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5-Formylcytosine
5-Formylcytosine (5fC) is a pyrimidine nitrogen base derived from cytosine. In the context of nucleic acid chemistry and biology, it is regarded as an epigenetic marker. Discovered in 2011 in mammalian embryonic stem cells by Thomas Carell's research group the modified nucleoside was more recently confirmed to be relevant both as an intermediate in the active demethylation pathway and as a standalone epigenetic marker. In mammals, 5fC is formed by oxidation of 5-hydroxymethylcytosine (5hmC) a reaction mediated by TET enzymes. Its molecular formula is C5H5N3O2. Localization Similarly to the related cytosine modifications 5-methylcytosine (5mC) and 5hmC, 5fC is broadly distributed across the mammalian genome, although it is much more rarely occurring. The specific concentration values vary significantly depending on the cell type. 5fC can be aberrantly expressed in distinct sets of tissue that can indicate different tumor onsets and canceration. Functions The exact functions o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
5-methylcytosine
5-Methylcytosine (5mC) is a methylation, methylated form of the DNA base cytosine (C) that regulates gene Transcription (genetics), transcription and takes several other biological roles. When cytosine is methylated, the DNA maintains the same sequence, but the Gene expression#DNA methylation and demethylation in transcriptional regulation, expression of methylated genes can be altered (the study of this is part of the field of epigenetics). 5-Methylcytosine is incorporated in the nucleoside 5-Methylcytidine, 5-methylcytidine. Discovery While trying to isolate the bacterial toxin responsible for tuberculosis, W.G. Ruppel isolated a novel nucleic acid named tuberculinic acid in 1898 from ''Mycobacterium tuberculosis, Tubercle bacillus''. The nucleic acid was found to be unusual, in that it contained in addition to thymine, guanine and cytosine, a methylated nucleotide. In 1925, Treat Baldwin Johnson, Johnson and Coghill successfully detected a minor amount of a methylated cytosi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
5-hydroxymethylcytosine
5-Hydroxymethylcytosine (5hmC) is a DNA pyrimidine nitrogen base derived from cytosine. It is potentially important in epigenetics, because the hydroxymethyl group on the cytosine can possibly switch a gene on and off. It was first seen in bacteriophages in 1952. However, in 2009 it was found to be abundant in human and mouse brains, as well as in embryonic stem cells. In mammals, it can be generated by oxidation of 5-methylcytosine, a reaction mediated by TET enzymes. Localization Every mammalian cell seems to contain 5-Hydroxymethylcytosine, but the levels vary significantly depending on the cell type. The highest levels are found in neuronal cells of the central nervous system. The amount of hydroxymethylcytosine increases with age, as shown in mouse hippocampus and cerebellum. Function The exact function of this nitrogen base is still not fully elucidated, but it is thought that it may regulate gene expression or prompt DNA demethylation. This hypothesis is supported by th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
5-Methylcytosine
5-Methylcytosine (5mC) is a methylation, methylated form of the DNA base cytosine (C) that regulates gene Transcription (genetics), transcription and takes several other biological roles. When cytosine is methylated, the DNA maintains the same sequence, but the Gene expression#DNA methylation and demethylation in transcriptional regulation, expression of methylated genes can be altered (the study of this is part of the field of epigenetics). 5-Methylcytosine is incorporated in the nucleoside 5-Methylcytidine, 5-methylcytidine. Discovery While trying to isolate the bacterial toxin responsible for tuberculosis, W.G. Ruppel isolated a novel nucleic acid named tuberculinic acid in 1898 from ''Mycobacterium tuberculosis, Tubercle bacillus''. The nucleic acid was found to be unusual, in that it contained in addition to thymine, guanine and cytosine, a methylated nucleotide. In 1925, Treat Baldwin Johnson, Johnson and Coghill successfully detected a minor amount of a methylated cytosi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
5-Hydroxymethylcytosine
5-Hydroxymethylcytosine (5hmC) is a DNA pyrimidine nitrogen base derived from cytosine. It is potentially important in epigenetics, because the hydroxymethyl group on the cytosine can possibly switch a gene on and off. It was first seen in bacteriophages in 1952. However, in 2009 it was found to be abundant in human and mouse brains, as well as in embryonic stem cells. In mammals, it can be generated by oxidation of 5-methylcytosine, a reaction mediated by TET enzymes. Localization Every mammalian cell seems to contain 5-Hydroxymethylcytosine, but the levels vary significantly depending on the cell type. The highest levels are found in neuronal cells of the central nervous system. The amount of hydroxymethylcytosine increases with age, as shown in mouse hippocampus and cerebellum. Function The exact function of this nitrogen base is still not fully elucidated, but it is thought that it may regulate gene expression or prompt DNA demethylation. This hypothesis is supported by th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pyrimidine
Pyrimidine (; ) is an aromatic, heterocyclic, organic compound similar to pyridine (). One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has nitrogen atoms at positions 1 and 3 in the ring. The other diazines are pyrazine (nitrogen atoms at the 1 and 4 positions) and pyridazine (nitrogen atoms at the 1 and 2 positions). In nucleic acids, three types of nucleobases are pyrimidine derivatives: cytosine (C), thymine (T), and uracil (U). Occurrence and history The pyrimidine ring system has wide occurrence in nature as substituted and ring fused compounds and derivatives, including the nucleotides cytosine, thymine and uracil, thiamine (vitamin B1) and alloxan. It is also found in many synthetic compounds such as barbiturates and the HIV drug zidovudine. Although pyrimidine derivatives such as alloxan were known in the early 19th century, a laboratory synthesis of a pyrimidine was not carried out until 1879, when Grimaux repor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nitrogen Base
Nucleotide bases (also nucleobases, nitrogenous bases) are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called ''primary'' or ''canonical''. They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings. In addition, some viruses have aminoadenine (Z) instead of adenine. It differs in having an extra amine group, crea ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cytosine
Cytosine () (symbol C or Cyt) is one of the four nucleotide bases found in DNA and RNA, along with adenine, guanine, and thymine ( uracil in RNA). It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). The nucleoside of cytosine is cytidine. In Watson–Crick base pairing, it forms three hydrogen bonds with guanine. History Cytosine was discovered and named by Albrecht Kossel and Albert Neumann in 1894 when it was hydrolyzed from calf thymus tissues. A structure was proposed in 1903, and was synthesized (and thus confirmed) in the laboratory in the same year. In 1998, cytosine was used in an early demonstration of quantum information processing when Oxford University researchers implemented the Deutsch–Jozsa algorithm on a two qubit nuclear magnetic resonance quantum computer (NMRQC). In March 2015, NASA scientists reported the formation of cytosine, alon ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thomas Carell
Thomas Carell (born 1966) is a German biochemist. Early life and education Carell was born in 1966 in Herford Germany, he studied chemistry from 1985 till 1990 at the University of Münster finishing with a diploma thesis at the Max Planck Institute for Medical Research Heidelberg. After his PhD thesis on Porphyrin chemistry at the same institute, he did his postdoctoral at the Massachusetts Institute of Technology in 1993. He finished his habilitation on DNA repair proteins at the ETH Zurich, Eidgenössischen Technischen Hochschule Zürich in 1998. Career From 2000 till 2004 he was Professor for organic chemistry at the University of Marburg until he became Professor for organic chemistry at the Ludwig Maximilian University of Munich. His main interest is still the DNA repair system. Awards and honors In 2004, he received the Gottfried Wilhelm Leibniz Prize of the Deutsche Forschungsgemeinschaft, which is the highest honour awarded in Germany, German research. In 2008, h ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TET Enzymes
The TET enzymes are a family of ten-eleven translocation (TET) 5-Methylcytosine, methylcytosine dioxygenases. They are instrumental in DNA demethylation. 5-Methylcytosine (see first Figure) is a methylation, methylated form of the DNA base cytosine (C) that often regulates gene Transcription (genetics), transcription and has several other functions in the genome. Demethylation by TET enzymes (see second Figure), can alter the regulation of transcription. The TET enzymes catalyze the hydroxylation of DNA 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and can further catalyse oxidation of 5hmC to 5-formylcytosine (5fC) and then to 5-carboxycytosine (5caC). 5fC and 5caC can be removed from the DNA base sequence by base excision repair and replaced by cytosine in the base sequence. TET enzymes have central roles in DNA demethylation required during embryogenesis, gametogenesis, Epigenetics in learning and memory, memory, learning, addiction and Nociception, pain pe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Demethylation
Demethylation is the chemical process resulting in the removal of a methyl group (CH3) from a molecule. A common way of demethylation is the replacement of a methyl group by a hydrogen atom, resulting in a net loss of one carbon and two hydrogen atoms. The counterpart of demethylation is methylation. In biochemistry : Demethylation is relevant to epigenetics. Demethylation of DNA is catalyst, catalyzed by demethylases. These enzymes oxidize N-methyl groups, which occur in histones, in lysine derivatives, and in some forms of DNA. :R2N-CH3 + O → R2N-H + CH2O One family of such oxidative enzymes is the cytochrome P450. Alpha-ketoglutarate-dependent hydroxylases are also active for demethylation of DNA, operating by a similar stoichiometry. These reactions, which proceed via hydroxylation, exploit the slightly weakened Carbon–hydrogen bond, C-H bonds of methylamines and methyl ethers. Demethylation of some sterols are steps in the biosynthesis of testosterone and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thymine-DNA Glycosylase
G/T mismatch-specific thymine DNA glycosylase is an enzyme that in humans is encoded by the TDG gene. Several bacterial proteins have strong sequence homology with this protein. Function The protein encoded by this gene belongs to the TDG/mug DNA glycosylase family. Thymine-DNA glycosylase (TDG) removes thymine moieties from G/T mismatches by hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of DNA and the mispaired thymine. With lower activity, this enzyme also removes thymine from C/T and T/T mispairings. TDG can also remove uracil and 5-bromouracil from mispairings with guanine. TDG knockout mouse models showed no increase in mispairing frequency suggesting that other enzymes, like the functional homologue MBD4, may provide functional redundancy. This gene may have a pseudogene in the p arm of chromosome 12. Additionally, in 2011, the human thymine DNA glycosylase (hTDG) was reported to efficiently excise 5-formylcytosine (5fC) and 5-carboxylcytosin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Base Excision Repair
Base excision repair (BER) is a cellular mechanism, studied in the fields of biochemistry and genetics, that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from the genome. The related nucleotide excision repair pathway repairs bulky helix-distorting lesions. BER is important for removing damaged bases that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication. BER is initiated by DNA glycosylases, which recognize and remove specific damaged or inappropriate bases, forming AP sites. These are then cleaved by an AP endonuclease. The resulting single-strand break can then be processed by either short-patch (where a single nucleotide is replaced) or long-patch BER (where 2–10 new nucleotides are synthesized). Lesions processed by BER Single bases in DNA can be chemically damaged by a variety of mechanisms, the most common ones being deamination, oxidation, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
