminates to form thymine, thus generating G/T mispairs in DNA. We investigated the way in ... These results attest to a specific mismatch repair pathway that restores G/C pairs lost through deamination of 5-methylcytosine ...
5.. Ronn T, Ling C. DNA methylation as a diagnostic and therapeutic target in the battle against type 2 diabetes. Epigenomics. ... As a well-established epigenetic mark, DNA methylation most often occurs at the 5′-cytosines of CpG dinucleotides [8, 9]. DNA ... Genomic 5-mC contents in peripheral blood leukocytes were independent protective factors for coronary artery disease with a ... Hyperglycemia affects global 5-methylcytosine and 5-hydroxymethylcytosine in blood genomic DNA through upregulation of SIRT6 ...
p,5-Methylcytosine (m,sup,5,/sup,C) is a well-characterized DNA modification, and is also predominantly reported in abundant ... m5C-RIP-seq analysis identified 6045 m5C peaks in 4465 expressed genes in young seedlings. We found that m5C is enriched in ... 5-Methylcytosine RNA Methylation in Arabidopsis Thaliana. Cui X. et al.. 5-Methylcytosine (m5C) is a well-characterized DNA ... Mutations in TRM4B display defects in root development and decreased m5C peaks. TRM4B affects the transcript levels of the ...
5-methylcytosine (5-mC) Monoclonal Antibody, clone 33D3 validated in MeDIP-seq, MeDIP, DB and IF. Batch-specific data available ... Zygotic epigenetic reprogramming entails genome-wide DNA demethylation that is accompanied by Tet methylcytosine dioxygenase 3 ... catalyzed by ten-eleven translocation methylcytosine dioxygenase (TET) occurs abundantly in neurons of mammals. However, the in ... Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain Amort T. et al.. Background Recent ...
  • One µg of the fragmented DNA was ligated to Illumina adapters and the resulting DNA was used for a standard MeDIP assay, using 2 µg of the Diagenode monoclonal against 5-mC (Cat. (diagenode.com)
  • The bisulfite method is a highly sensitive approach to 5-methylcytosine mapping that utilizes the capability of the polymerase chain reaction to exponentially amplify DNA. (nih.gov)
  • In this report we have identified, by sequencing of bisulfite-modified DNA of DLD-1 colon tumor cells, the specific 5-methylcytosine positions in the region of -46 to +251 bp from the transcription start site of RARbeta2. (nih.gov)
  • Genome-wide bisulfite sequencing in several cell types has established that the promoters of the most highly expressed genes show the lowest levels of CpG methylation and, conversely, that dense CpG methylation of promoters is associated with low gene expression ( 2 , 5 , 6 ). (frontiersin.org)
  • Recent advances in the field of epigenetics have identified 5-hydroxymethylcytosine (5-hmC) as a key factor in the regulation of gene expression, with substantial implications in the study of tissue differentiation, neurological development, and carcinogenesis. (thomassci.com)
  • We show here that TET1, a fusion partner of the MLL gene in acute myeloid leukemia, is a 2-oxoglutarate (2OG)- and Fe(II)-dependent enzyme that catalyzes conversion of 5mC to 5-hydroxymethylcytosine (hmC) in cultured cells and in vitro. (sciencemag.org)
  • Like TET1 and TET3 , TET2 modifies DNA by hydroxylating 5 methylcytosine. (jax.org)
  • Dnmt1 and Dnmt3a are expressed in motor neurons of adult mouse spinal cord, and, during their apoptosis induced by sciatic nerve avulsion, nuclear and cytoplasmic 5-methylcytosine immunoreactivity, Dnmt3a protein levels and Dnmt enzyme activity increased preapoptotically. (jneurosci.org)
  • We found that m 5 C is enriched in coding sequences with two peaks located immediately after start codons and before stop codons, and is associated with mRNAs with low translation activity. (diagenode.com)
  • ID No. 144 and sequences complementary thereto and/or chemically pretreated DNA of genes according to claim 2, wherein at least one oligomer according to any of the claims 3 through 5 is coupled to a solid phase. (google.com.au)
  • 6. A method according to claim 1 , characterised in that the polymerase has no 5′ to 3′ exonuclease activity in order to prevent degradation of the probe. (google.com)
  • Used by thousands of scientists worldwide, TaKaRa Ex Taq DNA Polymerase is a proofreading enzyme with 3' to 5' exonuclease activity, resulting in approximately 4.5-fold higher fidelity than Taq and high yield of product. (clontech.com)
  • We further discuss the potential of these initial studies to comprehensively determine the global but enzyme-specific cytosine-5 RNA methylome. (biomedcentral.com)
  • The original function elucidated for Dcm was in restriction enzyme biology where Dcm promotes the loss of plasmids containing the EcoRII restriction enzyme gene (which cleaves 5′CCWGG3′ sites) and protects cells from post-segregational killing by the EcoRII restriction enzyme [8 9 In addition Dcm protects phage lambda against DNA cleavage when EcoRII is introduced into the cell . (livingseas.org)
  • 5-azaC is phosphorylated upon cell entry and incorporated into both RNA and DNA [18 19 When 5-azaC is incorporated into DNA cytosine-5 DNA methyltransferases become covalently trapped on the DNA and are degraded and this limits the amount of enzyme available for the generation of 5-MeC [18 19 Thus 5 is a cytosine DNA methylation inhibitor. (livingseas.org)
  • Results Effects of 5-azaC on global DNA methylation levels First we determined the concentration dependence of DNA methylation inhibition by 5-azaC using Goat polyclonal to IgG (H+L). digestion of DNA with the restriction enzyme isoschizomers BstNI and PspGI (Fig.?1). (livingseas.org)
  • In the present study, we synthesized DNA duplexes containing MeC analogues with modified C-5 side chains and examined their ability to guide cytosine methylation by the human DNMT1 protein. (rsc.org)
  • The levels of 5-MeC and DNMT1 were assessed based on their immunoreactivities and then divided into low and high levels. (mdpi.com)
  • Results showed that 5-MeC levels were positively associated with DNMT1 levels in UC ( p = 0.0288). (mdpi.com)
  • Both 5-MeC and DNMT1 were low in approximately 50% (76/150) of UC. (mdpi.com)
  • Neither 5-MeC nor DNMT1 levels were associated with UC recurrence. (mdpi.com)
  • During apoptosis of NSC34 cells induced by camptothecin, levels of Dnmt1 and Dnmt3a increased fivefold and twofold, respectively, and 5-methylcytosine accumulated in nuclei. (jneurosci.org)
  • In human amyotrophic lateral sclerosis (ALS), motor neurons showed changes in Dnmt1, Dnmt3a, and 5-methylcytosine similar to experimental models. (jneurosci.org)
  • Here, we describe the development of a DNA polymerase variant that incorporates the canonical 2'-deoxyguanosine 5'-monophosphate (dGMP) opposite C with higher efficiency compared to 5mC. (uni-konstanz.de)
  • TRM4B affects the transcript levels of the genes involved in root development, which is positively correlated with their mRNA stability and m 5 C levels. (diagenode.com)
  • By studying a unique family of 5-methylcytosine oxidases, this proposal aims at providing novel reagents for better characterization of the DNA epigenomes and further understanding of their dynamic transitions. (grantome.com)
  • Abcam's Urine 5-methylcytosine Quantification Kit (Colorimetric) is a complete set of optimized buffers and reagents to colorimetrically quantify 5-mC in urine using an inhibitory competitive immunoassay method. (abcam.com)
  • The photochemical reactions of this nucleobase and its 2′‐deoxyribonucleoside, 5methyl‐2′‐deoxycytidine (II), in water have been studied. (edu.pl)
  • Mutations in TRM4B display defects in root development and decreased m 5 C peaks. (diagenode.com)