5-Methylcytosine
DNA Methylation
Thymine DNA Glycosylase
Methylation
DNA (Cytosine-5-)-Methyltransferase
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
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.
Pentoxyl
Dioxygenases
N-Glycosyl Hydrolases
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
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
Oligodeoxyribonucleotides
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
Nanopores
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
Azacitidine
Deoxyribonuclease (Pyrimidine Dimer)
Epigenomics
Endodeoxyribonucleases
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.
Deoxyribonuclease HpaII
Substrate Specificity
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
Cytidine
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).
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
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.
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 Text
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...
Frontiers | TET Methylcytosine Oxidases in T Cell and B Cell Development and Function | Immunology
5-MethylCytosine ELISA Kits: Novus Biologicals
Plus it
Active DNA demethylation in mammals. (a) The action of | Open-i
Most recent papers with the keyword 5 hydroxymethylcytosine | Read by QxMD
10th Transcription and Chromatin 2012
SNU Open Repository and Archive: Cellular response against expression of Arabidopsis DEMETER DNA demethylase in animal cells
RCSB PDB - 5L2G: Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th Position
DNA Demethylation in Development: 5mC, 5hmC, 5fC, 5caC and TET Proteins
Can 5-methylcytosine analogues with extended alkyl side chains guide DNA methylation? - Chemical Communications (RSC Publishing)
5-Methylcytosine RNA Methylation in Arabidopsis Thaliana
Structural insights into how 5-hydroxymethylation influences transcription factor binding - Chemical Communications (RSC...
Dealing with an Unconventional Genetic Code in Mitochondria: The Biogenesis and Pathogenic Defects of the 5‐Formylcytosine...
SALL4A Regulates DNA Demethylation at Enhancers----Institute of Biophysics Chinese Academy of Sciences
Methyl-DNA Binding Protein ChIP | EpiGentek
Plus it
The upper graph shows methylation position in colduntreated and handled Col-, and the lower graph shows colduntreated and...
5-hydroxymethylcytosine
Volume 4.25 | Jun 28 - Human Immunology News
RNA processing in Drosophila development
- Rutgers, The State University of New Jersey
Supplementary MaterialsadvancesADV2020001535-suppl1 | BX-795 inhibits HSV-1 and HSV-2 replication
AMG 900 | Role of NK1 and NK2 receptors in mouse gastric mechanical activity
Plus it
TET1P1 (human) | Gene Target - PubChem
Difference between revisions of E. coli genotypes - OpenWetWare
Difference between revisions of E. coli genotypes - OpenWetWare
Sci. Pharm. | Free Full-Text | Interaction of β-Cyclodextrin with DNA-Bases
Mutagenetix > Incidental...
Center For Life Sciences
Hydroxymethyl Collector (5-hmc, 5-hydroxymethylcytosine, hydroxymethylation enrichment kit)
Bioorthogonal labeling of 5-hydroxymethylcytosine in genomic DNA and diazirine-based DNA photo-cross-linking probes. - NDM...
Bisulfite sequencing - Wikipedia
cAMP signaling regulates DNA hydroxymethylation by augmenting the intracellular labile ferrous iron pool. - Helen Wills...
Early steps of active DNA demethylation initiated by ROS1 glycosylase require three putative helix-invading residues
DNA methylation in mycobacteria: Absence of methylation at GATC (Dam) and CCA/TGG (Dcm) sequences - [email protected]
Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. - NDM Research Building
Mechanisms of DNA Methyltransferases (DNMTs) and DNA Demethylases | EpiGentek
GSE79882 - Genome-wide map of DNA 5-Hydroxymethylcytosine in cardiomyocytes isolated from E14.5, Neonatal, Adult, pressure...
ENGINEERED DEMETER 5-METHYLCYTOSINE DNA GLYOSYLASE WITH IMPROVED YIELD, STABILITY AND SOLUBILITY - Patent application
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...
Data Availability StatementNot applicable - CYP17 inhibitors in prostate cancer
5-hmC (5-Hydroxymethylcytosine) (CAS 1123-95-1) (ab146141) |Abcam
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain | Genome Biology | Full Text
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain | Genome Biology | Full Text
ZFIN Publication: Yang et al., 2016
The potential influence of breast cancer estrogen receptors distribution on active DNA demethylation
IJMS | Free Full-Text | Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl...
5-Hydroxymethylcytosine in Neurodevelopment - Peng Jin
About DNA Methylation
Re often not methylated (5mC) but hydroxymethylated (5hmC) [80]. However, bisulfite-based methods - http://amparinhibitor.com
Selective Capture of 5-hydroxymethylcytosine from Genomic DNA | Protocol (Translated to Turkish)
Anti-5-Hydroxymethylcytosine Polyclonal Antibody
5-hydroxymethylcytosine in human cancer - Gerd Pfeifer
Selective Capture of 5-hydroxymethylcytosine from Genomic DNA | Protocol (Translated to Chinese)
Anti-Methylcytosine dioxygenase TET1 Antibody | 09-872
Anti-5-Hydroxymethylcytosine [AB3/63.3]
Information storage and transfer
SACOL RS06105 - AureoWiki
Vitamin C Stops Cancer
Sao Paulo Fashion Week A/W 10-11 | Dazed
Mutation bias
Bibcode:2003JMolE..56..373.. doi:10.1007/s00239-002-2455-5. ISSN 0022-2844. S2CID 7971705. Sayres, Melissa A. Wilson; Venditti ... Ehrlich, M; Wang, R. (1981-06-19). "5-Methylcytosine in eukaryotic DNA". Science. 212 (4501): 1350-1357. Bibcode:1981Sci... ...
DNA 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 ...
Arthur Riggs (geneticist)
ISBN 978-3-11-014830-5. Retrieved June 2, 2015. Riggs, Arthur D.; Bourgeois, Suzanne (June 1968). "On the assay, isolation and ... 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 ...
Hydroxymethylation
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/ ...
Tuberculinic 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 ...
Epitranscriptomic 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 ...
Transcriptional regulation
49 (5): 825-37. doi:10.1016/j.molcel.2013.01.038. PMC 3857148. PMID 23473601. de Napoles M, Mermoud JE, Wakao R, Tang YA, Endoh ... 7 (5): 663-76. doi:10.1016/j.devcel.2004.10.005. PMID 15525528. Lövkvist C, Dodd IB, Sneppen K, Haerter JO (June 2016). "DNA ... The most relevant study on limb evolution shows that the TAD at the 5' of the HoxD gene cluster in tetrapod genomes drives its ... 229 (5): 538-44. doi:10.1002/jcp.24483. PMID 24122273. S2CID 44613555. Chapman RD, Conrad M, Eick D (September 2005). "Role of ...
DNA methylation
N6-methylcytosine, 5-methylcytosine, and N6-methyladenine. In: Nucleic Acids Research. 13, 1985, S. 1399. PMID 4000939. PMC ... 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 ...
Regulatory 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-methyl-CpG, or 5-mCpG). ... TET enzymes can catalyze demethylation of 5-methylcytosine. When EGR1 transcription factors bring TET1 enzymes to EGR1 binding ... predominantly on cytosines within CpG dinucleotides, which consist of a cytosine is followed by a guanine reading in the 5′ to ...
Treat Baldwin Johnson
The Discovery of 5-Methyl-Cytosine in Tuberculinic Acid, the Nucleic Acid of the Tubercle Bacillus". Journal of the American ... Together with R. D. Coghill, Johnson was the first to discover the existence of 5-methylcytosine in nature, from tuberculinic ... Wyatt, G. R. (1950). "Occurrence of 5-Methyl-Cytosine in Nucleic Acids". Nature. 166 (4214): 237-238. Bibcode:1950Natur.166.. ...
DNA
... 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 ...
Epigenetics
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 ... 128 (4): 641-5. doi:10.1016/j.cell.2007.02.007. PMID 17320501. S2CID 6928707. Zaidi, S. K.; Lian, J. B.; Vanwijnen, A. J.; ... 18 (5): 299-314. doi:10.1038/nrm.2016.166. PMID 28144029. S2CID 3307731. Jang CW, Shibata Y, Starmer J, Yee D, Magnuson T (July ...
Deamination
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 ...
DNA 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, ...
Methylation
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.{{cite journal}}: CS1 maint: uses authors parameter (link) ...
Reprogramming
The Figure in this section indicates the central roles of ten-eleven translocation methylcytosine dioxygenases (TETs) in the ... 32 (5): 645-655. doi:10.1038/emboj.2012.357. PMC 3590984. PMID 23353889. Zhou X, Zhuang Z, Wang W, He L, Wu H, Cao Y, et al. ( ... 131 (5): 861-872. doi:10.1016/j.cell.2007.11.019. PMID 18035408. S2CID 8531539. David L, Polo JM (May 2014). "Phases of ... TET2 does not have an affinity for 5-methylcytosine in DNA. The CXXC domain of the full-length TET3, which is the predominant ...
Germline
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- ...
Nucleobase
"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 ... "Some viruses thwart bacterial defenses with a unique genetic alphabet". 5 May 2021. Berg JM, Tymoczko JL, Stryer L. "Section ...
DNA 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 ...
Anjana 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 ...
NSUN2
49 (6): 380-5. doi:10.1136/jmedgenet-2011-100686. PMC 4771841. PMID 22577224. "Body weight data for Nsun2". Wellcome Trust ... v t e (Articles with short description, Short description matches Wikidata, Genes on human chromosome 5, Human proteins, Genes ... 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. ...
Epigenomics
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 ... 403 (6765): 41-5. Bibcode:2000Natur.403...41S. doi:10.1038/47412. PMID 10638745. S2CID 4418993. Sedighi M, Sengupta AM ( ... In eukaryotes, methylation is most commonly found on the carbon 5 position of cytosine residues (5mC) adjacent to guanine, ...
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 ...
Shankar Balasubramanian
6 (5): 435-40. Bibcode:2014NatCh...6..435B. doi:10.1038/nchem.1893. PMC 4188980. PMID 24755596. "Corday-Morgan Prizes". Royal ... 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 ...
Jens H. Gundlach
"Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA". Proceedings of the National Academy ...
Mutational 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 ... 5 (3): e223833. doi:10.1001/jamanetworkopen.2022.3833. PMID 35319765. Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I ... 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 ...
Whole genome bisulfite sequencing
89 (5): 1827-1831. Bibcode:1992PNAS...89.1827F. doi:10.1073/pnas.89.5.1827. ISSN 0027-8424. PMC 48546. PMID 1542678. Clark, S J ... 5 (12): 1005-1010. doi:10.1038/nmeth.1270. ISSN 1548-7105. PMC 2610436. PMID 19034268. Wang, Qi; Gu, Lei; Adey, Andrew; ... As a result, specificity between 5-methylcytosine and 5-hydroxymethylcytosine is limited. Another potential source of bias ... doi:10.1038/s41598-019-46875-5. ISSN 2045-2322. PMC 6637168. PMID 31316107. Parle-Mcdermott, Anne; Harrison, Alan (2011). "DNA ...
Bisulfite sequencing
... methylcytosine, giving a map of the true methylation status in the DNA sample. Levels of 5‑hydroxymethylcytosine can also be ... PLOS ONE.2010;5(1):e8888. Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Jin, P., Ren, B., He, C. Tet-assisted bisulfite ... 29 (13): E65-5. doi:10.1093/nar/29.13.e65. PMC 55789. PMID 11433041. Ehrich M, Zoll S, Sur S, van den Boom D (2007). "A new ... 30 (5): 21e-21. doi:10.1093/nar/30.5.e21. PMC 101257. PMID 11861926. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, ...
MBD4
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 ...
I-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 ...
Hypothetical types of biochemistry
1-Methylcytosine for DNA).[9][10]. ... 978-0-375-50832-5. .. *^ a b c d Committee on the Limits of ... 978-0-375-50832-5. .. *^ a b c Sagan, Carl; Head, Tom (2006). Conversations with Carl Sagan. University Press of Mississippi. p ... Bibcode:2005AsBio...5..154D. doi:10.1089/ast.2005.5.154. PMID 15815166.. *^ Sagan, Carl; Agel, Jerome (2000). Carl Sagan's ... Bradley, Alex (5 December 2010). "Arsenate-based DNA: a big idea with big holes". scienceblogs.com/webeasties/. Archived from ...
Transcription factor
TET enzymes do not specifically bind to methylcytosine except when recruited (see DNA demethylation). Multiple transcription ... to act on methylcytosine (mC) and convert it to hydroxymethylcytosine hmC (and in most cases marking them for subsequent ... 2007: 1-5. doi:10.1155/2007/89017. PMC 2248278. PMID 18317533.. *^ Iwakuma T, Lozano G, Flores ER (July 2005). "Li-Fraumeni ... 5 (3): 130-8. doi:10.1159/000109183. PMID 8864058.. *^ Evan G, Harrington E, Fanidi A, Land H, Amati B, Bennett M (August 1994 ...
Neurogenesis
Methylcytosine demethylation is catalyzed in several stages 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.[11] ... 8 (5): a018820. doi:10.1101/cshperspect.a018820. PMC 4852803. PMID 27048191.. *^ Alvarez-Buylla, A; Lim, DA (4 March 2004). " ... 2006). Principles of neural science (5. ed.). Appleton and Lange: McGraw Hill. ISBN 978-0071390118. .. ...
Biomarkers of aging
doi:10.1038/s41591-019-0719-5. PMC 7301912. PMID 31932806.. *^ Van Neste D, Tobin DJ (2004). "Hair cycle and hair pigmentation ... In C. elegans, the loss of any of the three Trithorax proteins that catalyze the trimethylation of H3K4 such as, WDR-5 and the ... The cytosine base is methylated and becomes 5-methylcytosine, most often when in the CpG context. Hypermethylation of CpG ...
DNA repair
5 July 2017. Retrieved 7 November 2018.. *^ a b Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, ... 33 (5): 1268-74. doi:10.3892/ijmm.2014.1682. PMID 24590400.. *^ Krause A, Combaret V, Iacono I, Lacroix B, Compagnon C, ... 978-1-4419-9966-5. . PMC 3707278. PMID 22956494.. *^ Krishnan K, Steptoe AL, Martin HC, Wani S, Nones K, Waddell N, et al. ( ... First, two kinases, ATM and ATR are activated within 5 or 6 minutes after DNA is damaged. This is followed by phosphorylation ...
Mutation
38 (5): 1116-1129. doi:10.2307/2408444. JSTOR 2408444. PMID 28555784.. *^ Orr HA (April 2003). "The distribution of fitness ... 42 (5): 399-435. doi:10.1080/10409230701648502. PMC 3319127. PMID 17917874.. *^ Quinto-Alemany D, Canerina-Amaro A, Hernández- ... 5 (1): 109. arXiv:2110.00113. Bibcode:2022CmPhy...5..109S. doi:10.1038/s42005-022-00881-8. ISSN 2399-3650. S2CID 238253421.. ... Liou S (5 February 2011). "All About Mutations". HOPES. Huntington's Disease Outreach Project for Education at Stanford. ...
Neurogenesis
Methylcytosine demethylation is catalyzed in several stages 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.[11] ... 8 (5): a018820. doi:10.1101/cshperspect.a018820. PMC 4852803. PMID 27048191.. *^ Alvarez-Buylla, A; Lim, DA (4 March 2004). " ... 2006). Principles of neural science (5. ed.). Appleton and Lange: McGraw Hill. ISBN 978-0071390118. .. ...
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, ... DNA methylation forms 5-methylcytosines at the 5' pyrimidine ring of CpG cytosine residues. Some cancer genes are silenced by ... 5 (12): 1331-1341. doi:10.1021/acssynbio.5b00223. PMID 27346626. Chauhan V, Bahrudeen MN, Palma CS, Baptista IS, Almeida BL, ... In humans, DNA methylation occurs at the 5' position of the pyrimidine ring of the cytosine residues within CpG sites to form 5 ...
Hippocampus
5. Center for Inquiry. pp. 52-56. Archived from the original on 2020-04-29. Retrieved 2020-03-20. Rubin M, Shvil E, Papini S, ... 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 ( ... Sharp waves are frequently generated in sets, with sets containing up to 5 or more individual sharp waves and lasting up to 500 ...
Very 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. Then DNA Polymerase ...
Huda 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. Kavli Prize ... 75 (5): 799-809. doi:10.1016/j.neuron.2012.06.027. ISSN 0896-6273. PMC 3464459. PMID 22958821. Flora, Adriano; Klisch, Tiemo J ... 5: e14198. doi:10.7554/eLife.14198. PMC 4946897. PMID 27328321. Rodríguez, Ana María (5 September 2019). "Ataxin-1: One gene, ...
Fragaria vesca
... an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae". Horticulture Research. Nature + ... 52 (1): 5-7. doi:10.1038/s41588-019-0544-2. ISSN 1061-4036. PMC 6960091. PMID 31844320. S2CID 209381682. "Internet Archaeol 1. ...
DNA repair
5 July 2017. Retrieved 7 November 2018. Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J ... 5 (5): 503-09. doi:10.1038/sj.embor.7400127. PMC 1299048. PMID 15105825. de Boer J, Andressoo JO, de Wit J, Huijmans J, Beems ... 26 (5): 1143-53. doi:10.1093/molbev/msp029. PMC 2668831. PMID 19228922. Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick ... 5 (3): 43-49. doi:10.4251/wjgo.v5.i3.43. PMC 3648662. PMID 23671730. Narayanan L, Fritzell JA, Baker SM, Liskay RM, Glazer PM ( ...
Chromosome 13
... encoding protein Long intergenic non-protein coding RNA 346 LOC107984557 encoding protein Methylcytosine dioxygenase TET1-like ... 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 ...
Third-generation sequencing
examined 4-methylcytosine (4mC) and 6-methyladenine (6mA), along with 5mC, and also created software to directly visualize the ... 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 ...
Tet methylcytosine dioxygenase 2
... (TET2) is a human gene. It resides at chromosome 4q24, in a region showing recurrent ... "Entrez Gene: Tet methylcytosine dioxygenase 1". Retrieved 1 September 2012. Kriaucionis S, Heintz N (May 2009). "The nuclear ... TET2 encodes a protein that catalyzes the conversion of the modified DNA base methylcytosine to 5-hydroxymethylcytosine. The ... which it then activates by converting methylcytosine into 5-hydroxymethylcytosine at the genes' promoters. Additionally, ...
5-Methylcytidine
... is a modified nucleoside derived from 5-methylcytosine. It is found in ribonucleic acids of animal, plant, and ... Dunn, D. B. (1960). "Isolation of 5-methylcytidine from ribonucleic acid". Biochimica et Biophysica Acta. 38: 176-178. doi: ...
Alkb homolog 3, alpha-ketoglutaratedependent dioxygenase
ALKBH2 (MIM 610602) and ALKBH3 are E. coli AlkB homologs that catalyze the removal of 1-methyladenine and 3-methylcytosine ( ... 69 (4): 360-5. doi:10.1016/j.biopsych.2010.08.011. PMID 20970119. S2CID 41571515. Tasaki M, Shimada K, Kimura H, Tsujikawa K, ...
List of MeSH codes (D03)
5-tetrahydro-8-chloro-3-methyl-5-phenyl-1h-3-benzazepin-7-ol MeSH D03.438.079.800 - 2,3,4,5-tetrahydro-7,8-dihydroxy-1-phenyl- ... 5-amino-3-((5-nitro-2-furyl)vinyl)-1,2,4-oxadiazole MeSH D03.383.312.649.290 - fanft MeSH D03.383.312.649.308 - furagin MeSH ... 5-amino-3-((5-nitro-2-furyl)vinyl)-1,2,4-oxadiazole MeSH D03.383.129.462.580.400 - 4-chloro-7-nitrobenzofurazan MeSH D03.383. ... 5-dihydro-1-(3-(trifluoromethyl)phenyl)-1h-pyrazol-3-amine MeSH D03.383.129.539.200 - epirizole MeSH D03.383.129.539.487 - ...
Epigenetics in stem-cell differentiation
As soon as the TSA treatment was stopped, on day 4 the deacetylation was observed and the acetylation recovered on Day-5. The ... Global levels of 5-methylcytosine were compared between undifferentiated and differentiated embryonic stem cells in vitro. The ... H3K4 trimethylation coincides with the time of highest Brachyury gene expression since it only had gene expression on day 5. ... The morphological examination of the third group,' 5 nM TSA' showed the intermediate effect between the control and 10nM-TSA ...
5-Methyluridine
... contains a thymine base joined to a ribose pentose sugar. It is a white solid. 5-Methylcytosine 3-Methyluridine ... The chemical compound 5-methyluridine (symbol m⁵U or m5U), also called ribothymidine, is a pyrimidine nucleoside. It is the ... "5-Methyluridine". ChemSpider. Retrieved December 6, 2018. William M. Haynes (2016). CRC Handbook of Chemistry and Physics (97th ...
TET enzymes
The TET enzymes are a family of ten-eleven translocation (TET) methylcytosine dioxygenases. They are instrumental in DNA ... These are a ten-eleven translocation (TET) methylcytosine dioxygenase and thymine-DNA glycosylase (TDG). One particular TET ... 5-Methylcytosine (see first Figure) is a methylated form of the DNA base cytosine (C) that often regulates gene transcription ... They used a pain inducing model of intra plantar injection of 5% formalin into the dorsal surface of the mouse hindpaw and ...
5-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 ...
iRNA-m5C NB: A Novel Predictor to Identify RNA 5-Methylcytosine Sites Based on the Naive Bayes Classifier | IEEE Journals &...
TET proteins and 5-methylcytosine oxidation in hematological cancers
Eschweiler S, Ramírez-Suástegui C, Li Y, King E, Chudley L, Thomas J, Wood O, von Witzleben A, Jeffrey D, McCann K, Simon H, Mondal M, Wang A, Dicker M, Lopez-Guadamillas E, Chou TF, Dobbs NA, Essame L, Acton G, Kelly F, Halbert G, Sacco JJ, Schache AG, Shaw R, McCaul JA, Paterson C, Davies JH, Brennan PA, Singh RP, Loadman PM, Wilson W, Hackshaw A, Seumois G, Okkenhaug K, Thomas GJ, Jones TM, Ay F, Friberg G, Kronenberg M, Vanhaesebroeck B, Vijayanand P, Ottensmeier CH. ...
5-Methylcytosine (5-mC) antibody (mAb) | MyBio Ireland
MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion
Abdulkhaleg Ibrahim # 1 2 3 4 5 6 , Christophe Papin # 1 2 3 4 5 , Kareem Mohideen-Abdul # 1 3 4 5 7 , Stéphanie Le Gras 1 3 4 ... 5 , Isabelle Stoll 1 2 3 4 5 , Christian Bronner 1 2 3 4 5 , Stefan Dimitrov 8 9 , Bruno P Klaholz 10 3 4 5 7 , Ali Hamiche 10 ... with considerably modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg133, a key residue ...
Novel insights into the role of 5-Methylcytosine RNA methylation in human abdominal aortic aneurysm
The major 5-methylcytosine modulators, including NSUN2, NSUN5, and Aly/REF, which represented the major parameters related to ... Novel insights into the role of 5-Methylcytosine RNA methylation in human abdominal aortic aneurysm. Front. Biosci. (Landmark ... m5C, 5-Methylcytosine RNA methylation; AAA, abdominal aortic aneurysm; qRT-PCR, quantitative real-time polymerase chain ... Background: It remains largely unclear about the function of 5-methylcytosine (m5C) RNA modification in the context of ...
30th anniversary collection: top articles from the past 30 years
Quantitative assessment of Tet-induced oxidation products of 5-methylcytosine in cellular and tissue DNA<...
Moreover, 5-HmdC is present at a level that is approximately 2-3 and 3-4 orders of magnitude greater than 5-FodC and 5-CadC, ... Moreover, 5-HmdC is present at a level that is approximately 2-3 and 3-4 orders of magnitude greater than 5-FodC and 5-CadC, ... Moreover, 5-HmdC is present at a level that is approximately 2-3 and 3-4 orders of magnitude greater than 5-FodC and 5-CadC, ... Moreover, 5-HmdC is present at a level that is approximately 2-3 and 3-4 orders of magnitude greater than 5-FodC and 5-CadC, ...
Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease | Nature Communications
Figure 5: Repression of genes by the polycomb mark H3K27me3.. (a,b) IGV (integrative genomics viewer) traces of CpG methylation ... a,b) Heat maps of gene expression (a) and CpG methylation (b) of gene bodies and flanking regions (±5 kbp) with differential ... 5; Supplementary Fig. 12). Demethylated genes may also be repressed by de novo methylation, which is mediated by DNMT3A/B ( ... 5). This amounted to 5% of all CpGs in the mouse genome (Fig. 1e). Ninety percent of these CpGs were hypomethylated and 10% ...
Energetic DNA demethylation in mammals involves TET-mediated oxidation of 5-methylcytosine (5mC) - A genome-wide RNAi screen...
5-hydroxymethyl tolterodine Anisomycin AZ-960 BA554C12.1 BTLA Col11a1 DKK2 Dock4 EIF4G1 Goat polyclonal to IgG H+L)HRPO) HOXA2 ... 5 and Supplementary Take note 2). Even though the mechanism from the C-to-T changeover awaits potential investigations, we ... Energetic DNA demethylation in mammals involves TET-mediated oxidation of 5-methylcytosine (5mC). October 3, 2017. Tracy Porter ... Energetic DNA demethylation in mammals involves TET-mediated oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine ( ...
Epigenetic Approaches in Neuroblastoma Disease Pathogenesis | IntechOpen
In addition, several studies evaluated the 5-methylcytosine (5 mC) distribution patterns, which distinguish cancer cells from ... 5. :3316-3332. *9. Xie C, Fu L, Xie L, Liu N, Li Q. Rsf-1 overexpression serves as a prognostic marker in human hepatocellular ... A) TSP-1 gene expression levels were detected by RT-PCR analysis in NBL-W-S cells treated with vehicle or 1 or 5 μM of 5-Aza-dC ... 5. Lai AY, Wade PA. Cancer biology and NuRD: A multifaceted chromatin remodelling complex. Nature Review Cancer. 2011;. 11. : ...
Research - Epigenetics and Molecular Carcinogenesis | MD Anderson Cancer Center
5:42.. Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio MR, Takata Y, Lin K, Tomida MW, Shen J, Saha D, Gowher H, ... 2021 Mar;5(1):2. (Review). Yang F, Chen J, Liu B, Gao G, Sebastian M, Jeter C, Shen J, Person MD, Bedford MT. SPINDOC binds ... 58(5):863-9.. Kapoor P, Bao Y, Xiao J, Luo J, Shen J, Persinger J, Peng G, Ranish J, Bartholomew B, Shen X. (2015) Regulation ... 1(5):e201800117.. Das P, Veazey KJ, Van HT, Kaushik S, Lin K, Lu Y, Ishii M, Kikuta J, Ge K, Nussenzweig A, Santos MA. (2018) ...
Hydralazine hydrochloride, DNA methylation inhibitor. (CAS 304-20-1) (ab120863)
Frontiers | SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps...
4-methylcytosine (4mC) and 5-hydroxymethylcytosine (5-hmC), which can be identified by a series of methyltransferases at ... Dongbo Liu1,2,3,5*. *1Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural ... Ring 2 includes protein-coding genes (lasureous), rRNAs (blue) and tRNAs (red). ORFs are located on ring 3. Rings 4 and 5 shows ... Dawid, I. B. (1974). 5-methylcytidylic acid: absence from mitochondrial DNA of frogs and HeLa cells. Science 184, 80-81. doi: ...
Fernando RODRIGUEZ | Research Scientist | PhD | Marine Biological Laboratory, MA | MBL | Josephine Bay Paul Center for...
However, N4-methylcytosine (4mC) is confined to bacteria. Here we report that 4mC can serve as an epigenetic mark in eukaryotes ... In eukaryotes, modifications predominantly involve C5-methylcytosine (5mC) and occasionally N6-methyladenine (6mA), while ... bacteria frequently use N4-methylcytosine (4mC) in addition to 5mC and 6mA. Here we report that 4mC can serve as an epigenetic ... In eukaryotes, 5-methylcytosine is the predominant DNA base modification, followed by N6-methyladenine. ...
Zeitschrift für Naturforschung B Volume 33 Issue 3
Mn(CO) 5 Br and (Me 3 Si) 3 P react to give Mn 2 (CO) 8 (μBr) (μP(SiMe 3 ) 2 ) 3. Using methanol, both Si-P bonds of 3 can be ... Two tri- and tetraseleninato complexes of tin, RSn(O 2 SeR) 3 (1) and Sn(O 2 SeR) 4 (2) (R =C 6 H 5 ), are obtained from ... 2-Chloro-5-methoxy-p-benzoquinone [1] reacts with zinc mercaptide [2] to give 2-tri-fluoromethyl-8-methoxy phenothiazin-7-one ( ... The crystal structure of the [C 7 H 7 Fe(CO) 3 ] - anion stabilized with the [(C 6 H 5 ) 4 As] + cation has been determinated ...
Top 7 in genetics and genomics | The Scientist Magazine®
... www.molbiolcell.org/cgi/content/full/22/5/525 22:525-7, 2011. Evaluated by Etienne Joly, CNRS, France; Ferdinando Boero, ... linkurl:Free F1000 Evaluation;http://f1000.com/10134960?key=70w5gkxmhhy59y2 5. New role for GLRs. ... "Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain," linkurl:Cell,;http://www.ncbi. ...
The regulation of Ten-eleven translocation proteins (methylcytosine modifiers) by methyl-CpG binding domain proteins ...
The regulation of Ten-eleven translocation proteins (methylcytosine modifiers) by methyl-CpG binding domain proteins ( ... The regulation of Ten-eleven translocation proteins (methylcytosine modifiers) by methyl-CpG binding domain proteins ( ... The regulation of Ten-eleven translocation proteins (methylcytosine modifiers) by methyl-CpG binding domain proteins ( ... These results indicate that the fine balance between methylcytosine readers" and "erasers/writers" regulates transcriptional ...
Last Week's Sequencing-Related Papers of Note: Mar 11, 2014 | Genomeweb
Nucleic Acids Res. 2014 Mar 5. [Epub ahead of print] seqCNA: an R package for DNA copy number analysis in cancer using high- ... Hum Mutat. 2014 Mar 5. [Epub ahead of print] MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read ... PLOS One. 2014 Mar 5;9(3):e90581. Comparative analysis of methods for identifying somatic copy number alterations from deep ... Brief Bioinform. 2014 Mar 5. [Epub ahead of print] Next generation sequencing based development of intron-targeting markers in ...
ALKBH3 alkB homolog 3, alpha-ketoglutarate dependent dioxygenase [Homo sapiens (human)] - Gene - NCBI
ALKBH2 (MIM 610602) and ALKBH3 are E. coli AlkB homologs that catalyze the removal of 1-methyladenine and 3-methylcytosine ( ... ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine ... ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine ... BMC Cancer, 2017 Jul 5. PMID 28679371, Free PMC Article * AlkB homolog 3-mediated tRNA demethylation promotes protein synthesis ...
Itaconate Inhibits TET DNA Dioxygenases to Dampen Inflammatory Responses | Research Square
Ichiyama, K. et al. The methylcytosine dioxygenase Tet2 promotes DNA demethylation and activation of cytokine gene expression ... Here, we show that ITA is a potent inhibitor of the TET family DNA dioxygenases, which catalyze the conversion of 5- ... methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) during the process of active DNA demethylation. ITA binds to the same ... Several molecular processes are affected by ITA, including succinate dehydrogenase (SDH) inhibition5, resulting in succinate ...
NIOSHTIC-2 Search Results - Full View
Results: The Spearmans correlation coefficient for 5-mC and 5-hmC levels was 0.32 (p - value = 0.03) at visit 1 and 0.54 (p - ... Methods: % 5-methylcytosine (5-mC) and % 5-hydroxymethyl-cytosine (5-hmC) levels were measured by capture and detection ... The positive correlation of 5-mC and 5-hmC levels was confirmed in an independent study population. Conclusions: Our findings ...
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5-フルオレセインで精製された99-mer:. DharmaconのRNA合成に関する能力は、化学的に修飾された長いRNAオリゴヌクレオチドの日常的な合成をサポートします。UPLCおよびLC-MS分析は、得られた純度の標準レベルを示しています。 ... 5-LC-N-U. $100.00. $130.00. $145.00. $180.00. $320.00. Thiol Modifiers. Short Code. 0.05 µmol. 0.2 µmol. 0.4 µmol. 1.0 µmol. ... 5-P. $45.00. $52.00. $63.00. $78.00. $135.00. 2-Modifications. Short Code. 0.05 µmol. 0.2 µmol. 0.4 µmol. 1.0 µmol. 2.0 µmol ... 5-Cy3. Modification Code: Cy3 Description: Cy3 and Cy5 are the most popular cyanine dyes
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Frontiers | Caenorhabditis elegans as a Useful Model for Studying Aging Mutations
5. Golden TR, Melov S. Gene expression changes associated with aging in C. elegans. WormBook. (2007) 12:1-12. doi: 10.1895/ ... demonstrated that deletion of the spr-5 in C. elegans causes a trans-generational increase in lifespan through mis-regulation ... Greer EL, Becker B, Latza C, Antebi A, Shi Y. Mutation of C. elegans demethylase spr-5 extends transgenerational longevity. ... Riera CE, Dillin A. Can aging be drugged? Nat Med. (2015) 21:1400-5. doi: 10.1038/nm.4005 ...
February 2018 | What is Epigenetics?
Maybe Shes Born With it, Maybe its Epigenetics: 5 Tips for Beauty and Anti-Aging February 20, 2018 Bailey Kirkpatrick ... The erasure of Tet-oxidized 5-Methylcytosine (5-mC) is not only important during the reprogramming steps but as well as the ... 2017) have shown that the SOS response-associated peptidase domain protein, SRAP1, binds to Tet-oxidized forms of 5-mC in DNA ... Erasure of Tet-Oxidized 5-Methylcytosine by SRAP1 February 9, 2018 Estephany Ferrufino ...
Human trophoblasts are primarily distinguished from somatic cells by differences in the pattern rather than the degree of...
DNA methylation and methylcytosine oxidation in cell fate decisions. . Curr. Opin. Cell Biol. ... Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: an HPLC-based study ... Amount and distribution of 5-methylcytosine in human DNA from different types of tissues or cells ... and 5-hydroxymethylcytosine (5hmC), would aid in allowing a more complete understanding of human trophoblast methylation (Urich ...
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Epigenetics, DNA damage, and aging
Methylcytosine can be spontaneously oxidized or enzymatically modified by the TET enzymes to form 5-hydroxymethylcytosine and 5 ... 5-Hydroxymethylcytosine appears to be localized at sites of DNA damage (41), which may help identify sites requiring repair (41 ... TET enzymes and 5-hydroxymethylcytosine in neural progenitor cell biology and neurodevelopment. Front Cell Dev Biol. 2021;9: ... 5-Hydroxymethylcytosine marks sites of DNA damage and promotes genome stability. Cell Rep. 2016;14(6):1283-1292.. View this ...
5hmCModificationDioxygenaseOxidationDemethylationEnzymesTET2Conversion of 5-methylcytosineANTI-5-METHYLCYTOSINEHydroxylationMethyl groupMethyltransferasesTranslocationGenomicProteinsCalled 5-hydroxymethylcytosineEpigeneticsDeaminationGenesAntibodyHistone2017DetectionNSUN2MethyltransferaseMutationMethylation-sensitiveModificationsMRNAEukaryoticProteinEnzymeNucleosideThymine DNA GlycosyBlot analysisBasesResiduesImplicationsBisulfiteEncodesMoleculePredominantly5hmUQuantificationInvolvesPhosphatePatternsSignificantlyMammalianStructuralOccursMutationsEnzymaticallyPolymeraseCleavageErasers
5hmC19
- Energetic DNA demethylation in mammals involves TET-mediated oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5caC). (flora2world.com)
- Although, 5mC can be modified by Ten-eleven translocation (Tet) protein to 5-hydroxymethylcytosine (5hmC), which affects the binding ability of MBD proteins to DNA, the interplay of MBD proteins, Tet1 proteins and their substrate is still unknown. (tu-darmstadt.de)
- Here, we show that ITA is a potent inhibitor of the TET family DNA dioxygenases, which catalyze the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) during the process of active DNA demethylation. (researchsquare.com)
- Recently, researchers have rediscovered a mostly ignored epigenetic variant that results when a methyl group on a cytosine takes on a hydroxyl group to form 5-hydroxymethylcytosine (5hmC). (the-scientist.com)
- The DNA modification 5-hydroxymethylcytosine (5hmC) is now referred to as the sixth base of DNA with evidence of tissue-specific patterns and correlation with gene regulation and expression. (biomedcentral.com)
- 5-Hydroxymethylcytosine (5hmC) is a modified form of the DNA base cytosine. (biomedcentral.com)
- We attempted to develop effective and noninvasive methods using 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) markers from circulating cell-free DNA (cfDNA) for the detection of pancreatic ductal adenocarcinoma (PDAC). (biomedcentral.com)
- Bisulfite sequencing has been the gold standard for mapping DNA modifications including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) for decades. (pku.edu.cn)
- TAPS combines ten-eleven translocation (TET) oxidation of 5mC and 5hmC to 5-carboxylcytosine (5caC) with pyridine borane reduction of 5caC to dihydrouracil (DHU). (pku.edu.cn)
- Changes in DNA methylation were determined by immunohistochemistry using antibodies against 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). (elsevier.com)
- 5mC might be sequentially oxidized to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). (chipgrade.com)
- Quantitative immunofluorescence analysis and ultrasensitive LC-MS-based measurements revealed that oxidative DNA lesions in sperm impair active DNA demethylation at paternal pronuclei, without affecting 5-hydroxymethylcytosine (5hmC), a 5-methylcytosine modification that has been implicated in paternal active DNA demethylation in mouse zygotes. (biomedcentral.com)
- Bisulfite sequencing detects 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at single-base resolution. (france-genomique.org)
- In the first reaction, TET2 (Ten-eleven-translocation 2 = methylcytosine dioxygenase) and T4-BGT (T4 Phage β-glucosyltransferase) convert 5mC and 5hmC into products that cannot be deaminated by APOBEC3A (Apolipoprotéins B mRNA editing enzyme, catalytic polypeptide-like). (france-genomique.org)
- The Tet family of enzymes (Tet1/2/3) modify the DNA base 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and promote DNA demethylation and gene expression. (einsteinmed.edu)
- The three family members, TET1, TET2 and TET3, exhibit oxidizing activity and can catalyse the conversion of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) [42,43]. (nanoscience-europe.org)
- High-2HG tumors demonstrate reduced DNA levels of 5-hydroxymethylcytosine (5hmC), consistent with 2HG-mediated inhibition of ten-eleven translocation (TET) enzymes, which convert 5-methylcytosine (5mC) to 5hmC. (omicsdi.org)
- TET3 and TET1, changes the methylation position of the genome, controlling the transcription of particular genetics by changing 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and after that to 5-formylcytosine (5fC) and finally to 5-carboxylcytosine (5caC). (globaltechbiz.com)
- The TET methylcytosine dioxygenase enzymes (TET1/2/3) catalyze the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and can further oxidize 5hmC to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). (ox.ac.uk)
Modification15
- It remains largely unclear about the function of 5-methylcytosine (m5C) RNA modification in the context of abdominal aortic aneurysm (AAA). (imrpress.com)
- The major 5-methylcytosine modulators, including NSUN2, NSUN5 , and Aly/REF , which represented the major parameters related to the abnormal m5C modification level, were observed up-regulating in AAA tissues at both protein and mRNA levels. (imrpress.com)
- In eukaryotes, 5-methylcytosine is the predominant DNA base modification, followed by N6-methyladenine. (researchgate.net)
- The epigenetic information of 5-methylcytosine can be translated by cytosine modification readers, such as the methyl-CpG binding domain (MBD) proteins. (tu-darmstadt.de)
- Figure 1 shows that the Diagenode rabbit polyclonal antibody against 5-hmC is highly specific for the 5-hmC base modification (no IP with non-methylated or methylated C control fragments). (diagenode.com)
- RNA modification의 종류는 많습니다만, 주로 5가지 종류의 modification에 대하여 genome-wide한 RNA modification 을 찾는 연구가 활발히 이루어지고 있습니다. (github.io)
- In eukaryotes, the primary modification of DNA is found in cytosines (C), where DNA Methyltransferases mediate the transfer of a methyl group to cytosines, converting them to 5-methylcytosine (5-mC), minor modifications with broad implications for the activity of the DNA. (epigenie.com)
- 5-methylcytosine (5mC) is an epigenetic modification to DNA which modulates transcription. (chipgrade.com)
- In SMUG1 knock-down cells, immature and mature rRNAs accumulated 5-hydroxylmethyluridine (hm5U), a base modification recognized by SMUG1, pointing to SMUG1 as a possible new enzyme involved in the regulation of rRNA. (encyclopedia.pub)
- However, the picture was far from complete, focusing only on the most common and well-studied DNA modification, known as 5-methylcytosine (5-mC). (nih.gov)
- Ni Z, Nie X, Zhang H, Wang L, Geng Z, Du X, Qian H, Liu W, Liu T. Atranorin driven by nano materials SPION lead to ferroptosis of gastric cancer stem cells by weakening the mRNA 5-hydroxymethylcytidine modification of the Xc-/GPX4 axis and its expression. (medsci.org)
- The results of high performance liquid chromatography-mass spectrometry and Dot blotting showed that [email protected] significantly inhibited the mRNA 5‑hydroxymethylcytidine modification of GCSCs. (medsci.org)
- Meanwhile, the results of RNA immunoprecipitation-PCR also indicated that [email protected] significantly reduced the 5-hydroxymethylcytidine modification level of GPX4 and SLC7A11 mRNA 3' untranslated region in GCSCs, resulting in a decrease in their stability, shortening their half-lives and reducing translation activity. (medsci.org)
- Therefore, this study revealed that [email protected] induced ferroptosis of GCSCs by weakening the expression of the Xc-/GPX4 axis and the 5-hydroxymethylcytidine modification of mRNAs in the pathway, thereby achieving their therapeutic effect on gastric cancer. (medsci.org)
- One such DNA modification is mediated by DNA methyltransferases (DNMT) that covalently add a methyl group to the 5th carbon of a cytosine residue (5-methylcytosine, 5mC) [ 6 ]. (biomedcentral.com)
Dioxygenase3
- Quantitative real-time reverse transcription PCR and western blotting results showed that [email protected] not only reduced the expression levels of GCSC stem cell markers and cell proliferation and division markers, but also significantly inhibited the expression levels of key molecules in the cystine/glutamate transporter (Xc-)/glutathione peroxidase 4 (GPX4) and Tet methylcytosine dioxygenase (TET) family proteins. (medsci.org)
- The protein encoded by this gene is a methylcytosine dioxygenase that catalyzes the conversion of methylcytosine to 5-hydroxymethylcytosine. (utsouthwestern.edu)
- Rare cases involve mutations in the thrombopoietin gene (THPO), which are associated with autosomal dominant hereditary thrombocytosis, and somatic mutations in tet methylcytosine dioxygenase 2 (TET2). (medscape.com)
Oxidation1
- Removal of DNA methylation involves oxidation of 5-methyl-cytosine. (nature.com)
Demethylation6
- The robust analytical method built a solid foundation for dissecting the molecular mechanisms of active cytosine demethylation, for measuring these 5-mdC derivatives and assessing their involvement in epigenetic regulation in other organisms and for examining whether these 5-mdC derivatives can be used as biomarkers for human diseases. (umn.edu)
- Epigenetic modifications include DNA cytosine methylation to form 5-methylcytosine and 5-methylcytosine demethylation . (wikipedia.org)
- Methylcytosine demethylation is catalyzed in several stages 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. (wikipedia.org)
- DME encodes 5-methylcytosine DNA glycosylase, enzyme responsible for transcriptional activation of gliadins and low molecular weight glutenins (via demethylation of their promoter site). (biotechnologyforums.com)
- Active demethylation involves the removal of the methyl group from 5-methylcytosine (5mC) and is carried out by the ten-eleven translocation (TET) family of proteins. (nanoscience-europe.org)
- Co-staining for 5- hydroxymethylC did not show a dynamic pattern of staining and does not provide support for a role for this metabolite in global demethylation. (ktu.edu.tr)
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)
- While spontaneous deamination of cytosine forms uracil, which is recognized and removed by DNA repair enzymes, deamination of 5-methylcytosine forms thymine. (wikipedia.org)
- In another type of repair mechanism, nucleotide excision repair, enzymes replace incorrect bases by making a cut on both the 3′ and 5′ ends of the incorrect base. (dualjuridik.org)
TET25
- Like α-KG, which is a crucial co-substrate for the activity of TET2, ITA is also a dicarboxylic acid containing a 4- or 5-carboxylate that, in the case of α-KG, forms hydrogen and ionic bonds with H1416, R1896, and S1898 in TET2 11 . (researchsquare.com)
- The researchers concluded that their results suggest that TET2 is involved in conversion of 5-methylcytosine to 5-hydroxymethylcytosine in DNA. (theoncologypharmacist.com)
- This suggests that Tet2 is normally needed for methylcytosine dioxygenation in hematopoietic cells but that this function can end up being supplanted by Tet1 or Tet3 in various other. (globaltechbiz.com)
- Furthermore, the number of 5-hmC peaks were significantly decreased in Tet2-/-MSCs compared to WT MSCs based on whole genomic 5-hmC profiling. (ox.ac.uk)
- We then examined TET2 gene expression in MSCs derived from human myeloproliferative neoplasms (MPN) patients and healthy individuals and found that TET2 and 5-hmC was moderately down-regulated in MPN MSCs as compared to healthy controls. (ox.ac.uk)
Conversion of 5-methylcytosine1
- This results from the enzymatic conversion of 5-methylcytosine into 5-hydroxymethylcytosine by the TET family of oxygenases. (diagenode.com)
ANTI-5-METHYLCYTOSINE1
- Genomic DNA (gDNA) was isolated from the mammary tissue and immuno-precipitated using anti-5-methylcytosine antibodies. (desdaughter.com)
Hydroxylation1
- Methylation out of cytosine returns 5-methylcytosine, while the hydroxylation production 5-hydroxymethylcytosine. (bestbargainfurniture.com)
Methyl group8
- In 5-methylcytosine, a methyl group is attached to the 5th atom in the 6-atom ring, counting counterclockwise from the NH-bonded nitrogen at the six o'clock position. (wikipedia.org)
- This methyl group distinguishes 5-methylcytosine from cytosine. (wikipedia.org)
- S-Adenosylmethionine then donates a methyl group to carbon 5. (wikipedia.org)
- Cytosine, one of the four DNA bases, can be chemically modified by the addition of a molecule known as a methyl group to form 5-methylcytosine. (ludwigcancerresearch.org)
- 5mC (5-Methylcytosine) is a region of DNA that has been epigenetically modified through the addition of a methyl group at the 5th carbon position of cytosine. (chromatrap.com)
- Methyl group is added at 5' end of gene sequence in its cytosine ring, creating 5-methylcytosine. (scienceofhealthy.com)
- DNA methylation occurs by the covalent addition of a methyl group (CH3) on the 5-carbon of the cytosine ring by DNA methyltransferases (DNMTs), resulting in 5-methylcytosine (5-mC). (genzymediagnostics.com)
- 500579-04-4 manufacture Each of the last 3 items is normally regarded and excised by thymine DNA glycosylase (TDG), completing the removal of the 5-methyl group and regenerating unmodified cytosine (1). (globaltechbiz.com)
Methyltransferases2
- A universal mechanism-based probe for DNA (cytosine-5)-methyltransferases was used to screen tissues and cell types known to be active in de novo methylation for new species of DNA methyltransferase. (researchgate.net)
- DNA methyltransferase 3A (DNMT3A) belongs to a family of highly conserved DNA methyltransferases that catalyse 5-methylcytosine methylation. (medicineinnovates.com)
Translocation2
- Recent studies showed that Ten-eleven translocation (Tet) family dioxygenases can oxidize 5-methyl-2'-deoxycytidine (5-mdC) in DNA to yield the 5-hydroxymethyl, 5-formyl and 5-carboxyl derivatives of 2'-deoxycytidine (5-HmdC, 5-FodC and 5-CadC). (umn.edu)
- Since L-2-hydroxyglutaric acid is sufficiently similar in structure to 2-oxoglutarate (2OG), it is able to inhibit a range of 2OG-dependent dioxygenases, including histone lysine demethylases (KDMs) and members of the ten-eleven translocation (TET) family of 5-methylcytosine (5mC) hydroxylases. (hmdb.ca)
Genomic4
- Here we used a reversed-phase HPLC coupled with tandem mass spectrometry (LC-MS/MS/MS) method, along with the use of stable isotope-labeled standards, for accurate measurements of 5-HmdC, 5-FodC, 5-CadC and 5-HmdU in genomic DNA of cultured human cells and multiple mammalian tissues. (umn.edu)
- We found that overexpression of the catalytic domain of human Tet1 led to marked increases in the levels of 5-HmdC, 5-FodC and 5-CadC, but only a modest increase in 5-HmdU, in genomic DNA of HEK293T cells. (umn.edu)
- A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. (intbioinformaticsjr.com)
- Dim2 operates in a complex with Heterochromatin Protein-1 (Hp1) that recognizes and directs DNA methylation to genomic regions marked by tri-methylation of histone 3 lysine 9 (H3K9me3) that is deposited by the histone methyltransferase Deficient In Methylation-5 (Dim5) [ 11 , 12 ]. (biomedcentral.com)
Proteins5
- The aberrant interactions of MBD proteins with 5-methylcytosine cause diseases like Rett syndrome and also decrease genome stability, thus, the levels of both MBD protein and its substrate 5mC must be precisely regulated. (tu-darmstadt.de)
- MeCP2 and MBD2 are members of a family of proteins that possess a domain that selectively binds 5-methylcytosine in a CpG context. (nanosensors.com)
- In the article " DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices " Ming Liu, Saeid Movahed, Saroj Dangi, Hai Pan, Parminder Kaur, Stephanie M. Bilinovich, Edgar M. Faison, Gage O. Leighton, Hong Wang, David C. Williams Jr. and Robert Riehn demonstrate DNA compaction by MeCP2 while MBD2 does not affect DNA configuration. (nanosensors.com)
- Despite sharing a similar specific DNA-binding domain, the impact of full-length 5-methylcytosine-binding proteins can vary drastically between strong compaction of DNA and no discernible large-scale impact of protein binding. (nanosensors.com)
- Figure 6 from " DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices " by Ming Liu et al. (nanosensors.com)
Called 5-hydroxymethylcytosine1
- The new study, led by Kevin Johnson and Brock Christensen at the Geisel School of Medicine at Dartmouth College, Lebanon, NH, broke new ground by applying laboratory [2] and statistical approaches [3] that now make it possible to distinguish between 5-mC and another chemical mark called 5-hydroxymethylcytosine (5-hmC) to tumor samples. (nih.gov)
Epigenetics1
- Although its precise role has still to be shown, early evidence suggests a few putative mechanisms that could have big implications in epigenetics : 5-hydroxymethylcytosine may well represent a new pathway to demethylate DNA involving a repair mechanism converting 5-hmC to cytosine and, as such open up entirely new perspectives in epigenetic studies. (diagenode.com)
Deamination4
- 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)
- The implications of deamination on 5-hydroxymethylcytosine, on the other hand, remains less understood. (wikipedia.org)
- 5-methylcytosine is resistant to deamination by bisulfite treatment, which deaminates cytosine residues. (wikipedia.org)
- MBD4 is bifunctional, one domain acting as a DNA repair enzyme to minimize mutations caused by deamination of 5-methylcytosine, and a second domain acting to repress transcription in promotors containing 5-methylcytosine. (sfu.ca)
Genes7
- In mammalian cells, clusters of CpG at the 5' ends of genes are termed CpG islands. (wikipedia.org)
- PTMs include phosphorylation, methylation, and acetylation, which can lead to either silencing or activation of associated genes [ 5 ]. (hindawi.com)
- It seems more associated with activation of nearby genes, while 5-mC is more commonly involved with repression. (nih.gov)
- Indeed, 5-hmC popped up more frequently on genes with important roles in immunity and in stem cell biology. (nih.gov)
- The comparison revealed a significant enrichment of 5-hmC marks on genes that show increased activity in glioblastoma cells. (nih.gov)
- For example, the expression of p16, a well-known TSG, is downregulated due to its promoter hypermethylation [ 5 ], and DNA repair genes, such as BRCA1 and hMLH1 , are also hypermethylated, repressing their gene expression [ 6 ]. (genominfo.org)
- Within the last 5 years, advancements in B-cell lifestyle (21,C25) and sorting technology (26,C29) and the capability to recover antibody genes from one B cells (30,C32) possess resulted in the isolation of several potent and broadly reactive HIV-1 monoclonal antibodies (MAbs). (schwitzbiotech.com)
Antibody9
- Active Motif's 5-Methylcytosine (5-mC) antibody (mAb) (Clone 33D3) was raised in a Mouse host. (mybio.ie)
- Request a quote for a bulk order for 5-hydroxymethylcytosine (5-hmC) polyclonal antibody (rabbit) . (diagenode.com)
- Polyclonal antibody raised in rabbit against 5-hydroxymethylcytosine conjugated to KLH. (diagenode.com)
- Figure 1 hMeDIP results obtained with the Diagenode antibody directed against 5-hmC hMeDIP (hydroxymethylated DNA IP) was performed using the Diagenode antibody against 5-hydroxymethylcytosine (Cat. (diagenode.com)
- hMeDIP was performed with 3.5 μg of the rabbit 5-hmC antibody and the IP'd DNA was analysed by qPCR using primers specific for the 3 different control sequences. (diagenode.com)
- To determine the titer, an ELISA was performed using a serial dilution of the Diagenode antibody directed against 5-hmC (cat. (diagenode.com)
- To demonstrate the specificity of the Diagenode antibody against 5-hmC (cat. (diagenode.com)
- The results shown here illustrate the use of this unique monoclonal antibody against 5-hydroxymethylcytosine that has been fully validated in various technologies. (diagenode.com)
- Mouse anti 5-Methylcytidine antibody, clone 33D3 ( MCA2201 ) used for the detection of 5-meC in Zea mays root tip cells by immunofluorescence. (bio-rad-antibodies.com)
Histone2
- Briefly, posttranslational modifications (PTMs) of histone tails can alter chromatin structure and DNA accessibility, thereby impacting on gene transcription and ultimately cellular function [ 5 ]. (hindawi.com)
- Trichostatin A and 5-azacytidine both cause an increase in global histone H4 acetylation and a decrease in global DNA and H3K9 methylation during mitosis in maize. (bio-rad-antibodies.com)
20173
- BMC Cancer, 2017 Jul 5. (nih.gov)
- 2017) have shown that the SOS response-associated peptidase domain protein, SRAP1, binds to Tet-oxidized forms of 5-mC in DNA and selectively cleave DNA containing Tet-oxidized 5-methylcytosine. (whatisepigenetics.com)
- 2017. Medium throughput bisulfite sequencing for accurate detection of 5-methylcytosine and 5-hydroxymethylcytosine. . (mcgill.ca)
Detection1
- Methods: % 5-methylcytosine (5-mC) and % 5-hydroxymethyl-cytosine (5-hmC) levels were measured by capture and detection antibodies followed by colorimetric quantification. (cdc.gov)
NSUN21
- NSun2 is an RNA methyltransferase introducing 5-methylcytosine into tRNAs, mRNAs, and noncoding RNAs, thereby influencing the levels or function of these RNAs. (jbc.org)
Methyltransferase2
- DNA (cytosine-5)-methyltransferase in mouse cells and tissue. (researchgate.net)
- DNA methylation refers to the chemical conversion of a cytosine nucleotide in DNA to 5-methylcytosine by DNA methyltransferase. (genominfo.org)
Mutation3
- The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with considerably modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg 133 , a key residue whose mutation causes Rett syndrome. (nih.gov)
- The disorder-causing mutation is the amplification of a cytosine-guanine-guanine (CGG) repeat in the 5' untranslated region of FMR1 located at Xq27.3 1 . (cdc.gov)
- I have looked through the topic of 'How can I mutate cytosine to 5-methylcytosine' and processed the adenine to 3-methyladenine according the protocol for mutation the cytosine. (x3dna.org)
Methylation-sensitive1
- Global DNA methylation levels were examined using 5-methylcytosine dot blot and methylation-sensitive Southern blot analysis. (kribb.re.kr)
Modifications3
- In eukaryotes, modifications predominantly involve C5-methylcytosine (5mC) and occasionally N6-methyladenine (6mA), while bacteria frequently use N4-methylcytosine (4mC) in addition to 5mC and 6mA. (researchgate.net)
- DNA methylation is an important type of epigenetic modifications, where 5- methylcytosine (5mC), 6-methyadenine (6mA) and 4-methylcytosine (4mC) are the most common types. (pacb.com)
- DNA accessibility for the transcriptional machinery is regulated in part by chemical modifications to histones that can alter chromatin structure or nucleosome positioning, and by direct DNA modifications that can alter transcription factor-binding sites [ 5 ]. (biomedcentral.com)
MRNA1
- Transfected mRNA was modified with pseudouridine and 5-methylcytosine and encoded 2x NLS (Nand C-terminal) Cas9. (neb-online.de)
Eukaryotic1
- 5-Methylcytosine in eukaryotic DNA. (wikidata.org)
Protein1
- Several molecular processes are affected by ITA, including succinate dehydrogenase (SDH) inhibition 5 , resulting in succinate accumulation and metabolic reprogramming 6 , 7 , and alkylation of protein cysteine residues, inducing the electrophilic stress response mediated by NRF2 and IκBζ 8 , 9 and impairing aerobic glycolysis 10 . (researchsquare.com)
Enzyme1
- 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)
Nucleoside2
- 5-Methylcytosine is incorporated in the nucleoside 5-methylcytidine. (wikipedia.org)
- 5-Methylcytidine is a modified nucleoside derived from 5-methylcytosine. (alchetron.com)
Thymine DNA Glycosy1
- After their formation at CpG dinucleotide sites, these oxidized pyrimidine nucleosides, particularly 5-FodC, 5-CadC, and 5-HmdU, may be cleaved from DNA by thymine DNA glycosylase, and subsequent action of base-excision repair machinery restores unmethylated cytosine. (umn.edu)
Blot analysis3
- No. pAb-HMC-050), a Dot blot analysis was performed using the hmC, mC and C controls from the Diagenode "5-hmC, 5-mC & cytosine DNA Standard Pack" (Cat No. AF-101-0002). (diagenode.com)
- HBx-mediated DNA methylation abnormalities were confirmed in patient HCC samples using methyl-specific polymerase chain reaction and 5-methylcytosine dot blot analysis. (kribb.re.kr)
- The accumulation of DAC and 5-mC were detected using LC-MS, and the amount of 5-hmC was determined by dot blot analysis. (thno.org)
Bases7
- One hundred to 4 ng (equivalent of 5 to 0.2 pmol of C-bases) of the controls were spotted on a membrane (Amersham Hybond-N+). (diagenode.com)
- So far, the 5-hmC bases have been identified in Purkinje neurons, in granule cells and embryonic stem cells where they are present at high levels (up to 0,6% of total nucleotides in Purkinje cells). (diagenode.com)
- Due to the structural similarity between 5-mC and 5-hmC, these bases are experimentally almost indistinguishable. (diagenode.com)
- Furthermore, the electrical resistance of a pore is determined by the bases present within multiple nucleotides that reside in the pore's narrowest point (approximately five nucleotides for the R9.4 pore), yielding a large number of possible states: 4 5 = 1024 for a standard four-base model. (biomedcentral.com)
- When modified bases are present, e.g. 5-methylcytosine, the number of possible states can grow even higher: 5 5 = 3125. (biomedcentral.com)
- These epigenetically marked bases, called 5-methylcytosines (5mCs), help to determine how hundreds of cell types in the human body differentiate and maintain their identities, despite having the same genetic backgrounds. (the-scientist.com)
- Cleavage by EnGen Lba Cas12a (Cpf1) occurs ~18 bases 3′ of the PAM and leaves 5′ overhanging ends. (neb-online.de)
Residues1
- The phosphate group connects successive sugar residues by bridging the 5′-hydroxyl group on one sugar to the 3′-hydroxyl group of the next sugar in the chain. (en-academic.com)
Implications1
- Finally, we demonstrate that the C-terminal region of FOXN1 is required for high-affinity DNA binding and that FOXN1 has a significantly reduced affinity for DNA that contains 5'-methylcytosine, which may have implications for the role of FOXN1 in thymic involution. (ox.ac.uk)
Bisulfite2
- Recent articles demonstrated that the most common approaches (e.g. enzymatic approaches, bisulfite sequencing) do not account for 5-hmC. (diagenode.com)
- 2] Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA by oxidative bisulfite on an array (OxBS-array) . (nih.gov)
Encodes1
- The single ORF of canonical EN+ PLEs encodes RT and a C-terminal GIY-YIG endonuclease (EN) that enables intrachromosomal integration, while EN-PLEs lack endonuclease and are generally r. (researchgate.net)
Molecule1
- In certain embodiments, the molecule comprises a 5′-triphosphate or a 5′-diphosphate. (justia.com)
Predominantly1
- 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)
5hmU1
- Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. (encyclopedia.pub)
Quantification2
- Product Overview The MethylFlash Methylated DNA Quantification Package (Fluorometric) is a whole set of optimized buffers and reagents to fluorometrically quantify international DNA methylation by particularly measuring ranges of 5-methylcytosine (5-mC) in a microplate-based format. (computablegenomix.com)
- Product Overview The MethylFlash Methylated DNA Quantification Bundle (Fluorometric) is an entire set of optimized buffers and reagents to fluorometrically quantify worldwide DNA methylation by significantly measuring ranges of 5-methylcytosine (5-mC) in a microplate-based format. (cellexusinc.com)
Involves1
- [4] [5] Following RGC proliferation, neurogenesis involves a final cell division of the parent RGC, which produces one of two possible outcomes. (wikipedia.org)
Phosphate3
- Yeast RNA polymerase I (Pol I) contains approximately 15 phosphate groups, distributed to 5 of the 14 subunits. (cipsm.de)
- This cleavage reduces an other apoptosis in resulting available 5'-phosphate of at least a axis of key NOS under high-level syndromes( Wang X et al. (evakoch.com)
- In both cases the end product is a nucleotide carrying a phosphate attached to the 5′ carbon on the sugar. (en-academic.com)
Patterns4
- In addition, several studies evaluated the 5-methylcytosine (5 mC) distribution patterns, which distinguish cancer cells from normal cells, and how CpG methylation contributes to the oncogenic phenotype. (intechopen.com)
- The presence of 5-methylcytosine in I8 DNA was indicated from the restriction patterns of MspI and HpaII. (ias.ac.in)
- Global DNA methylation and cellular 5-methylcytosine and H4 acetylated patterns in primary and secondary dormant seeds of Capsella bursa-pastoris (L.) Medik. (bl.uk)
- Those analyses showed that the tumor DNA had widespread losses of 5-hmC compared to healthy brain cells, suggesting a link between changes in the epigenetic patterns and glioblastoma. (nih.gov)
Significantly1
- With the increasing of severity of carotid plaque, a stepwise upward trend was observed in 5-mC and 5-hmC levels from PBMCs, which were significantly correlated with the risk factors, Crouse score and Gensini score. (aging-us.com)
Mammalian1
- 5-hydroxymethylcytosine (5-hmC) has been recently discovered in mammalian DNA. (diagenode.com)
Structural3
- Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence. (nih.gov)
- Structural insights into the specific recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL effectors. (taleffectors.com)
- 5 Most structural birth defects develop early in embryogenesis, during the first 10 weeks of pregnancy, and the majority of these defects occur in isolation affecting only one organ system. (cdc.gov)
Occurs2
- Furthermore, the formation of longer than full-length nucleic acid sequences occurs when the activation of phosphoramidite monomers by a weak acid prompts the premature cleavage of the acid-labile 5′-hydroxyl protecting group of the newly extended nucleic acid sequence. (justia.com)
- [4] [5] Thus, the generation of neurons occurs in a specific tissue compartment or 'neurogenic niche' occupied by their parent stem cells. (wikipedia.org)
Mutations2
- 2009) Interaction between the mismatch repair and nucleotide excision repair pathways in the prevention of 5-azacytidine-induced CG-to-GC mutations in Escherichia coli. (sfu.ca)
- MPL mutations have been associated with only about 3-5% of essential thrombocytosis cases. (medscape.com)
Enzymatically2
Polymerase1
- Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta. (expasy.org)
Cleavage1
- Double-stranded DNA breaks can be generated with reduced off-target cleavage by targeting two sites in close proximity (generally 0-20 bp apart) and with PAMs facing outward to leave 5' overhangs. (neb-online.de)
Erasers1
- These results indicate that the fine balance between methylcytosine readers" and "erasers/writers" regulates transcriptional noise and genome stability. (tu-darmstadt.de)