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5-MethylcytosineCytosineDeaminationDNA MethylationThymine DNA GlycosylaseMethylationDNA (Cytosine-5-)-MethyltransferaseSulfitesThymineDNAOsmiumDNA GlycosylasesDNA-Cytosine MethylasesPentoxylDioxygenasesAdenineN-Glycosyl HydrolasesCpG IslandsBase SequenceDNA Restriction EnzymesDinucleoside PhosphatesOligodeoxyribonucleotidesEpigenesis, GeneticDNA Modification MethylasesMethyltransferasesNanoporesNucleic Acid DenaturationDeoxycytidine MonophosphateAzacitidineUracilDeoxyribonuclease (Pyrimidine Dimer)EpigenomicsEndodeoxyribonucleasesDNA RepairGuanineDeoxyribonuclease HpaIISubstrate SpecificityGardner SyndromeGenomeCytidineBase Pair MismatchPhotochemical ProcessesOxidation-ReductionDNA-Binding ProteinsMolecular Sequence DataZygoteOligonucleotidesEnzyme-Linked Immunosorbent AssayReagent Kits, DiagnosticSensitivity and SpecificityEmbryonic Stem Cells
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.
Thymine
DNA
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.
Uracil
Deoxyribonuclease (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.
Guanine
Deoxyribonuclease 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)

Genome-wide analysis reveals TET-and TDG-mediated 5-methylcytosine oxidation dynamics | Epigenetics & Chromatin | Full TextGenome-wide analysis reveals TET-and TDG-mediated 5-methylcytosine oxidation dynamics | Epigenetics & Chromatin | Full Text
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 ...
https://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/1756-8935-6-S1-P75
TET proteins and 5-methylcytosine oxidation in the immune systemTET proteins and 5-methylcytosine oxidation in the immune system
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https://www.lji.org/publication-type/tet-proteins-and-5-methylcytosine-oxidation-in-the-immune-system/
DNA Methylation Analysis | Methylated Cytosine: 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) | T4 Beta...DNA Methylation Analysis | Methylated Cytosine: 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) | T4 Beta...
Frontiers | TET Methylcytosine Oxidases in T Cell and B Cell Development and Function | ImmunologyFrontiers | TET Methylcytosine Oxidases in T Cell and B Cell Development and Function | Immunology
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.
https://www.frontiersin.org/articles/10.3389/fimmu.2017.00220/full
5-MethylCytosine ELISA Kits: Novus Biologicals5-MethylCytosine ELISA Kits: Novus Biologicals
5-MethylCytosine ELISA Kits available through Novus Biologicals. Browse our 5-MethylCytosine ELISA Kits all backed by our Guarantee+.
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Plus itPlus it
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 ...
http://cancerres.aacrjournals.org/content/74/19_Supplement/396
Active DNA demethylation in mammals. (a) The action of | Open-iActive DNA demethylation in mammals. (a) The action of | Open-i
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
https://openi.nlm.nih.gov/detailedresult.php?img=PMC2864560_gb-2010-11-3-110-1&req=4
Most recent papers with the keyword 5 hydroxymethylcytosine | Read by QxMDMost recent papers with the keyword 5 hydroxymethylcytosine | Read by QxMD
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 ...
https://www.readbyqxmd.com/keyword/14723
10th Transcription and Chromatin 201210th Transcription and Chromatin 2012
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 ...
https://epigenie.com/conferences/10th-transcription-and-chromatin-2012/
SNU Open Repository and Archive: Cellular response against expression of Arabidopsis DEMETER DNA demethylase in animal cellsSNU Open Repository and Archive: Cellular response against expression of Arabidopsis DEMETER DNA demethylase in animal cells
Epigenetics refers to heritable changes of phenotype or gene expression without the modification of DNA sequence. DNA methylation, a prominent epigenetic marks, is associated with gene expression, X chromosome inactivation, gene imprinting and developmental process. DNA methylation occurs by DNA methyltransferase to add methyl group at the 5th carbon of a cytosine to produce 5-methylcytosine (5mC), which is achieved by a similar mechanism in both the plants and animals. However, DNA demethylation pathways are fundamentally different in plant and animal. In animals, DNA demethylation is achieved by several enzymatic pathways, where TET1 catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and successive oxidation of 5hmC to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC), and deamination by AID/APOBEC. More efficient DNA demethylation is accomplished in plants by the DEMETER 5-methylcytosine DNA glycosylase, which mediates direct excision of 5mC from double strand DNA ...
https://s-space.snu.ac.kr/handle/10371/140815
RCSB PDB - 5L2G: Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th PositionRCSB PDB - 5L2G: Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th Position
As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
https://www.rcsb.org/structure/5L2G
DNA Demethylation in Development: 5mC, 5hmC, 5fC, 5caC and TET ProteinsDNA Demethylation in Development: 5mC, 5hmC, 5fC, 5caC and TET Proteins
This ebook provides an introduction to the key cytosine base modifications: 5-methylcytosine, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) that have been at the center of intense study in recent years.
https://epigenie.com/ebook-dna-demethylation-in-development/
Can 5-methylcytosine analogues with extended alkyl side chains guide DNA methylation? - Chemical Communications (RSC Publishing)Can 5-methylcytosine analogues with extended alkyl side chains guide DNA methylation? - Chemical Communications (RSC Publishing)
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
http://pubs.rsc.org/en/content/articlelanding/2018/cc/c7cc06867k
5-Methylcytosine RNA Methylation in Arabidopsis Thaliana5-Methylcytosine RNA Methylation in Arabidopsis Thaliana
|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...
https://www.diagenode.com/en/publications/view/3297
Structural insights into how 5-hydroxymethylation influences transcription factor binding - Chemical Communications (RSC...Structural insights into how 5-hydroxymethylation influences transcription factor binding - Chemical Communications (RSC...
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
http://pubs.rsc.org/en/Content/ArticleLanding/2014/CC/C3CC48151D?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+rss%2FCC+%28RSC+-+Chem.+Commun.+latest+articles%29
Dealing with an Unconventional Genetic Code in Mitochondria: The Biogenesis and Pathogenic Defects of the 5‐Formylcytosine...Dealing with an Unconventional Genetic Code in Mitochondria: The Biogenesis and Pathogenic Defects of the 5‐Formylcytosine...
Human mitochondria contain their own genome, which uses an unconventional genetic code. In addition to the standard AUG methionine codon, the single mitochondrial tRNA Methionine (mt‐tRNA$^{Met}$) also recognises AUA during translation initiation and elongation. Post‐transcriptional modifications of tRNAs are important for structure, stability, correct folding and aminoacylation as well as decoding. The unique 5‐formylcytosine (f$^{5}$C) modification of position 34 in mt‐tRNA$^{Met}$ has been long postulated to be crucial for decoding of unconventional methionine codons and efficient mitochondrial translation. However, the enzymes responsible for the formation of mitochondrial f$^{5}$C have been identified only recently. The first step of the f$^{5}$C pathway consists of methylation of cytosine by NSUN3. This is followed by further oxidation by ABH1. Here, we review the role of f$^{5}$C, the latest breakthroughs in our understanding of the biogenesis of this unique mitochondrial tRNA ...
https://www.repository.cam.ac.uk/handle/1810/264195
SALL4A Regulates DNA Demethylation at Enhancers----Institute of Biophysics Chinese Academy of SciencesSALL4A Regulates DNA Demethylation at Enhancers----Institute of Biophysics Chinese Academy of Sciences
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 ...
http://english.ibp.cas.cn/rh/rp/201705/t20170505_176781.html
Methyl-DNA Binding Protein ChIP | EpiGentekMethyl-DNA Binding Protein ChIP | EpiGentek
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...
https://www.epigentek.com/catalog/methyl-dna-binding-protein-chip-c-75_22_56.html
Plus itPlus it
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 ...
http://cancerdiscovery.aacrjournals.org/content/early/2016/09/07/2159-8290.CD-RW2016-158
The upper graph shows methylation position in colduntreated and handled Col-, and the lower graph shows colduntreated and...The upper graph shows methylation position in colduntreated and handled Col-, and the lower graph shows colduntreated and...
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. ...
http://www.bet-bromodomain.com/2016/09/25/the-upper-graph-shows-methylation-position-in-colduntreated-and-handled-col-and-the-lower-graph-shows-colduntreated-and-handled-rpt2a-2-no-transgene-b-mean-levels-of-dna-methylation-in-diverse/
5-hydroxymethylcytosine5-hydroxymethylcytosine
Methylation, in the form of 5-methylcytosine or 5mC, is both a control button for turning genes off and a sign of their off state. 5hmC looks like 5mC, except it has an extra oxygen. That could be a tag for a removal, or a signal that a gene is poised to be turned on.. Two recent papers on this topic:. Please recall that an enriched environment (exercise and mental stimulation) is good for learning and memory, for young and old. In the journal Genomics, Jin and his team show that exposing mice to an enriched environment - a running wheel and a variety of toys - leads to a 60 percent reduction in 5hmC in the hippocampus, a region of the brain critical for learning and memory.  The changes in 5hmC were concentrated in genes having to do with axon guidance. Hat tip to the all-things-epigenetic site Epigenie.. In Genes and Development, structural biologist Xiaodong Cheng and colleagues demonstrate that two regulatory proteins that bind DNA (Egr1 and WT1) respond primarily to oxidation of ...
https://www.emoryhealthsciblog.com/tag/5-hydroxymethylcytosine/
Volume 4.25 | Jun 28 - Human Immunology NewsVolume 4.25 | Jun 28 - Human Immunology News
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 ...
http://www.humanimmunologynews.com/issue/volume-4-25-jun-28/
RNA processing in Drosophila development - Rutgers, The State University of New JerseyRNA processing in Drosophila development - Rutgers, The State University of New Jersey
Abstract The aim of our proposal is to elucidate the mechanisms that link transcription of specific RNAs in the nucleus to their translation (RNA processing). ?We have identified and characterized a novel and highly conserved gene, ?Zfrp8/PDCD2, ?and shown that it is essential in stem cells in flies, mouse, and human, and that it is also required for growth of cancer cells. We discovered ?Zfrp8/PDCD2 ?is required for the nuclear export of select mRNAs and TE transcripts. Also it interacts with the small ribosomal subunit and forms a complex with mRNA binding proteins. Our data suggest that Zfrp8/PDCD2 controls subcellular localization of select RNAs and the association of mRNA-RNPs with ribosomes. We also have identified Tet/TET1 as a new Zfrp8/PDCD2 interacting protein. In vertebrates, TET proteins function in DNA demethylation converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), modifications that are not detected in Drosophila DNA. A recent study shows that vertebrate Tet ...
https://www.researchwithrutgers.com/en/projects/rna-processing-in-drosophila-development-3
Supplementary MaterialsadvancesADV2020001535-suppl1 | BX-795 inhibits HSV-1 and HSV-2 replicationSupplementary MaterialsadvancesADV2020001535-suppl1 | BX-795 inhibits HSV-1 and HSV-2 replication
Supplementary MaterialsadvancesADV2020001535-suppl1. peaks were more many and pronounced than in normoxia. Among the genes, was upregulated in hypoxia specifically. We discovered 2 HIF-1 binding sites in by chromatin immunoprecipitation of HIF-1 accompanied by sequencing, and upregulation was abrogated with deletion of both sites, indicating that is clearly a direct HIF-1 focus on. Finally, we demonstrated that lack of one or both these HIF-1 binding sites in K562 cells disrupted erythroid differentiation in hypoxia and reduced cell viability. This ongoing function offers a molecular hyperlink between O2 availability, epigenetic changes of chromatin, and erythroid differentiation. Visible Abstract Open up in another window Intro 5-Hydroxymethylcytosine (5-hmC) can be an epigenetic tag that regulates chromosome framework and promotes transcription.1-3 The Ten-eleven translocation dioxygenases (TETs) convert 5-methylcytosine (5-mC) to 5-hmC inside a reaction that will require air (O2), Fe(II), and ...
http://bx-795.com/%EF%BB%BFsupplementary-materialsadvancesadv2020001535-suppl1/
AMG 900 | Role of NK1 and NK2 receptors in mouse gastric mechanical activityAMG 900 | Role of NK1 and NK2 receptors in mouse gastric mechanical activity
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 ...
http://stopvivisection.info/tag/amg-900/
Plus itPlus it
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 ...
http://www.plantcell.org/content/20/5/1278
TET1P1 (human) | Gene Target - PubChemTET1P1 (human) | Gene Target - PubChem
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.
https://pubchem.ncbi.nlm.nih.gov/target/gene/TET1P1
E. coli genotypes - OpenWetWareE. coli genotypes - OpenWetWare
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 ...
https://openwetware.org/wiki/?title=E._coli_genotypes&oldid=573219
Difference between revisions of E. coli genotypes - OpenWetWareDifference between revisions of E. coli genotypes - OpenWetWare
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 ...
https://openwetware.org/wiki/?title=E._coli_genotypes&diff=prev&oldid=401783
Sci. Pharm. | Free Full-Text | Interaction of β-Cyclodextrin with DNA-BasesSci. Pharm. | Free Full-Text | Interaction of β-Cyclodextrin with DNA-Bases
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. [...]
http://www.mdpi.com/2218-0532/78/3/590
Mutagenetix > Incidental...Mutagenetix > Incidental...
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a nuclear protein which is involved in cell-cycle regulation. The encoded protein is a ubiquitin-ligase capable of ubiquinating PCNP (PEST-containing nuclear protein), and together they may play a role in tumorigenesis. The encoded protein contains an NIRF_N domain, a PHD finger, a set- and ring-associated (SRA) domain, and a RING finger domain and several of these domains have been shown to be essential for the regulation of cell proliferation. This protein may also have a role in intranuclear degradation of polyglutamine aggregates. Alternative splicing results in multiple transcript variants some of which are non-protein coding. [provided by RefSeq, Feb 2012 ...
https://mutagenetix.utsouthwestern.edu/incidental/incidental_rec.cfm?mid=603852
Center For Life SciencesCenter For Life Sciences
The ten-eleven translocation (TET)-dependent generation and removal of oxidized derivatives of 5-methylcytosine (5mC), namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), uncovered a new paradigm of active DNA demethylation in mammalian genomes. Besides acting as demethylation intermediates, these oxidized variants of 5mC may also play functional roles. Emerging evidence has suggested 5hmC as a stable epigenetic modification implicated in many biological processes and various diseases. 5fC and 5caC, further oxidation products of 5hmC, accumulate at distal regulatory elements as active DNA demethylation intermediates and can be removed through base excision repair by mammalian thymine DNA glycosylase (TDG). My laboratory recently developed fC-CET, a bisulfite-free, base-resolution method for the genome-wide identification of 5fC sites. We will continue to develop robust and sensitive sequencing technologies, including those applicable to single-cell ...
http://www.cls.edu.cn/english/PrincipalInvestigator/pi/index1608.shtml
Hydroxymethyl Collector (5-hmc, 5-hydroxymethylcytosine, hydroxymethylation enrichment kit)Hydroxymethyl Collector (5-hmc, 5-hydroxymethylcytosine, hydroxymethylation enrichment kit)
Hydroxymethyl Collector Kit is designed for the detection and enrichment of 5-hydroxymethylcytosine (5-hmC) DNA for whole-genome or gene specific hydroxymethylation analyis.
https://www.activemotif.com/catalog/775/hydroxymethyl-collector-trade
Bioorthogonal labeling of 5-hydroxymethylcytosine in genomic DNA and diazirine-based DNA photo-cross-linking probes. - NDM...Bioorthogonal labeling of 5-hydroxymethylcytosine in genomic DNA and diazirine-based DNA photo-cross-linking probes. - NDM...
DNA is not merely a combination of four genetic codes, namely A, T, C, and G. It also contains minor modifications that play crucial roles throughout biology. For example, the fifth DNA base, 5-methylcytosine (5-mC), which accounts for ∼1% of all the nucleotides in mammalian genomic DNA, is a vital epigenetic mark. It impacts a broad range of biological functions, from development to cancer. Recently, an oxidized form of 5-methylcytosine, 5-hydroxymethylcytosine (5-hmC), was found to constitute the sixth base in the mammalian genome; it was believed to be another crucial epigenetic mark. Unfortunately, further study of this newly discovered DNA base modification has been hampered by inadequate detection and sequencing methods, because current techniques fail to differentiate 5-hmC from 5-mC. The immediate challenge, therefore, is to develop robust methods for ascertaining the positions of 5-hmC within the mammalian genome. In this Account, we describe our development of the first bioorthogonal,
https://www.ndmrb.ox.ac.uk/research/research/publications/628455/
Bisulfite sequencing - WikipediaBisulfite sequencing - Wikipedia
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 ...
https://en.wikipedia.org/wiki/Bisulfite_sequencing
cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool. - Helen Wills...cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool. - Helen Wills...
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 ...
http://neuroscience.berkeley.edu/publications/camp-signaling-regulates-dna-hydroxymethylation-by-augmenting-the-intracellular-labile-ferrous-iron-pool/
Early steps of active DNA demethylation initiated by ROS1 glycosylase require three putative helix-invading residuesEarly steps of active DNA demethylation initiated by ROS1 glycosylase require three putative helix-invading residues
Active DNA demethylation is crucial for epigenetic control, but the underlying enzymatic mechanisms are incompletely understood. REPRESSOR OF SILENCING 1 (ROS1) is a 5-methylcytosine (5-meC) DNA glycosylase/lyase that initiates DNA demethylation in plants through a base excision repair process. The enzyme binds DNA nonspecifically and slides along the substrate in search of 5-meC. In this work, we have used homology modelling and biochemical analysis to gain insight into the mechanism of target location and recognition by ROS1. We have found that three putative helix-intercalating residues (Q607, R903 and M905) are required for processing of 5-meC:G pairs, but dispensable for excision of mismatched 5-meC. Mutant proteins Q607A, R903A and M905G retain the capacity to process an abasic site opposite G, thus suggesting that all three residues play a critical role in early steps of the base extrusion process and likely contribute to destabilization of 5-meC:G pairs. While R903 and M905 are not ...
https://helvia.uco.es/handle/10396/15731
DNA methylation in mycobacteria: Absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences - ePrints@IIScDNA methylation in mycobacteria: Absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences - [email protected]
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. ...
http://eprints.iisc.ernet.in/1017/
Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. - NDM Research BuildingIntegrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. - NDM Research Building
Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the role of 5-hmC in the epigenomic landscape of pluripotent cells, here we profile the genome-wide 5-hmC distribution and correlate it with the genomic profiles of 11 diverse histone modifications and six transcription factors in human ES cells. By integrating genomic 5-hmC signals with maps of histone enrichment, we link particular pluripotency-associated chromatin contexts with 5-hmC. Intriguingly, through additional correlations with defined chromatin signatures at promoter and enhancer subtypes, we show distinct enrichment of 5-hmC at enhancers marked with H3K4me1 and H3K27ac. These results suggest potential
https://www.ndmrb.ox.ac.uk/research/research/publications/628452/
Mechanisms of DNA Methyltransferases (DNMTs) and DNA Demethylases | EpiGentekMechanisms of DNA Methyltransferases (DNMTs) and DNA Demethylases | EpiGentek
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. ...
https://www.epigentek.com/catalog/mechanisms-of-dna-methyltransferases-dnmts-and-dna-demethylases-n-8.html
GSE79882 - Genome-wide map of DNA 5-Hydroxymethylcytosine in cardiomyocytes isolated from E14.5, Neonatal, Adult, pressure...GSE79882 - Genome-wide map of DNA 5-Hydroxymethylcytosine in cardiomyocytes isolated from E14.5, Neonatal, Adult, pressure...
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
https://www.omicsdi.org/dataset/geo/GSE79882
ENGINEERED DEMETER 5-METHYLCYTOSINE DNA GLYOSYLASE WITH IMPROVED YIELD, STABILITY AND SOLUBILITY - Patent applicationENGINEERED DEMETER 5-METHYLCYTOSINE DNA GLYOSYLASE WITH IMPROVED YIELD, STABILITY AND SOLUBILITY - Patent application
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 ...
http://www.patentsencyclopedia.com/app/20120149023
A similar effect of P16 hydroxymethylation and true-methylation on the prediction of malignant transformation of oral...A similar effect of P16 hydroxymethylation and true-methylation on the prediction of malignant transformation of oral...
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
https://bmccancer.biomedcentral.com/articles/10.1186/s12885-018-4787-6/tables/2
A similar effect of P16 hydroxymethylation and true-methylation on the prediction of malignant transformation of oral...A similar effect of P16 hydroxymethylation and true-methylation on the prediction of malignant transformation of oral...
Fingerprint Dive into the research topics of A similar effect of P16 hydroxymethylation and true-methylation on the prediction of malignant transformation of oral epithelial dysplasia: Observation from a prospective study 11 Medical and Health Sciences 1112 Oncology and Carcinogenesis. Together they form a unique fingerprint. ...
https://augusta.pure.elsevier.com/en/publications/a-similar-effect-of-p16-hydroxymethylation-and-true-methylation-o/fingerprints/
Data Availability StatementNot applicable - CYP17 inhibitors in prostate cancerData Availability StatementNot applicable - CYP17 inhibitors in prostate cancer
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 ...
http://tak-700.info/%EF%BB%BFdata-availability-statementnot-applicable/
5-hmC (5-Hydroxymethylcytosine) (CAS 1123-95-1) (ab146141) |Abcam5-hmC (5-Hydroxymethylcytosine) (CAS 1123-95-1) (ab146141) |Abcam
5-hmC (5-Hydroxymethylcytosine), DNA pyrimidine nitrogen base (CAS 1123-95-1). Join researchers using our high quality biochemicals.
https://www.abcam.com/5-hmc-5-hydroxymethylcytosine-dna-pyrimidine-nitrogen-base-ab146141.html
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain | Genome Biology | Full TextDistinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain | Genome Biology | Full Text
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,
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1139-1/metrics
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain | Genome Biology | Full TextDistinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain | Genome Biology | Full Text
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,
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1139-1/tables/1
ZFIN Publication: Yang et al., 2016ZFIN Publication: Yang et al., 2016
It has been considered that epigenetic modulation can affect a diverse array of cellular activities, in which ten eleven translocation (TET) methylcytosine dioxygenase family members refer to a group of fundamental components involved in catalyzation of 5-hydroxymethylcytosine and modification of gene expression. Even though the function of TET proteins has been gradually revealed, their roles in immune regulation are still largely unknown. Recent studies provided clues that TET2 could regulate several innate immune-related inflammatory mediators in mammals. This study sought to explore the function of TET family members in potential T-helper (Th) cell differentiation involved in adaptive immunity by utilizing a zebrafish model. As shown by results, soluble antigens could induce expression of zebrafish IL-4/13A (i.e. a pivotal Th2-type cytokine essential in Th2 cell differentiation and functions), and further trigger the expression of Th1- and Th2-related genes. It is noteworthy that this ...
https://zfin.org/ZDB-PUB-160716-6
The potential influence of breast cancer estrogen receptors distribution on active DNA demethylationThe potential influence of breast cancer estrogen receptors distribution on active DNA demethylation
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...
https://www.termedia.pl/The-potential-influence-of-breast-cancer-estrogen-receptors-distribution-on-active-DNA-demethylation,3,36708,1,1.html
IJMS | Free Full-Text | Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl...IJMS | Free Full-Text | Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl...
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.
http://www.mdpi.com/1422-0067/15/7/11799/htm
5-Hydroxymethylcytosine in Neurodevelopment - Peng Jin5-Hydroxymethylcytosine in Neurodevelopment - Peng Jin
Cytosine methylation serves as a critical epigenetic mark by modifying DNA-protein interactions that influence transcriptional states and cellular identity. 5-m...
http://grantome.com/grant/NIH/R01-NS079625-03
About DNA MethylationAbout DNA Methylation
Measuring the 5-methylcytosine (5-mC) base in DNA allows researchers to investigate the role DNA methylation plays in various biological processes.
http://www.epigenweb.com
Re often not methylated (5mC) but hydroxymethylated (5hmC) [80]. However, bisulfite-based methods - http://amparinhibitor.comRe often not methylated (5mC) but hydroxymethylated (5hmC) [80]. However, bisulfite-based methods - http://amparinhibitor.com
Re often not methylated (5mC) but hydroxymethylated (5hmC) [80]. However, bisulfite-based methods of cytosine modification detection (including RRBS) are unable to distinguish these two types of modifications [81]. The presence of 5hmC in a gene body may be the GDC-0152 site reason why a fraction of CpG dinucleotides has a significant positive SCCM/E value. Unfortunately, data on genome-wide distribution of 5hmC in humans is available for a very limited set of cell types, mostly developmental [82,83], preventing us from a direct study of the effects of 5hmC on transcription and TFBSs. At the current stage the 5hmC data is not available for inclusion in the manuscript. Yet, we were able to perform an indirect study based on the localization of the studied cytosines in GW433908G site various genomic regions. We tested whether cytosines demonstrating various SCCM/E are colocated within different gene regions (Table 2). Indeed,CpG traffic lights are located within promoters of GENCODE [84] ...
https://amparinhibitor.com/2017/11/27/re-often-not-methylated-5mc-but-hydroxymethylated-5hmc-80-however-bisulfite-based-methods/
Selective Capture of 5-hydroxymethylcytosine from Genomic DNA | Protocol (Translated to Turkish)Selective Capture of 5-hydroxymethylcytosine from Genomic DNA | Protocol (Translated to Turkish)
Açıklanan kolay ve yoğunluk bağımsız zenginleştirme için bir biyotin bağlayıcının aktarmak tıkırtı kimya ve ardından, 5-HMC için bir...
https://www.jove.com/video/4441/genomik-dna-5-hydroxymethylcytosine-seici-yakalama?language=Turkish
Anti-5-Hydroxymethylcytosine Polyclonal AntibodyAnti-5-Hydroxymethylcytosine Polyclonal Antibody
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
https://www.zymoresearch.com/products/anti-5-hydroxymethylcytosine-polyclonal-antibody
5-hydroxymethylcytosine in human cancer - Gerd Pfeifer5-hydroxymethylcytosine in human cancer - Gerd Pfeifer
Cell differentiation, reprogramming and malignant transformation are major events characterized by remarkable changes in the epigenome and involve remodeling of...
http://grantome.com/grant/NIH/R01-CA160965-02
Selective Capture of 5-hydroxymethylcytosine from Genomic DNA | Protocol (Translated to Chinese)Selective Capture of 5-hydroxymethylcytosine from Genomic DNA | Protocol (Translated to Chinese)
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 - ...
https://www.jove.com/video/4441/dna5-?language=Chinese
Anti-Methylcytosine dioxygenase TET1 Antibody | 09-872Anti-Methylcytosine dioxygenase TET1 Antibody | 09-872
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.
http://www.merckmillipore.com/INTL/en/product/Anti-Methylcytosine-dioxygenase-TET1-Antibody,MM_NF-09-872
Anti-5-Hydroxymethylcytosine [AB3/63.3]Anti-5-Hydroxymethylcytosine [AB3/63.3]
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http://absoluteantibody.com/ab/Anti-5-Hydroxymethylcytosine-AB363-3/
Information storage and transferInformation storage and transfer
Throughout its lifetime, the DNA in a cell is under constant metabolic and environmental assault leading to damage. The ultraviolet (UV) component of sunlight, ionizing radiation and numerous genotoxic chemicals, including the (by)products of normal cellular metabolism (e.g. reactive oxygen species such as superoxide anions, hydroxyl radicals and hydrogen peroxide), constitute a permanent enemy to DNA integrity. Hydrolysis of nucleotide residues leaves non-instructive abasic sites. Spontaneous or induced deamination of cytosine, adenine, guanine or 5-methylcytosine converts these bases to the miscoding uracil, hypoxanthine, xanthine and thymine, respectively. Left unchecked, the resulting genomic instability initiates cancer and other age-related disorders. Inherited or acquired deficiencies in genome maintenance systems contribute significantly to the onset of cancer. Over time, DNA accumulates changes that activate proto-oncogenes and inactivate tumor-suppressor genes. Cells have evolved ...
https://www.asbmb.org/education/core-concept-teaching-strategies/foundational-concepts/information-storage
SACOL RS06105 - AureoWikiSACOL RS06105 - AureoWiki
16S rRNA (cytosine1402-N4)-methyltransferaseS-adenosyl-L-methionine + cytosine1402 in 16S rRNA = S-adenosyl-L-homocysteine + N4-methylcytosine1402 in 16S rRNA ...
http://aureowiki.med.uni-greifswald.de/SACOL_RS06105
Vitamin C Stops CancerVitamin C Stops Cancer
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 ...
http://healthimpactnews.com/2017/vitamin-c-stops-cancer/print/
Mutation biasMutation bias
Bibcode:2003JMolE..56..373.. doi:10.1007/s00239-002-2455-5. ISSN 0022-2844. Sayres, Melissa A. Wilson; Venditti, Chris; Pagel, ... Ehrlich, M; Wang, R. (1981-06-19). "5-Methylcytosine in eukaryotic DNA". Science. 212 (4501): 1350-1357. Bibcode:1981Sci... ...
https://en.wikipedia.org/wiki/Mutation_bias
DNA sequencingDNA sequencing
6 (5): 1-9. doi:10.1093/gigascience/gix024. PMC 5467036. PMID 28379488. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, ... Retrieved 5 July 2018. Huang YF, Chen SC, Chiang YS, Chen TH, Chiu KP (2012). "Palindromic sequence impedes sequencing-by- ... 5 (23): 2638-49. doi:10.1002/smll.200900976. PMID 19904762. Schadt EE, Turner S, Kasarskis A (2010). "A window into third- ... 48 (5): 1295-302. doi:10.1016/0006-291X(72)90852-2. PMID 4560009. Wu R, Tu CD, Padmanabhan R (1973). "Nucleotide sequence ...
https://en.wikipedia.org/wiki/DNA_sequencing
Arthur Riggs (geneticist)Arthur Riggs (geneticist)
Riggs, AD; Jones, PA (1983). "5-methylcytosine, gene regulation, and cancer". Advances in Cancer Research. 40: 1-30. doi: ... examining the DNA methylation pattern of the entire genome in an attempt to find patterns of the epigenetic mark 5- ... methylcytosine. DNA methylation is believed to pass information from parent cells to daughter cells, functioning as a secondary ...
https://en.wikipedia.org/wiki/Arthur_Riggs_(geneticist)
HydroxymethylationHydroxymethylation
Tetrakis(hydroxymethyl)phosphonium chloride ([P(CH2OH)4]Cl) is produced in this way from phosphine (PH3). 5-Methylcytosine is a ... 10-Dimethyl-5,9-Undecadien-1-Yne and (E)-7,11-Dimethyl-6,10-Dodecadien-2-yn-1-ol". Organic Syntheses. 69: 120. doi:10.15227/ ...
https://en.wikipedia.org/wiki/Hydroxymethylation
Tuberculinic acidTuberculinic acid
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 ...
https://en.wikipedia.org/wiki/Tuberculinic_acid
Epitranscriptomic sequencingEpitranscriptomic sequencing
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 ...
https://en.wikipedia.org/wiki/Epitranscriptomic_sequencing
DNA methylationDNA methylation
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 SJ ... 24 (5): 821-30. doi:10.1101/gr.162412.113. PMC 4009611. PMID 24558263. Zhang G, Huang H, Liu D, Cheng Y, Liu X, Zhang W, Yin R ... 5-Aza-2'-deoxycytidine (decitabine) is a nucleoside analog that inhibits DNMTs by trapping them in a covalent complex on DNA by ... 17 (5): 625-31. doi:10.1101/gr.6163007. PMC 1855171. PMID 17420183. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin ...
https://en.wikipedia.org/wiki/DNA_methylation
Regulatory sequenceRegulatory sequence
5-methylcytosine (5-mC) is a methylated form of the DNA base cytosine (see Figure). 5-mC is an epigenetic marker found ... In most tissues of mammals, on average, 70% to 80% of CpG cytosines are methylated (forming 5-methylCpG or 5-mCpG). Methylated ... TET enzymes can catalyse demethylation of 5-methylcytosine. When EGR1 transcription factors bring TET1 enzymes to EGR1 binding ... predominantly on cytosines within CpG dinucleotides, where 5' cytosine is followed by 3' guanine (CpG sites). About 28 million ...
https://en.wikipedia.org/wiki/Regulatory_sequence
Transcription (biology)Transcription (biology)
This use of only the 3' → 5' DNA strand eliminates the need for the Okazaki fragments that are seen in DNA replication. This ... ISBN 0-7167-8724-5. Watson JD, Baker TA, Bell SP, Gann AA, Levine M, Losick RM (2013). Molecular Biology of the Gene (7th ed ... 17 (5): 515-523. doi:10.1038/s41592-020-0797-9. PMC 7205578. S2CID 214810294. Raj A, van Oudenaarden A (October 2008). "Nature ... The antisense strand of DNA is read by RNA polymerase from the 3' end to the 5' end during transcription (3' → 5'). The ...
https://en.wikipedia.org/wiki/Transcription_(biology)
DNADNA
... methyladenine N6-methyadenine Modified Guanine 7-Deazaguanine 7-Methylguanine Modified Cytosine N4-Methylcytosine 5- ... 13 (5): 212-20. doi:10.1016/j.tim.2005.03.010. PMID 15866038. Nickle DC, Learn GH, Rain MW, Mullins JI, Mittler JE (January ... Retrieved 5 March 2015. Hunt, Katie (17 February 2021). "World's oldest DNA sequenced from a mammoth that lived more than a ... Therefore, any DNA strand normally has one end at which there is a phosphate group attached to the 5′ carbon of a ribose (the 5 ...
https://en.wikipedia.org/wiki/DNA
EpigeneticsEpigenetics
71 (5): 865-73. doi:10.1016/0092-8674(92)90561-P. PMID 1423634. S2CID 5995820. Chuang LS, Ian HI, Koh TW, Ng HH, Xu G, Li BF ( ... 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 ... 12 (5): 432-44. doi:10.1016/j.ccr.2007.10.014. PMC 4657456. PMID 17996647. Tabish AM, Poels K, Hoet P, Godderis L (2012). ... 5-Methylcytosine performs much like a regular cytosine, pairing with a guanine in double-stranded DNA. However when methylated ...
https://en.wikipedia.org/wiki/Epigenetics
DeaminationDeamination
This can occur in vitro through the use of bisulfite, which deaminates cytosine, but not 5-methylcytosine. This property has ... A DNA polymerase may perform this replacement via nick translation, a terminal excision reaction by its 5'⟶3' exonuclease ... Spontaneous deamination of 5-methylcytosine results in thymine and ammonia. This is the most common single nucleotide mutation ...
https://en.wikipedia.org/wiki/Deamination
DNA damage theory of agingDNA damage theory of aging
6 (5): 836-43. doi:10.1016/j.celrep.2014.01.031. PMC 4010117. PMID 24582957. Kanfi Y, Naiman S, Amir G, Peshti V, Zinman G, ... 134 (5-6): 261-9. doi:10.1016/j.mad.2013.03.006. PMID 23562424. S2CID 25146054. Theil AF, Nonnekens J, Steurer B, Mari PO, de ... 5 (5): 503-9. doi:10.1038/sj.embor.7400127. PMC 1299048. PMID 15105825. Reiling E, Dollé ME, Youssef SA, Lee M, Nagarajah B, ... 37 (5): 1043-53. doi:10.1016/j.biocel.2004.10.006. PMID 15743677. MacRae SL, Croken MM, Calder RB, Aliper A, Milholland B, ...
https://en.wikipedia.org/wiki/DNA_damage_theory_of_aging
MethylationMethylation
5-methylcytosine (5-mC) also commonly occurs in various RNA molecules. Recent data strongly suggest that m6A and 5-mC RNA ... 480 (7378): 490-5. doi:10.1038/nature11086. PMID 22170606. Rotondo JC, Selvatici R, Di Domenico M, Marci R, Vesce F, Tognon M, ... This 5-O-methylation affects the flavonoid´s water solubility. Examples are 5-O-methylgenistein, 5-O-methylmyricetin or 5-O- ... 5 (19): 19. doi:10.1186/1472-6807-5-19. PMC 1282579. PMID 16225687.CS1 maint: uses authors parameter (link) Fustin, J.M.; Ye, S ...
https://en.wikipedia.org/wiki/Methylation
ReprogrammingReprogramming
The Figure in this section indicates the central roles of ten-eleven translocation methylcytosine dioxygenases (TETs) in the ... TET2 does not have an affinity for 5-methylcytosine in DNA. The CXXC domain of the full-length TET3, which is the predominant ... In the case of methylation, this is a short step that results in the methylation of cytosine to 5-methylcytosine. Stage 3: Base ... EGR1 binds to DNA at sites with the motifs 5′-GCGTGGGCG-3′ and 5'-GCGGGGGCGG-3′ and these motifs occur primarily in promoter ...
https://en.wikipedia.org/wiki/Reprogramming
GermlineGermline
This usually occurs in the DNA sequence CpG, changing the DNA at the CpG site from CpG to 5-mCpG. Methylation of cytosines in ... 80 (5): 1387-1391. Bibcode:1983PNAS...80.1387B. doi:10.1073/pnas.80.5.1387. ISSN 0027-8424. PMC 393602. PMID 6572396. Ohno M, ... The mutation frequencies for cells in different stages of gametogenesis are about 5 to 10-fold lower than in somatic cells both ... Yamaguchi S, Hong K, Liu R, Inoue A, Shen L, Zhang K, Zhang Y (March 2013). "Dynamics of 5-methylcytosine and 5- ...
https://en.wikipedia.org/wiki/Germline
NucleobaseNucleobase
"Role of 5' mRNA and 5' U snRNA cap structures in regulation of gene expression" - Research - Retrieved 13 December 2010. Nguyen ... In DNA, the most common modified base is 5-methylcytosine (m5C). In RNA, there are many modified bases, including those ...
https://en.wikipedia.org/wiki/Nucleobase
DNA demethylationDNA demethylation
These are a ten-eleven translocation methylcytosine dioxygenase (TET) and thymine-DNA glycosylase (TDG). One particular TET ... by ten-eleven translocation methylcytosine dioxygenases (TET enzymes). The molecular steps of this initial demethylation are ... In short patch repair, 5′ dRP lyase trims the 5′ dRP end to form a phosphorylated 5′ end. This is followed by DNA polymerase β ... The human genome contains about 28 million CpG sites, and roughly 60% of the CpG sites are methylated at the 5 position of the ...
https://en.wikipedia.org/wiki/DNA_demethylation
Anjana RaoAnjana Rao
"TET methylcytosine oxidases: new insights from a decade of research". Journal of Biosciences. 45 (1): 21. doi:10.1007/s12038- ... replacement of 5-methylcytosine by cytosine. At the La Jolla Institute, her lab demonstrated the importance of TET enzymes in ... "Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1". Science. 324 (5929): 930-935. ... "Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2". Nature. 468 (7325): 839-843. Bibcode:2010Natur ...
https://en.wikipedia.org/wiki/Anjana_Rao
NSUN2NSUN2
49 (6): 380-5. doi:10.1136/jmedgenet-2011-100686. PMC 4771841. PMID 22577224. "Body weight data for Nsun2". Wellcome Trust ... The protein is a methyltransferase that catalyzes the methylation of cytosine to 5-methylcytosine (m5C) at position 34 of ... July 2019). "NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs". Nucleic Acids Research. 47 (16): 8720-8733. ... July 2019). "Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs". Nucleic Acids Research. 47 (16): 8734-8745 ...
https://en.wikipedia.org/wiki/NSUN2
EpigenomicsEpigenomics
14 (13): 2921-5. doi:10.1021/bi00684a020. PMID 1148185. Zhou W, Sherwood B, Ji Z, Xue Y, Du F, Bai J, Ying M, Ji H (October ... 7 (6): 461-5. doi:10.1038/nmeth.1459. PMC 2879396. PMID 20453866. Yang Y, Scott SA (2017). DNA Methylation Profiling Using Long ... 403 (6765): 41-5. Bibcode:2000Natur.403...41S. doi:10.1038/47412. PMID 10638745. Sedighi M, Sengupta AM (November 2007). " ... In eukaryotes, methylation is most commonly found on the carbon 5 position of cytosine residues (5mC) adjacent to guanine, ...
https://en.wikipedia.org/wiki/Epigenomics
Yi Zhang (biochemist)Yi Zhang (biochemist)
128 (5): 889-900. doi:10.1016/j.cell.2007.02.013. ISSN 0092-8674. PMID 17320163. S2CID 1412135. Liang, Gaoyang; He, Jin; Zhang ... 14 (5): 457-466. doi:10.1038/ncb2483. ISSN 1476-4679. PMC 3544197. PMID 22522173. Matoba, Shogo; Liu, Yuting; Lu, Falong; ... Inoue, Azusa; Zhang, Yi (2011-10-14). "Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos ... to 5-hydroxymethylcytosine (5hmC), 5fC, and 5caC in a cyclic manner in mouse embryonic stem cells. He continued to reveal the ...
https://en.wikipedia.org/wiki/Yi_Zhang_(biochemist)
Shankar BalasubramanianShankar Balasubramanian
6 (5): 435-40. Bibcode:2014NatCh...6..435B. doi:10.1038/nchem.1893. PMC 4188980. PMID 24755596. Royal Society of Chemistry, ... 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. Honours and awards include: 1998 Glaxo Wellcome Award for Innovative Organic ...
https://en.wikipedia.org/wiki/Shankar_Balasubramanian
Mutational signaturesMutational signatures
46 (5): 487-91. doi:10.1038/ng.2955. PMC 4137149. PMID 24728294. Yang B, Li X, Lei L, Chen J (September 2017). "APOBEC: From ... Signature 5 has a predominance of T>C substitutions in the ApTpN trinucleotide context with transcriptional strand bias. ... Taking the information from the 5' and 3' adjacent bases (also called flanking base pairs or trinucleotide context) lead to 96 ... Genotoxins Endogenous cellular (e.g. spontaneous 5-methylcytosine deamination leads to C>T transition (genetics)) mutations ( ...
https://en.wikipedia.org/wiki/Mutational_signatures
MBD4MBD4
9 (2): 393-5. doi:10.3892/or.9.2.393. PMID 11836615. Jost JP, Thiry S, Siegmann M (2002). "Estradiol receptor potentiates, in ... 78 (2): 151-5. doi:10.1007/bf00278187. PMID 3338800. S2CID 41948691. Sanders MA, Chew E, et al. (Jul 2018). "MBD4 guards ... 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 ...
https://en.wikipedia.org/wiki/MBD4
I-motif DNAI-motif DNA
At a pH of 5, these regions contracted to form i-motifs, tightening the ring in a fashion similar to closing a trash bag. At a ... Chemical modifications to the C:C+ base pair in which halogenated analogs (5-fluoro, 5-bromo, and 5-iodo) took the place of ... However, no significant differences in stability occurred with the addition of 5 mM Mg+, Ca+, Zn+, Li+ or K+ cations in the ... Methylation of cytosine at position 5 increased pH of mid-transition and Tm of i-motifs. On the other hand, hydroxymethylation ...
https://en.wikipedia.org/wiki/I-motif_DNA
Expanded genetic codeExpanded genetic code
23 (5): 751-7. doi:10.1016/j.copbio.2011.12.027. PMID 22237016. Neumann H, Wang K, Davis L, Garcia-Alai M, Chin JW (March 2010 ... 105 (3): 211-5. doi:10.1263/jbb.105.211. PMID 18397770. Anderson JC, Wu N, Santoro SW, Lakshman V, King DS, Schultz PG (May ... 11 (5): 537-42. doi:10.1016/j.cbpa.2007.08.011. PMID 17884697. Wang Q, Parrish AR, Wang L (March 2009). "Expanding the genetic ... 80 (5): 1718-25. doi:10.1128/AEM.03417-13. PMC 3957627. PMID 24375139. Chin JW, Cropp TA, Anderson JC, Mukherji M, Zhang Z, ...
https://en.wikipedia.org/wiki/Expanded_genetic_code
Nucleoside-modified messenger RNANucleoside-modified messenger RNA
5 (1): a014035. doi:10.1101/cshperspect.a014035. PMC 4292072. PMID 25301935. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, ... These sequences at the 5′ and 3′ ends of an mRNA strand are called untranslated regions (UTRs). The two UTRs at their strand ... Some of these, such as pseudouridine and 5-methylcytosine, occur naturally in eukaryotes. Inclusion of these modified ... and cytosine can be replaced by 5-methylcytosine. ...
https://en.wikipedia.org/wiki/Nucleoside-modified_messenger_RNA
Citric acid cycleCitric acid cycle
5 (11): e1000662. doi:10.1371/journal.ppat.1000662. PMC 2773412. PMID 19936047. Zhang S, Bryant DA (December 2011). "The ... 5: 2221-2233. doi:10.1021/acsomega.9b03352. PMC 7016920. PMID 32064383. Garrett, Reginald H.; Grisham, Charles M. (2013). ... ordinarily TETs hydroxylate 5-methylcytosines to prime them for demethylation. However, in the absence of alpha-ketoglutarate ...
https://en.wikipedia.org/wiki/Citric_acid_cycle
DNA sequencingDNA sequencing
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- ...
https://en.wikipedia.org/wiki/Sequencing_technology
EpigeneticsEpigenetics
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 ...
https://en.wikipedia.org/wiki/Epigenetic
Single cell sequencingSingle cell sequencing
... and 4mC 4-methylcytosine (4mC). In eukaryotes, especially animals, 5mC is widespread along the genome and plays an important ... doi:10.1038/s41467-018-08126-5. PMC 6341120. PMID 30664627.. *^ Dal Molin A, Di Camillo B (July 2019). "How to design a single- ... doi:10.1038/s41467-020-16821-5. PMC 7298005. PMID 32546686.. *^ Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, ... There are several known types of methylation that occur in nature, including 5-methylcytosine (5mC), 5-hydroymethylcytosine ( ...
https://en.wikipedia.org/wiki/Single_cell_sequencing?source=post_page---------------------------
CpG siteCpG site
It was proposed that the CpG deficiency is due to an increased vulnerability of methylcytosines to spontaneously deaminate to ... 33 (5): 1268-74. doi:10.3892/ijmm.2014.1682. PMID 24590400.. *^ Krause A, Combaret V, Iacono I, Lacroix B, Compagnon C, ... ISBN 0-7637-1511-5.. *^ Fatemi M, Pao MM, Jeong S, Gal-Yam EN, Egger G, Weisenberger DJ, Jones PA (2005). "Footprinting of ... CpG is shorthand for 5'-C-phosphate-G-3' , that is, cytosine and guanine separated by only one phosphate group; phosphate links ...
https://en.wikipedia.org/wiki/CpG_island
Nucleic acid sequenceNucleic acid sequence
23 (5): 373-378. doi:10.1209/0295-5075/23/5/012.. *^ a b Pinho, A; Garcia, S; Pratas, D; Ferreira, P (Nov 21, 2013). "DNA ... 5 (10203): 10203. doi:10.1038/srep10203. PMC 4434998. PMID 25984837.. *^ Troyanskaya, O; Arbell, O; Koren, Y; Landau, G; ... doi:10.1016/0092-8674(81)90522-5. PMID 6263489.. *^ Peng, C.-K.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Sciortino, F ... By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, the sense strand is used. Because ...
https://en.m.wikipedia.org/wiki/Genetic_information
DNA methyltransferaseDNA methyltransferase
m5C - those that generate C5-methylcytosine EC 2.1.1.37 m6A and m4C methyltransferases are found primarily in prokaryotes ( ... m4C - those that generate N4-methylcytosine EC 2.1.1.113. * ... C-5 cytosine-specific DNA methylase. structure of human dnmt2, ... m5C methyltransferases (C-5 cytosine-specific DNA methylase) (C5 Mtase) are enzymes that specifically methylate the C-5 carbon ... of cytosines in DNA to produce C5-methylcytosine.[8][9][10] In mammalian cells, cytosine-specific methyltransferases methylate ...
https://en.wikipedia.org/wiki/DNA_methyltransferase
Development of the nervous systemDevelopment of the nervous system
Methylcytosine demethylation is catalyzed in several sequential steps by TET enzymes that carry out oxidative reactions (e.g. 5 ... methylcytosine to 5-hydroxymethylcytosine) and enzymes of the DNA base excision repair (BER) pathway.[15] ... Kandel, Eric R. (2006). Principles of neural science (5. ed.). Appleton and Lange: McGraw Hill. ISBN 978-0071390118. .. [page ... The 3′ (3 prime end) genes in the Hox cluster are induced by retinoic acid in the hindbrain, whereas the 5′ (5 prime end) Hox ...
https://en.wikipedia.org/wiki/Neural_development
Promoter (genetics)Promoter (genetics)
5: S2. doi:10.1186/1752-0509-5-S1-S2.. *^ a b Shu, J.; Jelinek, J; Chang, H; Shen, L; Qin, T; Chung, W; Oki, Y; Issa, J. P. ( ... 1: RNA Polymerase, 2: Repressor, 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA. Top: The gene is essentially ... doi:10.1016/s1369-5274(03)00036-5.. *^ Copland JA, Sheffield-Moore M, Koldzic-Zivanovic N, Gentry S, Lamprou G, Tzortzatou- ... 103 (5): 1412-7. Bibcode:2006PNAS..103.1412S. doi:10.1073/pnas.0510310103. PMC 1345710. PMID 16432200.. ...
https://en.wikipedia.org/wiki/Promoter_
EpigeneticsEpigenetics
302 (1): 5-18. doi:10.1002/jez.b.20002. PMID 14760651.. *^ Alvarez-Buylla ER, Chaos A, Aldana M, Benítez M, Cortes-Poza Y, ... 978-0-19-515619-5. .. *^ Gray RD, Oyama S, Griffiths PE (2003). Cycles of Contingency: Developmental Systems and Evolution ( ... doi:10.1016/S0022-5193(05)80287-5. PMID 2359317.. *^ Lynch M (May 2007). "The frailty of adaptive hypotheses for the origins of ... 978-0-12-809324-5. .. *^ Robison AJ, Nestler EJ (November 2011). "Transcriptional and epigenetic mechanisms of addiction". Nat ...
https://en.m.wikipedia.org/wiki/Epigenetic
Subventricular zoneSubventricular zone
8 (5): a018820. doi:10.1101/cshperspect.a018820. ISSN 1943-0264. PMC 4852803. PMID 27048191.. ... The conversion of cytosine to 5-methylcytosine (5mC) in DNA by DNA methyltransferase DNMT3A appears to be an important type of ... The adult SVZ is composed of four distinct layers[5] of variable thickness and cell density as well as cellular composition. ... It is identified by a high presence of myelin in the region.[5] ... 5] Layer II[edit]. The secondary layer (Layer II) provides for ...
https://en.wikipedia.org/wiki/Subventricular_zone
MutationMutation
38 (5): 1116-1129. doi:10.2307/2408444. JSTOR 2408444. PMID 28555784.. *^ Orr HA (April 2003). "The distribution of fitness ... 57 (3): 683-5, discussion 686-9. doi:10.1554/0014-3820(2003)057[0683:tarmom]2.0.co;2. JSTOR 3094781. PMID 12703958.. ... Liou, Stephanie (February 5, 2011). "All About Mutations". HOPES. Huntington's Disease Outreach Project for Education at ... Examples include C → U and A → HX (hypoxanthine), which can be corrected by DNA repair mechanisms; and 5MeC (5-methylcytosine ...
https://en.m.wikipedia.org/wiki/Genetic_mutation
DNA methylationDNA methylation
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 ...
https://en.wikipedia.org/wiki/DNA_methylation?wprov=sfti1
Very short patch repairVery short patch repair
Very short patch (VSP) repair is a DNA repair system that removes GT mismatches created by the deamination of 5-methylcytosine ... and it creates a nick on a single strand by cleaving the phosphate backbone on the 5' side of the thymine.[1] Then DNA ...
https://en.m.wikipedia.org/wiki/Very_short_patch_repair
DNA, ang malayang ensiklopedyaDNA, ang malayang ensiklopedya
Ang asimetrikong mga dulo ng mga strandong DNA ay tinatawag na 5′ (limang prime) at 3′ (tatlong prime) mga dulo na ang 5' dulo ... Kahit sa kahalagahan ng 5-methylcytosine, ito ay maaaring mag-deamina upang mag-iwan ng baseng thymine kaya ang methyladong ... Halimbawa, ang ensaymn na EcoRV ay kumikilala ng 6-na baseng sekwensiyang 5′-GAT,ATC-3′ at gumagawa ng pagputol sa bertikal na ... Dahil sa ang mga DNA polymerase ay maaari lamang magpalawig ng stranding DNA sa direksiyong 5′ hanggang 3′, ang iba ibang mga ...
https://tl.wikipedia.org/wiki/DNA
Planococcus citriPlanococcus citri
Ferraro, M., Buglia, G. & Predazzi, V. (1998) Analysis of methylcytosine distribution along the chromosomes of {Planococcus ... 5) [v. 5]. The Pseudococcidae (Part I)., *↑ Williams, D.J. (1962) The British Pseudococcidae (Homoptera: Coccoidea)., Bulletin ...
https://war.wikipedia.org/wiki/Planococcus_citri
Succinic acidSuccinic acid
... (/səkˈsɪnɪk/) is a dicarboxylic acid with the chemical formula (CH2)2(CO2H)2.[5] The name derives from Latin ... In living organisms, primarily succinate, not succinic acid, is found.[5]. As a radical group it is called a succinyl (/ˈsʌksɪn ... 51 (5): 545. doi:10.1007/s002530051431. S2CID 38868987.. *^ "Overview of pharmaceutical excipients used in tablets and capsules ... Succinic acid is a white, odorless solid with a highly acidic taste.[5] In an aqueous solution, succinic acid readily ionizes ...
https://en.m.wikipedia.org/wiki/Succinic_acid
Ostra białaczka szpikowa, wolna encyklopediaOstra białaczka szpikowa, wolna encyklopedia
2,5 1,7 0,7 Czynniki chemiczne[edytuj , edytuj kod]. Zawodowy kontakt z benzenem zwiększa ryzyko zachorowania na ostrą ... 5 lub del(5q). −7; abnl(17p). złożony kariotyp Rokowanie[edytuj , edytuj kod]. Największe szanse mają chorzy z korzystnymi ... Leukemia". 13 (5), s. 679-86, May 1999. PMID: 10374870. *↑ FG. Behm, SC. Raimondi, JL. Frestedt, Q. Liu i inni. Rearrangement ... Oncotarget". 5 (1), s. 7-8, Jan 2014. PMID: 24473927. *↑ SR. Wolman, H. Gundacker, FR. Appelbaum, ML. Slovak. Impact of trisomy ...
https://pl.wikipedia.org/wiki/Ostra_białaczka_szpikowa
Nukleyobase, ang malayang ensiklopedyaNukleyobase, ang malayang ensiklopedya
"Role of 5' mRNA and 5' U snRNA cap structures in regulation of gene expression" - Research - Retrieved 13 December 2010. ... Sa DNA, ang karamihan ng mga karaniwang nabagong base ang 5-methylcytosine (m5C). Sa RNA, mayroon maraming mga nabagong base ... Ang dalawang mga baseng ito ay magkatulad maliban na uracil ay nagkukulang sa pangkat 5' methyl. Ang adenine at guanine ay ... ay tinatawag na isang nukleyosida at ang isang nukleyosida na may isa o higit pang mga pangkat na pospata na nakakabit sa 5' ...
https://tl.wikipedia.org/wiki/Nukleyobase
Promoter (genetics)Promoter (genetics)
5 Suppl 1: S2. doi:10.1186/1752-0509-5-S1-S2. PMC 3121118. PMID 21689477. Shu J, Jelinek J, Chang H, Shen L, Qin T, Chung W, ... 103 (5): 1412-7. Bibcode:2006PNAS..103.1412S. doi:10.1073/pnas.0510310103. PMC 1345710. PMID 16432200. Deaton AM, Bird A (May ... In humans, DNA methylation occurs at the 5' position of the pyrimidine ring of the cytosine residues within CpG sites to form 5 ... methylcytosines. The presence of multiple methylated CpG sites in CpG islands of promoters causes stable silencing of genes. ...
https://en.wikipedia.org/wiki/Promoter_(genetics)
HippocampusHippocampus
5. Center for Inquiry. pp. 52-56. Rubin M, Shvil E, Papini S, Chhetry BT, Helpman L, Markowitz JC, Mann JJ, Neria Y (June 2016 ... 44 (1): 5-21. doi:10.1016/j.neuron.2004.09.012. PMID 15450156. S2CID 79844. Matsumura N, Nishijo H, Tamura R, Eifuku S, Endo S ... ISBN 978-1-292-02320-5. Jatzko A, Rothenhöfer S, Schmitt A, Gaser C, Demirakca T, Weber-Fahr W, Wessa M, Magnotta V, Braus DF ( ... 11 (5): 508-19. doi:10.1002/hipo.1067. PMID 11732704. S2CID 2502525. Nishioka N, Arnold SE (2004). "Evidence for oxidative DNA ...
https://en.wikipedia.org/wiki/Hippocampus
Huda ZoghbiHuda Zoghbi
5 (9): 1207-1216. doi:10.1093/hmg/5.9.1207. PMID 8872459. Bermingham, Nessan A.; Hassan, Bassem A.; Price, Steven D.; Vollrath ... 178 (5): 1159-1175.e17. doi:10.1016/j.cell.2019.07.043. PMC 6726125. PMID 31442405 - via Elsevier Science Direct. "The Brain ... 5: e14198. doi:10.7554/eLife.14198. PMC 4946897. PMID 27328321. Rodríguez, Ana María (5 September 2019). "Ataxin-1: One gene, ... Recently, Zoghbi confirmed that the MECP2 protein also bound 5-methylcytosine not in CpG sites, and that restoring the level of ...
https://en.wikipedia.org/wiki/Huda_Zoghbi
Chromosome 13Chromosome 13
... encoding protein KIAA1704 LOC107984557 encoding protein Methylcytosine dioxygenase TET1-like MBNL2: encoding protein ... 11 (5): 206. doi:10.1186/gb-2010-11-5-206. PMC 2898077. PMID 20441615. "Statistics & Downloads for chromosome 13". HUGO Gene ... Glypican 5: encoding protein Glypican-5 HTR2A: 5-HT2A receptor INTS6: encoding protein Integrator complex subunit 6 GPALPP1: ... encoding protein SLIT and NTRK-like protein 5 SLITRK6: encoding protein SLIT and NTRK-like protein 6 SOX21: Transcription ...
https://en.wikipedia.org/wiki/Chromosome_13
Third-generation sequencingThird-generation sequencing
examined 4-methylcytosine (4mC) and 6-methyladenine (6mA), along with 5mC, and also created a software to directly visualize ... Here they found that in E. coli, which has a known methylome, event windows of 5 base pairs long can be used to divide and ... was used to analyze MinION data to detect 5-methylcytosine (5mC) DNA modification. The model was trained using synthetically ...
https://en.wikipedia.org/wiki/Third-generation_sequencing
5-Methylcytosine - Wikipedia5-Methylcytosine - Wikipedia
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 (C) that regulates gene transcription and takes several other ...
https://en.wikipedia.org/wiki/5-Methylcytosine
DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases | PNASDEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases | PNAS
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 ...
https://www.pnas.org/content/103/18/6853?ijkey=49701a400ea1ff85482fc3ee9d2b32b76d45c7ea&keytype2=tf_ipsecsha
5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3. - PubMed - NCBI5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3. - PubMed - NCBI
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- ...
https://www.ncbi.nlm.nih.gov/pubmed/24678721
Urine 5-methylcytosine Quantification Kit (Colorimetric) (ab156903)Urine 5-methylcytosine Quantification Kit (Colorimetric) (ab156903)
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 ...
https://www.abcam.com/urine-5-methylcytosine-quantification-kit-colorimetric-ab156903.html
5-MethylCytosine ELISA Kits: Novus Biologicals5-MethylCytosine ELISA Kits: Novus Biologicals
5-MethylCytosine ELISA Kits available through Novus Biologicals. Browse our 5-MethylCytosine ELISA Kits all backed by our ...
https://www.novusbio.com/elisa-kits/5-methylcytosine?promotional_item=No
5 methylcytosine Protocols and Video...'5 methylcytosine' Protocols and Video...
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 ...
https://www.jove.com/keyword/5+methylcytosine
A bisulfite method of 5-methylcytosine mapping that minimizes template degradationA bisulfite method of 5-methylcytosine mapping that minimizes template degradation
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 ...
https://pubmed.ncbi.nlm.nih.gov/7785768/?dopt=Abstract
RCSB PDB - Protein Feature View - 5-methylcytosine-specific restriction enzyme A - P24200 (MCRA ECOLI)RCSB PDB - Protein Feature View - 5-methylcytosine-specific restriction enzyme A - P24200 (MCRA ECOLI)
Restriction of 5-methyl and 5-hydroxymethylcytosines at the specific DNA sequence C(me)CGG. UniProt ...
https://www.rcsb.org/pdb/protein/P24200
JCI - Mutations in 5-methylcytosine oxidase TET2 and RhoA cooperatively disrupt T cell homeostasisJCI - Mutations in 5-methylcytosine oxidase TET2 and RhoA cooperatively disrupt T cell homeostasis
Mutations in 5-methylcytosine oxidase TET2 and RhoA cooperatively disrupt T cell homeostasis. ... Mutations in 5-methylcytosine oxidase TET2 and RhoA cooperatively disrupt T cell homeostasis. ... and loss-of-function mutations in the 5-methylcytosine oxidase TET2. Here, we have demonstrated that TET2 loss and RhoAG17V ...
https://www.jci.org/articles/view/92026/sd/2
Global DNA Methylation Assay Kit (5 Methyl Cytosine, Colorimetric) (ab233486)Global DNA Methylation Assay Kit (5 Methyl Cytosine, Colorimetric) (ab233486)
The level of 5-mC in plants generally accounts for 0.5-2% and can be as high as 8% of total DNA in some other species. The ... Levels of 5-mC are variable in animal genomes, ranging from undetectable amounts in some insects to about 2% of total DNA in ... Kit - Global DNA Methylation Assay Kit (5 Methyl Cytosine, Colorimetric) (ab233486) Biochemical - Hydralazine hydrochloride, ... Accurate quantification of 5-mC content of various DNA samples from different species using Global DNA Methylation Assay Kit (5 ...
https://www.abcam.com/global-dna-methylation-assay-kit-5-methyl-cytosine-colorimetric-ab233486.html
Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution | ScienceQuantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution | Science
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 ...
https://science.sciencemag.org/content/336/6083/934
Quantification of global DNA methylation level using 5-methylcytosine dioxygenase | SpringerLinkQuantification of global DNA methylation level using 5-methylcytosine dioxygenase | SpringerLink
5.. Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, Endo TA, et al. The SRA protein Np95 mediates epigenetic ... Taka, N., Yoshida, W. Quantification of global DNA methylation level using 5-methylcytosine dioxygenase. Anal Bioanal Chem 412 ... Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;324:930-5. ... TET proteins mediate DNA demethylation through the oxidation of 5-methylcytosine (5mC) in CpG in mammalian cells. Succinate is ...
https://link.springer.com/article/10.1007/s00216-020-02745-y?error=cookies_not_supported&code=5eb9c3c9-1400-4f05-a2f4-f69b40b1ed8a
RCSB PDB - 5L2G: Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th PositionRCSB PDB - 5L2G: Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th Position
DNA (5-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3). A, B. 12. synthetic construct. ... Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th Position. *DOI: 10.2210/pdb5L2G/pdb ... the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5- ... methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion ... ...
https://www.rcsb.org/structure/5L2G
5-Methylcytosine & 5-Hydroxymethylcytosine DNA Standard Set5-Methylcytosine & 5-Hydroxymethylcytosine DNA Standard Set
The 5-Methylcytosine & 5-Hydroxymethylcytosine DNA Standard Set is a set of three standards that are linear dsDNA at a length ... The 5-Methylcytosine & 5-Hydroxymethylcytosine DNA Standard Set is a set of three standards that are linear dsDNA at a length ... Control DNA for 5-methylcytosine and 5-hydroxymethylcytosine quantitation applications (ex. mass spectrometry, HPLC, TLC, etc ... or 5-hydroxymethylcytosines. Since the sequence and extent of cytosine modification is known, this DNA standard set is ideal ...
https://www.zymoresearch.com/products/5-methylcytosine-5-hydroxymethylcytosine-dna-standard-set
Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1 | ScienceConversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1 | Science
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 ...
https://science.sciencemag.org/content/324/5929/930?ijkey=fc07ee37ed10a21cc48e985382cdaa5bac066f57&keytype2=tf_ipsecsha
Can 5-methylcytosine analogues with extended alkyl side chains guide DNA methylation? - Chemical Communications (RSC Publishing)Can 5-methylcytosine analogues with extended alkyl side chains guide DNA methylation? - Chemical Communications (RSC Publishing)
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. ...
http://pubs.rsc.org/en/content/articlelanding/2018/cc/c7cc06867k
Discrimination between 5-hydroxymethylcytosine and 5-methylcytosine by a chemically designed peptide - Chemical Communications ...Discrimination between 5-hydroxymethylcytosine and 5-methylcytosine by a chemically designed peptide - Chemical Communications ...
The Sp1 zinc finger peptide substituted by phosphotyrosine effectively discriminated between 5-methylcytosine, 5- ... 5-methylcytosine. by a chemically designed peptide A. Nomura, K. Sugizaki, H. Yanagisawa and A. Okamoto, Chem. Commun., 2011, ... 5-hydroxymethylcytosine. (hmC) and unmethylated cytosine. The DNA recognition properties of the peptide. differ from those of ... Discrimination between 5-hydroxymethylcytosine and 5-methylcytosine by a chemically designed peptide† ...
https://pubs.rsc.org/en/Content/ArticleLanding/CC/2011/C1CC12131F
IJMS | Free Full-Text | Reduced 5-Methylcytosine Level as a Potential Progression Predictor in Patients with T1 or Non-Invasive...IJMS | Free Full-Text | Reduced 5-Methylcytosine Level as a Potential Progression Predictor in Patients with T1 or Non-Invasive...
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- ...
https://www.mdpi.com/1422-0067/16/1/677
Accurate Measurement of 5-Methylcytosine and 5-Hydroxymethylcytosine in Human Cerebellum DNA by Oxidative Bisulfite on an Array...Accurate Measurement of 5-Methylcytosine and 5-Hydroxymethylcytosine in Human Cerebellum DNA by Oxidative Bisulfite on an Array...
However, the bisulfite (BS) reaction commonly used with the 450K array cannot distinguish between 5-methylcytosine (5mC) and 5- ...
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118202
5-Methylcytosine content of nuclear DNA during chemical hepatocarcinogenesis and in carcinomas which result. - PubMed - NCBI5-Methylcytosine content of nuclear DNA during chemical hepatocarcinogenesis and in carcinomas which result. - PubMed - NCBI
5-Methylcytosine content of nuclear DNA during chemical hepatocarcinogenesis and in carcinomas which result.. Lapeyre JN, ...
https://www.ncbi.nlm.nih.gov/pubmed/454420?dopt=Abstract
Characterizing 5-methylcytosine in the mammalian epitranscriptome | Genome Biology | Full TextCharacterizing 5-methylcytosine in the mammalian epitranscriptome | Genome Biology | Full Text
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 ...
https://genomebiology.biomedcentral.com/articles/10.1186/gb4143
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosineTet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable ... 5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins. Here, we show that, in ... Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine Science. 2011 Sep 2;333(6047):1300-3. doi ... 5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable ...
https://pubmed.ncbi.nlm.nih.gov/21778364/
Quantification of Leukocyte Genomic 5-Methylcytosine Levels Reveals Epigenetic Plasticity in Healthy Adult Cloned CattleQuantification of Leukocyte Genomic 5-Methylcytosine Levels Reveals Epigenetic Plasticity in Healthy Adult Cloned Cattle
DNA Methylation Analysis | Methylated Cytosine: 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) | T4 Beta...DNA Methylation Analysis | Methylated Cytosine: 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) | T4 Beta...
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) ...
http://www.clontech.com/US/Products/Cell_Biology_and_Epigenetics/Epigenetics/DNA_Preparation/Cytosine_Methylation_Modification_Enzyme?sitex=10020:22372:US&PEBCL1=DoFghEfNOTLyNuZNn56qGyTLZd&PEBCL1_pses=ZG6E8563D094033B57A24ADA3E46B022206866D35941FCBFAAAA6EBD532311950CAF559C922C30E95997A1BFA728758268B9596856EC5FF62F
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...
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 ...
http://cancerres.aacrjournals.org/content/78/24/6728.figures-only
Hydroquinone increases 5-hydroxymethylcytosine formation through ten eleven translocation 1 (TET1) 5-methylcytosine dioxygenase...Hydroquinone increases 5-hydroxymethylcytosine formation through ten eleven translocation 1 (TET1) 5-methylcytosine dioxygenase...
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 ...
https://www.kennedykrieger.org/node/88516
A specific mismatch repair event protects mammalian cells from loss of 5-methylcytosine - Zurich Open Repository and ArchiveA specific mismatch repair event protects mammalian cells from loss of 5-methylcytosine - Zurich Open Repository and Archive
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 ...
https://www.zora.uzh.ch/id/eprint/34297/
Hyperglycemia affects global 5-methylcytosine and 5-hydroxymethylcytosine in blood genomic DNA through upregulation of SIRT6...Hyperglycemia affects global 5-methylcytosine and 5-hydroxymethylcytosine in blood genomic DNA through upregulation of SIRT6...
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 ...
https://rd.springer.com/article/10.1186%2Fs13148-019-0660-y
Reactome | TET1,2,3 oxidizes 5-methylcytosine to 5-hydroxymethylcytosineReactome | TET1,2,3 oxidizes 5-methylcytosine to 5-hydroxymethylcytosine
Ascorbate induces ten-eleven translocation (Tet) methylcytosine dioxygenase-mediated generation of 5-hydroxymethylcytosine ... Dynamics of 5-hydroxymethylcytosine and chromatin marks in Mammalian neurogenesis Hahn, MA, Qiu, R, Wu, X, Li, AX, Zhang, H, ... Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain Guo, JU, Su, Y, Zhong, C, Ming, ... Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2 Ko, M, Huang, Y, Jankowska, AM, Pape, UJ, ...
https://reactome.org/content/detail/R-HSA-5221014
5-Methylcytosine RNA Methylation in Arabidopsis Thaliana 5-Methylcytosine RNA Methylation in Arabidopsis Thaliana
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 ...
https://www.diagenode.com/en/publications/view/3297
Oxidation of 5-methylcytosine5hmCThymineAntibodyDioxygenaseCytosinesAbstractGenomicOxidize the 5-methyl groupMethyltransferasesTET1MethyltransferaseEnzymesModificationDeamination of cytosineResiduesMonoclonalUracilTranslocationEpigeneticsProteinsDinucleotideBisulfiteGlobal DNA methylationTET2Position of cytosineEukaryotesArabidopsisColorimetricSequencesOccursReagentsDNMTMammalian cellsRecognitionMethyl CytosineAssayDioxygenasesRegulationTranscriptome-wideRestriction enzymeQuantificationStabilityQuantitationDemethylationEmbryonicHypomethylationBaseOxidativeTumorigenesisHydrochlorideGene expression
Oxidation of 5-methylcytosine6
  • TET proteins mediate DNA demethylation through the oxidation of 5-methylcytosine (5mC) in CpG in mammalian cells. (springer.com)
  • Recently, methylated CpG sites have been established as mutational hotspots in DNA, one reason of which being oxidation of 5-methylcytosine. (radioprotection.org)
  • Oxidation of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) was suggested to be an intermediate step in the DNA demethylation pathway. (vub.be)
  • A sixth base, 5‑hydroxymethylcytosine (5hmC), is formed by the oxidation of 5‑methylcytosine (5mC) via the catalysis of the ten‑eleven translocation (TET) protein family in cells. (spandidos-publications.com)
  • Furthermore, 5hmC is generated by the oxidation of 5-methylcytosine (5mC) by ten-eleven translocation protein (TET), and 5hmC serves critical roles in various tissues ( 2 , 13 , 15 - 22 ). (spandidos-publications.com)
  • Tet methylcytosine dioxygenase 1 (TET1) catalyses the sequential oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine, (5hmC) leading to eventual DNA demethylation. (portlandpress.com)
5hmC17
  • Methylated cytosine can be enzymatically oxidized to 5-hydroxymethylcytosine (5hmC), which may function as a distinct epigenetic mark-possibly involved in pluripotency-and it may also be an intermediate in active DNA demethylation. (sciencemag.org)
  • p. 934 , published online 26 April) developed a 5hmC sequencing chemistry that selectively oxidizes 5hmC to 5-formylcytosine and then to uracil while leaving 5mC unchanged. (sciencemag.org)
  • 5-Methylcytosine can be converted to 5-hydroxymethylcytosine (5hmC) in mammalian DNA by the ten-eleven translocation (TET) enzymes. (sciencemag.org)
  • Selective chemical oxidation of 5hmC to 5-formylcytosine (5fC) enables bisulfite conversion of 5fC to uracil. (sciencemag.org)
  • Here, we show that, in addition to 5hmC, the Tet proteins can generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic activity-dependent manner. (nih.gov)
  • MspI/HpaII) digestion or immunodetection can be used identify β-glucosyl-5-hydroxymethylcytosine (ß-glu-5hmC) at particular loci, or genome-wide analyses can be accomplished by selective pull-down of β-glu-5hmC. (clontech.com)
  • However, the dynamic regulation of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in diabetic peripheral blood DNA remains to be elucidated. (springer.com)
  • In addition to the generally repressive methylcytosine DNA alteration, 5-hydroxymethylation of cytosine (5hmC) is recognized as an epigenetic mark associated with active chromatin. (scienceopen.com)
  • 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 and 5-methylcytosine (5mC). (scienceopen.com)
  • It does this by starting a series of oxidation reactions that convert the methylated cytosine on the DNA from 5-methyl cytosine (5mC) into 5-hydroxymethylcytosine (5hmC). (wikipedia.org)
  • The study shows that TET3 as well as its product, 5-hydroxymethylcytosine (5hmC), are expressed more after focal ischemia in order to demethylate and turn on genes associated with DNA repair in neurons. (wikipedia.org)
  • 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. (biomedcentral.com)
  • Recently, the ten-eleven translocation (TET) family of methylcytosine dioxygenases was shown to mediate this process by catalyzing the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and, subsequently, to 5-formylcytosine and 5-carboxylcytosine, critical enzymatic steps necessary for generating unmodified cytosines ( 20 - 22 ). (jimmunol.org)
  • We observed that overall 5-hydroxymethylcytosine (5hmC) abundance in the cortex of the temporal lobe of rat pups was decreased significantly after hypoxic-ischemic injury, and the reduced expression of Tet1 and Tet2 enzymes might be responsible for this change. (frontiersin.org)
  • 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. (frontiersin.org)
  • Previous studies have reported that a sixth base, 5-hydroxymethylcytosine (5hmC), is present in a number of tissues, including the muscle, lung, kidney and heart, and is highly expressed in the brain and embryonic cells ( 2 , 12 - 15 ). (spandidos-publications.com)
  • Recently, TET-family proteins were identified as enzymes that convert 5mC to 5-hydroxymethylcytosine (5hmC),[ 6, 7 ] and further to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)[ 8, 9 ] through consecutive oxidation reactions. (wiley.com)
Thymine10
  • While spontaneous deamination of cytosine forms uracil, which is recognized and removed by DNA repair enzymes, deamination of 5-methylcytosine forms thymine. (wikipedia.org)
  • DME and ROS1 show a preference for 5-meC over thymine in the symmetric dinucleotide CpG context, where most plant DNA methylation occurs. (pnas.org)
  • A 5-meC DNA glycosylase activity was first identified in chicken embryos ( 15 ) and found to copurify with a protein homologous to human thymine DNA glycosylase (TDG) ( 16 , 17 ). (pnas.org)
  • Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. (springer.com)
  • In a computational search for enzymes that could modify 5-methylcytosine (5mC), we identified TET proteins as mammalian homologs of the trypanosome proteins JBP1 and JBP2, which have been proposed to oxidize the 5-methyl group of thymine. (sciencemag.org)
  • Supplementary Figure 1 - Deamination of Cytosine or 5-methylcytosine to Uracil or Thymine respectively. (aacrjournals.org)
  • 5-Methylcytosine spontaneously deaminates to form thymine, thus generating G/T mispairs in DNA. (uzh.ch)
  • Spontaneous deamination of 5-methylcytosine converts it to thymine. (wikipedia.org)
  • In turn, AICDA causes deamination of 5-methylcytosine to thymine at position c.2369 to generate the T790M mutation. (elsevier.com)
  • On the other hand, 5-methylcytosine is potentially mutagenic because thymine produced during the methylation process converts C:G pairs to T:A pairs. (britannica.com)
Antibody18
  • 5-methylcytosine (5-mC) Antibody - clone 33D3 to my shopping cart. (diagenode.com)
  • Request a quote for a bulk order for 5-methylcytosine (5-mC) monoclonal antibody 33D3 - Premium . (diagenode.com)
  • Monoclonal antibody raised in mouse against 5-mC (5-methylcytosine) conjugated to ovalbumine (33D3 clone). (diagenode.com)
  • Visual inspection of the peak profiles in a genome browser reveals high enrichment of CA simple repeats in affinity-enriched methylated fragments after MeDIP with the Diagenode 5-mC monoclonal antibody. (diagenode.com)
  • MeDIP (Methylated DNA immunoprecipitation) was performed on 1 µg fragmented human genomic DNA using 0.2 µg of the Diagenode monoclonal antibody against 5-mC (cat. (diagenode.com)
  • To demonstrate the specificity of the Diagenode antibody against 5-mC (cat. (diagenode.com)
  • HeLa cells were stained with the Diagenode antibody against 5-mC (Cat. (diagenode.com)
  • The cells were immunofluorescently labelled with the 5-mC antibody (middle) diluted 1:500 in blocking solution followed by an anti-mouse antibody conjugated to Alexa594. (diagenode.com)
  • Immunofluorescence staining with 5-methylcytosine antibody (anti-5mc) clone 33D3. (epigentek.com)
  • Methylated DNA successfully captured by 5-methylcytosine antibody (anti-5mc) clone 33D3 during MeDIP. (epigentek.com)
  • Synthesized oligos containing different numbers of 5-methylcytosines were captured with the Clone 33D3 anti-5-methylcytosine antibody (Cat No. A-1014) and then colorimetrically detected. (epigentek.com)
  • The results show that the oligos containing as few as two 5-mCs can still be captured and oligos with four or more 5-mCs can be fully captured by the antibody. (epigentek.com)
  • Results show Epigentek's 5-mC antibody has the highest sensitivity and specificity in capturing methylated DNA fragments. (epigentek.com)
  • 5-mC is considered the "fifth" DNA base and this 5-methylcytosine mouse monoclonal antibody is ideal for discriminating between the unmodified cytosine base (C) and the methylated cytosine base (5-mC) for DNA methylation studies. (epigentek.com)
  • Mouse monoclonal antibody to 5-methylcytosine (5-mC), clone 33D3, MeDIP/ChIP-grade, used in DNA methylation studies. (epigentek.com)
  • The mouse Anti-5-Methylcytosine monoclonal antibody (clone 10G4) has been developed to facilitate differentiation between methylated and non-methylated cytosines in DNA. (thomassci.com)
  • For enrichment of methylated DNA fragments containing 5-methylcytosine, Active Motif offers the antibody-based MeDIP Assay in which an antibody specific for 5-methylcytosine is used to bind and immunoprecipitate methylated DNA fragments. (activemotif.com)
  • An alternative non-antibody-based method for enrichment that uses methyl-CpG binding proteins (MBD) to specifically bind DNA fragments containing 5-methylcytosine within a CpG dinucleotide. (activemotif.com)
Dioxygenase4
  • Hydroquinone increases 5-hydroxymethylcytosine formation through ten eleven translocation 1 (TET1) 5-methylcytosine dioxygenase. (kennedykrieger.org)
  • This work demonstrates that hydroquinone exposure leads to active and functional DNA demethylation in HEK293 cells in a mechanism involving reactive oxygen species and Ten Eleven Translocation 1 5-methylcytosine dioxygenase. (kennedykrieger.org)
  • Tet methylcytosine dioxygenase 3 is a protein that in humans is encoded by the TET3 gene. (wikipedia.org)
  • In this article, we demonstrate that the methylcytosine dioxygenase ten-eleven translocation (TET)2 regulates CD8 + T cell differentiation. (jimmunol.org)
Cytosines4
  • All DNA standards have the same sequence (see protocol for sequence), the only difference being that each standard contains either 100% unmodified cytosines, 5-methylcytosines, or 5-hydroxymethylcytosines. (zymoresearch.com)
  • 1 Up to 4% of the cytosines in DNA are 5-methylcytosine (m 5 C). 2 The ionization potential of m 5 C is comparable to that of guanine and m 5 C may compete with guanine as a hole trap. (radioprotection.org)
  • 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) are modified cytosines found in mammals that are involved in the regulation of gene expression . (bvsalud.org)
  • Bisulfite conversion is a process in which genomic DNA is treated with sodium bisulfite, leading to deamination of unmethylated cytosines into uracils, while methylated cytosines (both 5-methylcytosine and 5-hydroxymethylcytosine) are protected from deamination and remain unchanged. (activemotif.com)
Abstract1
  • Abstract-The nucleobase 5‐methylcytosine (I) is a minor component of eukaryotic DNA thought to be important in regulation of gene expression. (edu.pl)
Genomic4
  • 5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable elements. (nih.gov)
  • Addition of glucose to 5-hydroxymethylcytosine (to create β-glucosyl-5-hydroxymethylcytosine) in mammalian or plant genomic DNA. (clontech.com)
  • Since 5-methylcytosine (5mC) is an important epigenetic marker in mammalian genomic DNA, these enzymes should enable many creative experiments, e.g., direct sequencing of the epigenome, because they functionalize the chemically inert 5mC. (grantome.com)
  • For researchers interested in assaying global DNA methylation, Active Motif's Global DNA Methylation Assay - LINE-1 is a convenient ELISA-based assay for the detection and quantification of global 5-mC levels in human genomic DNA. (activemotif.com)
Oxidize the 5-methyl group1
  • TET1, TET2, and TET3 each oxidize the 5-methyl group of 5-methylcytosine (5-mC) in DNA using molecular oxygen and 2-oxoglutarate as substrates and Fe(II) as a cofactor to yield 5-hydroxymethylcytosine (5-hmC), carbon dioxide, and succinate (Tahiliani et al. (reactome.org)
Methyltransferases6
  • Nucleobase 5-methylcytosine (5-mC), a modified form of cytosine converted by cytosine methyltransferases, is widespread both in DNA and different cellular RNAs. (abcam.com)
  • DNA methylation occurs by the covalent addition of a methyl group at the 5-carbon of the cytosine ring by DNA methyltransferases, resulting in 5-methylcytosine (5-mC). (abcam.com)
  • Me C is produced via enzymatic methylation of the C-5 position of cytosine by DNA-methyltransferases (DNMT) which use S -adenosylmethionine (SAM) as a cofactor. (rsc.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)
  • Thus the physiology of 5-azaC treated cells is not identical to cells lacking cytosine DNA methyltransferases. (livingseas.org)
  • Until recently, the only known modified base in DNA was 5-methylcytosine (5mC), an epigenetic mark established by the DNA methyltransferases (DNMTs) DNMT1, DNMT3a, and DNMT3b ( 1 ) (Figure 1 ). (frontiersin.org)
TET13
  • Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. (springer.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)
  • TET1,TET2, and TET3 are involved in establishing the increased level of 5-hmC that is characteristic of adult neurons (Guo et al. (reactome.org)
Methyltransferase4
  • We examined the relationship among 5-MeC levels, DNA (cytosine-5)-methyltransferase 1 (DNMT1) immunostaining levels, and clinicopathologic features. (mdpi.com)
  • We further demonstrated that an RNA (cytosine-5)-methyltransferase, tRNA-specific methyltransferase 4B (TRM4B), exhibits m 5 C RNA methyltransferase activity. (diagenode.com)
  • K-12 strains the only known cytosine-5 Ursolic acid DNA methyltransferase is DNA cytosine methyltransferase (Dcm) [3 4 Dcm methylates the second cytosine in 5′CCWGG3′ sequences [3]. (livingseas.org)
  • Researchers interested in studying the DNA methyltransferase enzymes, DNMT1, DNMT3a and DNMT3b, that are responsible for transferring the methyl group to the fifth carbon of cytosine to produce 5-methylcytosine should use the DNMT Activity / Inhibition Assay . (activemotif.com)
Enzymes3
  • The function of this chemical varies significantly among species: In bacteria, 5-methylcytosine can be found at a variety of sites, and is often used as a marker to protect DNA from being cut by native methylation-sensitive restriction enzymes. (wikipedia.org)
  • Both enzymes cut DNA at Dcm recognition sites (5′CCWGG3′) but PspGI is blocked by Dcm-mediated methylation of the second cytosine. (livingseas.org)
  • However, research has shown that the Tet family of cytosine oxygenase enzymes are involved in oxidizing 5-methylcytosine into 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). (activemotif.com)
Modification13
  • Methylation of cytosine at carbon 5 of the pyrimidine ring [5-methylcytosine (5-meC)] is an epigenetic modification that guides formation of transcriptionally silent chromatin and allows transmission of specific patterns of gene activity across cellular divisions ( 1 , 2 ). (pnas.org)
  • The biological importance of DNA 5-mC methylation as a major epigenetic modification in phenotype and gene expression has been widely recognized. (abcam.com)
  • The biological importance of 5-mC as a major epigenetic modification in phenotype and gene expression has been recognized widely. (abcam.com)
  • 5-Methylcytosine ( Me C) is an endogenous modification of DNA that plays a crucial role in DNA-protein interactions, chromatin structure, epigenetic regulation, and DNA repair. (rsc.org)
  • The post-transcriptional modification 5-methylcytosine (m 5 C) occurs in a wide range of coding and non-coding RNAs. (biomedcentral.com)
  • 5-hydroxymethylcytosine (5-hmC) is an epigenetic modification (methylated cytosine) that is thought to be a derivative of 5-methylcytosine (5-mC). (clontech.com)
  • 5-Methylcytosine (m 5 C) is a well-characterized DNA modification, and is also predominantly reported in abundant non-coding RNAs in both prokaryotes and eukaryotes. (diagenode.com)
  • LC-MS/MS and dot blot analyses reveal a dynamic pattern of m 5 C mRNA modification in various tissues and at different developmental stages. (diagenode.com)
  • Our results suggest that m 5 C in mRNA is a new epitranscriptome marker inArabidopsis, and that regulation of this modification is an integral part of gene regulatory networks underlying plant development. (diagenode.com)
  • Post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m 5 C) is an important modification that regulates RNA metabolism and occurs in both eukaryotes and prokaryotes. (beds.ac.uk)
  • 5-methylcytosine (m 5 C) is a modification that occurs both on DNA and RNA. (beds.ac.uk)
  • [6] [7] Depending on the sequencing technique, a particular modification, e.g., the 5mC ( 5 methyl cytosine ) common in humans, may or may not be detected. (wikipedia.org)
  • Historically, 5-methylcytosine (5mC) is considered as a highly stable chemical modification that is mainly required for long-term epigenetic memory. (upenn.edu)
Deamination of cytosine1
  • In addition, active enzymatic deamination of cytosine or 5-methylcytosine by the APOBEC family of cytosine deaminases could have beneficial implications on various cellular processes as well as on organismal evolution. (wikipedia.org)
Residues4
  • 5-methylcytosine is resistant to deamination by bisulfite treatment, which deaminates cytosine residues. (wikipedia.org)
  • Direct removal of the methyl group from 5-meC residues has been claimed ( 11 ), but this mechanism, which involves a thermodynamically unfavorable breakage of the carbon-carbon bond, has been questioned ( 12 ) and could not be independently reproduced ( 13 , 14 ). (pnas.org)
  • These results attest to a specific mismatch repair pathway that restores G/C pairs lost through deamination of 5-methylcytosine residues. (uzh.ch)
  • The most characteristic epigenetic change is the DNA methylation that consists of transferring a methyl group from methyl donors to cytosine residues from CpG islands in 5′ positions [ 2 ]. (hindawi.com)
Monoclonal1
  • 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)
Uracil1
  • Supplementary Figure 5 - Uracil-DNA glycosylase (UDG) hydrolysis assay. (aacrjournals.org)
Translocation2
  • Hydroquinone also caused an increase in Ten Eleven Translocation 1 activity and global levels of 5-hydroxymethylcytosine. (kennedykrieger.org)
  • Ten Eleven Translocation-1 knockdown decreased 5-hydroxymethylcytosine formation following hydroquinone exposure as well as the induction of glutamate-cysteine ligase catalytic subunit and 14-3-3σ. (kennedykrieger.org)
Epigenetics1
  • 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)
Proteins1
  • Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. (springer.com)
Dinucleotide3
  • In somatic cells, 5-mC is found almost exclusively in the context of paired symmetrical methylation of the dinucleotide CpG, whereas in embryonic stem (ES) cells, a substantial amount of 5-mC is also observed in non-CpG contexts. (abcam.com)
  • 5-methylcytosine (5mC) is a minor base in mammalian DNA: It constitutes ~1% of all DNA bases and is found almost exclusively as symmetrical methylation of the dinucleotide CpG ( 1 ). (sciencemag.org)
  • In higher eukaryotes, DNA can be methylated at cytosine mainly in the context of CpG dinucleotide sequences, producing 5-methylcytosine (5mC), the accumulation of which at promoter regions is often associated with the repressive state of gene loci as well as its stable maintenance, known as gene silencing. (wiley.com)
Bisulfite2
  • 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)
  • 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)
Global DNA methylation3
  • Global DNA Methylation Assay Kit (5 Methyl Cytosine, Colorimetric) (ab233486) contains all reagents necessary for the quantification of global DNA methylation. (abcam.com)
  • 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)
  • The 96-well assay utilizes a unique hybridization approach that quantitates 5-mC levels of Long Interspersed Nucleotide Element 1 (LINE-1) repeats as a surrogate measure for global DNA methylation. (activemotif.com)
TET23
  • Recent exome sequencing in patients with AITL has revealed the frequent coexistence of somatic mutations in the Rho GTPase RhoA (RhoAG17V) and loss-of-function mutations in the 5-methylcytosine oxidase TET2. (jci.org)
  • Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX. (springer.com)
  • 2013). The crystal structure of TET2 indicates that it binds specifically to 5-mC in CG dinucleotides and flips the base out of the helix into proximity of the catalytic Fe(II) where it is oxidized (Hu et al. (reactome.org)
Position of cytosine1
  • Traditional DNA methylation involves the transfer of a methyl group to the carbon 5 position of cytosine to produce 5-methylcytosine (5-mC). (activemotif.com)
Eukaryotes3
  • In eukaryotes, DNA methylation is detected in protists, fungi, plants, and animals ( 3 ) and plays important roles in the establishment of developmental programs ( 4 , 5 ) and in genome defense against parasitic mobile elements ( 6 ). (pnas.org)
  • Although 5-azaC has been routinely used to demethylate DNA in a variety of eukaryotes to assess the consequences of cytosine DNA methylation loss [25 26 this is the first report Ursolic acid of the response of the entire transcriptome to 5-azaC in a bacterial organism. (livingseas.org)
  • In higher eukaryotes, 5-methylcytosine controls many cellular phenomena by preventing DNA transcription. (britannica.com)
Arabidopsis4
  • 5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and DML3. (nih.gov)
  • Here, we report transcriptome-wide profiling of RNA m 5 C in Arabidopsis thaliana by applying m 5 C RNA immunoprecipitation followed by a deep-sequencing approach (m 5 C-RIP-seq). (diagenode.com)
  • Using the plant model Arabidopsis thaliana , we identified a total of 39 highly methylated m 5 C sites in predicted structural positions of nuclear tRNAs and 7 m 5 C sites in rRNAs from nuclear, chloroplast and mitochondrial transcriptomes. (beds.ac.uk)
  • Here we characterize 5 members of the RNA 5-methylcytosine family in Arabidopsis and extend the functional characterization of TRDMT1 and NOP2A/OLI2. (beds.ac.uk)
Colorimetric1
  • 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)
Sequences3
  • 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. (wikipedia.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)
Occurs1
  • 5-mC generally occurs on cytosine bases that are followed by guanines, which are referred to as "CpGs", although non-CpG methylation has been identified in embryonic stem cells 2 . (activemotif.com)
Reagents2
  • It is suggested that urinary 5-mC might be applicable as a biological marker for detecting some types of cancer and monitoring cancer progression after treatment with radiation or demethylation reagents. (abcam.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)
DNMT1
  • A base in the DNMT enzyme deprotonates the residual hydrogen on carbon 5 restoring the double bond between carbon 5 and 6 in the ring, producing the 5-methylcytosine base pair. (wikipedia.org)
Mammalian cells1
  • In mammalian cells, clusters of CpG at the 5' ends of genes are termed CpG islands. (wikipedia.org)
Recognition1
  • Recent data strongly suggests that RNA 5-mC methylation is also involved in the regulation of various biological processes including tRNA stability/recognition and mRNA translation. (abcam.com)
Methyl Cytosine1
  • Semiclassical Dynamics Simulation and CASSCF Calculation for 5-Methyl Cytosine and Cytosine[J].Acta Phys. (pku.edu.cn)
Assay2
  • 5-mC standard was added into the assay wells at different concentrations and then measured with ab156903. (abcam.com)
  • The assay is ideally suited for screening relative changes in 5-mC levels across multiple samples resulting from variables such as treatment conditions, patient history and clinical prognosis. (activemotif.com)
Dioxygenases1
  • α-Hydroxyglutaric acid is a competitive inhibitor of multiple α-ketoglutarate-dependent dioxygenases, including histone demethylases and the TET family of 5 -methlycytosine ( 5 mC) hydroxylases . (medchemexpress.com)
Regulation4
  • 5-Methyl-2'-deoxycytosine, the most common epigenetic marker of DNA in eukaryotic cells, plays a key role in gene regulation and affects various cellular processes such as development and carcinogenesis. (uni-konstanz.de)
  • The occurrence of 5-methyl-2'-deoxycytosine (5mC) as well as the distribution pattern of this epigenetic marker were shown to be crucial for gene regulation and can serve as important biomarkers for diagnostics. (uni-konstanz.de)
  • In addition we have identified new targets of 5-methylcytosine-mediated regulation of gene expression. (livingseas.org)
  • For the first time , the levels of 5-mC and 5-hmC in Bos taurus indicus were characterized, which may contribute to our understanding of the mechanisms of epigenetic regulation in the placenta . (bvsalud.org)
Transcriptome-wide2
  • We describe transcriptome-wide approaches to capture the global m 5 C RNA methylome. (biomedcentral.com)
  • Yet, to date, no transcriptome-wide identification of m 5 C sites has been undertaken in plants. (beds.ac.uk)
Restriction enzyme2
  • Detection of 5-hydroxymethylcytosine when coupled with digestion with a restriction enzyme that is sensitive to β-glucosyl-5-hydroxymethylcytosine. (clontech.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 [10]. (livingseas.org)
Quantification2
  • 5-mC and 5-hmC levels were determined using MethylFlash Methylated/Hydroxymethylated DNA Quantification Kit, respectively. (bvsalud.org)
  • Os níveis de 5-mC e 5-hmC foram determinados usando os kits MethylFlash Methylated/Hydroxymethylated DNA Quantification, respectivamente. (bvsalud.org)
Stability3
  • 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)
  • However, epigenetic changes through chromatin remodeling are also important to the stability of the differentiated phenotype ( 5 ). (jimmunol.org)
  • DNA cytosine methylation (5-methylcytosine) is an evolutionarily conserved epigenetic mark and has a profound impact on transcription, development and genome stability. (upenn.edu)
Quantitation1
  • Control DNA for 5-methylcytosine and 5-hydroxymethylcytosine quantitation applications (ex. (zymoresearch.com)
Demethylation2
  • These findings suggest that a function of ROS1 and DME is to initiate erasure of 5-meC through a base excision repair process and provide strong biochemical evidence for the existence of an active DNA demethylation pathway in plants. (pnas.org)
  • However, they have been shown to have a very weak activity on 5-meC·G pairs compared with their activities toward U·G and T·G mismatches ( 18 , 20 , 21 ), and hence their roles in DNA demethylation remain unclear. (pnas.org)
Embryonic1
  • A few novel modified nucleotides, 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5carboxycytosine (5-caC), have been detected in human and mouse tissues as well as embryonic stem cells. (abcam.com)
Hypomethylation2
  • For example, global decrease in 5-mC content (DNA hypomethylation) is likely caused by methyldeficiency due to a variety of environmental influences, and has been proposed as a molecular marker in multiple biological processes such as cancer. (abcam.com)
  • DNA hypomethylation (decreased 5-methylcytosine, 5-mC) was observed in pediatric HGG by multiple studies ( 13, 18-22 ). (aacrjournals.org)
Base6
  • 5-Methylcytosine is a methylated form of the DNA base cytosine (C) that regulates gene transcription and takes several other biological roles. (wikipedia.org)
  • Another proposed mechanism is disruption of the labile N -glycosidic bond between the 5-meC base and the deoxyribose moiety in DNA, followed by replacement with an unmodified cytosine. (pnas.org)
  • Like 5-methylcytosine, base J has an association with gene silencing: It is present in silenced copies of the genes encoding the variable surface glycoprotein (VSG) responsible for antigenic variation in the host but is absent from the single expressed copy ( 6 ). (sciencemag.org)
  • Modified base 5-methylcytosine (5-mC), a broad range of species. (epigentek.com)
  • A presença de 5-hmC em tecidos somáticos sugerem que essa base pode ter sua própria função biológica, sendo não somente um sub-produto da oxidação da 5-mC. (bvsalud.org)
  • 5-methylcytosine was the first DNA methylation variant discovered and is the most abundant modified DNA base - it is also the most widely studied form of DNA methylation. (activemotif.com)
Oxidative1
  • The gradual loss of homeostatic mechanisms associated with ageing is hypothetically due to an accumulation of molecular oxidative damage [ 5 - 7 ]. (mdpi.com)
Tumorigenesis2
  • DNA methylation patterns are highly dysregulated in cancer: Changes in methylation status have been postulated to inactivate tumor suppressors and activate oncogenes, thus contributing to tumorigenesis ( 5 ). (sciencemag.org)
  • Genome-wide reduction in 5-methylcytosine is an epigenetic hallmark of human tumorigenesis. (aacrjournals.org)
Hydrochloride1
  • Single crystals of 5-methylcytosine hemihydrate and 5-methylcytosine hydrochloride have been X-irradiated at 8-10 K and studied at this and elevated temperatures using EPR, ENDOR, and EIE spectroscopy in addition to single molecule- and cluster DFT calculations at the B3LYP level. (radioprotection.org)
Gene expression5
  • Methylation of cytosine to 5-methylcytosine (5mC) is important for gene expression, gene imprinting, X-chromosome inactivation, and transposon silencing. (nih.gov)
  • In summary our data indicate that 5-azacytidine impacts the composition of the bacterial transcriptome and the primary effect is increased gene expression at early stationary phase. (livingseas.org)
  • Based on the important role of 5-MeC in eukaryotic transcription and the fact that there is little known about the relationship between 5-MeC and gene expression in bacteria Dcm has been recently evaluated for an impact on the composition of the transcriptome. (livingseas.org)
  • As the only known function of Dcm is cytosine DNA methylation the simplest model is that Dcm mediates gene expression changes via the generation of 5-MeC. (livingseas.org)
  • In order to test the model that Dcm-mediated cytosine DNA methylation directly influences gene expression in and identify new genes impacted by DNA methylation we analyzed the transcriptome in the absence and presence of 5-azacytidine (5-azaC)?treatment. (livingseas.org)
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Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a | PNAS (pnas.org)
Epigenetic differences arise during the lifetime of monozygotic twins | PNAS
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Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1 | Science
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