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*  Reduced representation bisulfite sequencing
When an unconverted cytosine is observed, it is challenging to differentiate between lack of methylation and an artifact. The ... a non-proofreading polymerase must be used as a proof-reading enzyme would stop at uracil residues found in the ssDNA template ... This is unfortunate in regards to methylation studies, as these repeated sequences often contain methylated cytosines. This is ... The methylated adapter oligonucleotides have all cytosines replaced with 5'methyl-cytosines, in order to prevent the ...
*  Bisulfite sequencing
... treatment introduces specific changes in the DNA sequence that depend on the methylation status of individual cytosine residues ... Treatment of DNA with bisulfite converts cytosine residues to uracil, but leaves 5-methylcytosine residues unaffected. ... In animals it predominantly involves the addition of a methyl group to the carbon-5 position of cytosine residues of the ... Olek A, Oswald J, Walter J (December 1996). "A modified and improved method for bisulphite based cytosine methylation analysis ...
*  Epigenetic therapy
The first is DNA methylation, where a cytosine residue that is followed by a guanine residue (CpG) is methylated. In general, ... A number of cardiac dysfunctions have been linked to cytosine methylation patterns. DNMT deficient mice show upregulation of ... where they seem to inhibit these methylation patterns with some success at reducing symptoms. The DNA methylation inhibitor ... Decreased LINE-1 methylation is a strong predictive indicator of ischemic heart disease and stroke, although the mechanism is ...
*  Epigenetics in learning and memory
... cytosine residue. This usually occurs at cytosines that form part of a cytosine-guanine dinucleotide (CpG sites). Methylation ... In the case of DNA methylation, it was found that increases in H3K4 trimethylation correlate with altered DNA methylation of ... The current hypothesis for how DNA methylation contributes to the storage of memories is that dynamic DNA methylation changes ... Epigenetic mechanisms such as DNA methylation and histone modifications (methylation, acetylation, and deacetylation) have been ...
*  Epitranscriptomic sequencing
... following methylation of the residue. For 5-aza-C, due to a nitrogen substitution in the C5 position of cytosine, the RNA ... 2008). "RNA cytosine methylation analysis by bisulphite sequencing". Nucleic Acids Research. 37 (2): e12. doi:10.1093/nar/ ... Methylation of adenosine does not affect its ability to base-pair with thymidine or uracil, so N6-methyladenosine (m6A) cannot ... Each cluster can contain up to 15 m6A residues. In 2013, a modified version of m6A-seq based on the previous two methods m6A- ...
*  Cellular differentiation
... in which the DNA methyltransferase-mediated methylation of cytosine residues in CpG dinucleotides maintains heritable ... By comparing these regions of differential methylation with regions of cytosine methylation in the original somatic cells, 44- ... In addition, somatic cells possessed minimal levels of cytosine methylation in non-CG dinucleotides, while induced pluripotent ... Methylation is not as straightforward, as neither methylation nor demethylation consistently correlate with either gene ...
*  CpG site
In humans, DNA methylation occurs at the 5 position of the pyrimidine ring of the cytosine residues within CpG sites to form 5- ... TLR9, detector of unmethylated CpG sites DNA methylation age Jabbari K, Bernardi G (May 2004). "Cytosine methylation and CpG, ... A C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the cytosines in such ... Cytosines in CpG dinucleotides can be methylated to form 5-methylcytosine. In mammals, methylating the cytosine within a gene ...
*  Promoter (genetics)
In humans, DNA methylation occurs at the 5' position of the pyrimidine ring of the cytosine residues within CpG sites to form 5 ... see DNA methylation in cancer). DNA methylation causing silencing in cancer typically occurs at multiple CpG sites in the CpG ... Silencing of a gene may be initiated by other mechanisms, but this is often followed by methylation of CpG sites in the ... 50%, and have regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide and this occurs frequently in the ...
*  Regulation of transcription in cancer
In humans, DNA methylation occurs at the 5' position of the pyrimidine ring of the cytosine residues within CpG sites to form 5 ... see DNA methylation in cancer). DNA methylation causing silencing in cancer typically occurs at multiple CpG sites in the CpG ... Silencing of transcription of a gene may be initiated by other mechanisms, but this is often followed by methylation of CpG ... Beggs AD, Jones A, El-Bahrawy M, El-Bahwary M, Abulafi M, Hodgson SV, Tomlinson IP (2013). "Whole-genome methylation analysis ...
*  Combined bisulfite restriction analysis
... depending on whether the cytosine residue was originally methylated or not, respectively. Due to the methylation-independent ... During sodium bisulfite treatment, unmethylated cytosine residues are converted to uracil, while methylated cytosine residues ... resulting in cytosine residues at originally methylated positions, and thymine residues at originally unmethylated position ( ... Quantitative: This is in contrast to methylation-specific PCR, which is qualitative. With COBRA, DNA methylation levels can be ...
*  DNA methylation
Cytosine methylation is widespread in both eukaryotes and prokaryotes, even though the rate of cytosine DNA methylation can ... with different consequences depending on their methylation. Methylated C residues spontaneously deaminate to form T residues ... maintenance methylation and de novo methylation. Maintenance methylation activity is necessary to preserve DNA methylation ... DNA methylation in plants differs from that of mammals: while DNA methylation in mammals mainly occurs on the cytosine ...
*  5-Methylcytosine
... which deaminates cytosine residues. This property is often exploited to analyze DNA cytosine methylation patterns with ... In addition, active enzymatic deamination of cytosine or 5-methylcytosine by the APOBEC family of cytosine deaminases could ... by which he detected a unique methylated cytosine, quite distinct from conventional cytosine and uracil. After seven decades, ... When cytosine is methylated, the DNA maintains the same sequence, but the expression of methylated genes can be altered (the ...
*  Epigenetics of schizophrenia
These -CH3 groups are added to cytosine residues by the DNMT (DNA Methytransferases) enzymes. The binding methyl group to ... DNA methylation is one of the most well studied epigenetic mechanisms and there have been several findings linking it to ... Methylation of BDNF DNA has also been shown to be affected by post-natal social experiences, stressful environment, and social ... DNA methylation can also affect expression of BDNF (brain derived neurotrophic factor). The BDNF protein is important for ...
*  DNA base flipping
Chloroacetaldehyde is used to detect cytosine residues flipped out by the HhaI DNA cytosine-5 methyltransferase (M. HhaI). DNA ... DNA methylation is the process in which a methyl group is added to either a cytosine or adenine. This process causes the ... Potassium permanganate is used to detect thymine residues that have been flipped out by cytosine-C5 and adenine-N6 ... It was first observed in 1994 using X-ray crystallography in a methyltransferase enzyme catalyzing methylation of a cytosine ...
*  Regulation of gene expression
Methylation of DNA is a common method of gene silencing. DNA is typically methylated by methyltransferase enzymes on cytosine ... Methylated cytosine residues are unchanged by the treatment, whereas unmethylated ones are changed to uracil. The differences ... Often, DNA methylation and histone deacetylation work together in gene silencing. The combination of the two seems to be a ... Abnormal methylation patterns are thought to be involved in oncogenesis. Histone acetylation is also an important process in ...
*  Vault RNA
It has been shown that vault non-coding RNAs contain multiple cytosine residues that have been methylated by the NSUN2 protein ... In NSUN2 deficient cells, the loss of cytosine-5 methylation causes incorrect processing into small RNA fragments that end up ... Hussain, Shobir; Sajini, Abdulrahim; Blanco, Sandra (July 25, 2013). "NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding ...
*  DNMT3L
DNA (cytosine-5)-methyltransferase 3-like is an enzyme that in humans is encoded by the DNMT3L gene. CpG methylation is an ... This protein is not thought to function as a DNA methyltransferase as it does not contain the amino acid residues necessary for ... However, this protein does stimulate de novo methylation by DNA cytosine methyltransferase 3 alpha and it is thought to be ... 2007). "Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation". Nature. 449 (7159): 248-51. doi: ...
*  Iridoviridae
Members of the Lymphocystivirus, Megalocytivirus, and Ranavirus genera have genomes with about 25% of their cytosine residues ... Members of this family differ in their degree of genome methylation. The genera Chloriridovirus and Iridovirus lack a highly ...
*  Epigenetics of neurodegenerative diseases
In mammals, methylation occurs on DNA and histone proteins. DNA methylation occurs on the cytosine of CpG dinucleotides in the ... The effects of histone methylation are residue dependent (e.g. which amino acid on which histone tail is methylated) therefore ... most commonly on lysine residues (Bradley et al., 2007). CpG refers to a dinucleotide composed of a cytosine deoxynucleotide ... and the variability of methylation in AD brains. DNA methylation-directed treatments Folate and other B vitamins B vitamins are ...
*  Epigenetics of physical exercise
The methyl groups bound to the cytosine residues lie in the major groove of DNA, the same region most transcription factors use ... As one ages, the amount of DNA methylation slowly begins to decrease. Studies have also looked at methyl deoxycytidine residues ... CpG methylation is an important mechanism of transcriptional silencing. Methylation of CpG islands is shown to reduce gene ... Thus, aging is related to a significant loss in DNA methylation. However, this loss of DNA methylation appears to be slowed by ...
*  Methylated DNA immunoprecipitation
DNA methylation, referring to the reversible methylation of the 5 position of cytosine by methyltransferases, is a major ... which rely on the treatment of DNA with bisulfite to convert unmethylated cytosine residues to uracil. Other methods mapping ... The DNA methylation level estimations can be confounded by varying densities of methylated CpG sites across the genome when ... The coverage of these extended reads can be used to estimate the methylation level of the region. A genome browser such as ...
*  Primary transcript
In addition to acetylation patterns of histones, methylation patterns at promoter regions of DNA can regulate RNA polymerase ... RNA polymerase II constructs the primary transcript using a set of four specific ribonucleoside monophosphate residues ( ... incapable of synthesizing a primary transcript if the targeted gene's promoter region contains specific methylated cytosines- ... residues that hinder binding of transcription-activating factors and recruit other enzymes to stabilize a tightly bound ...
*  CREB
However, the majority of these sites remain unbound due to cytosine methylation which physically obstructs protein binding. A ... These leucine residues tightly bind to leucine residues of another CREB protein forming a dimer. This chain of leucine residues ... and Ca2+/calmodulin-dependent protein kinases on the Serine 133 residue. When activated, CREB protein recruits other ...
*  Riboswitch
In the guanine riboswitch this residue is always a cytosine (i.e. C74), in the adenine residue it is always a uracil (i.e. U74 ... to regulate genes involved in recycling this metabolite that is produced when S-adenosylmethionine is used in methylation ...
*  Epigenomics
In eukaryotes, methylation is most commonly found on the carbon 5 position of cytosine residues (5mC) adjacent to guanine, ... The distinction between methylated and unmethylated cytosine residues is carried out by specific DNA-binding proteins. Binding ... Sodium bisulfate and alkaline treatment does this by converting unmethylated cytosine residues into uracil while leaving ... DNA methylation patterns vary greatly between species and even within the same organism. The usage of methylation among animals ...
*  DNA damage theory of aging
Cai Q, Fu L, Wang Z, Gan N, Dai X, Wang Y (2014). "α-N-methylation of damaged DNA-binding protein 2 (DDB2) and its function in ... DNA damage is any physical abnormality in the DNA, such as single and double strand breaks, 8-hydroxydeoxyguanosine residues ... The mitochondrial DNA base composition is though to reflect its nucleotide-specific (guanine, cytosine, thymidine and adenine) ...
*  Epigenetics of human development
DNA methylation in humans and most other mammals refers to the methylation of a CpG. Methylation of these cytosines are common ... Histone modifications are modifications made to the amino acid residues in the tails of the histones that either restrict the ... Methylation, meanwhile, is when a protein adds a methyl group to a lysine in a histone tail, although more than one methyl ... Regions in which cytosines prior to guanines are clustered and highly unmethylated are called CpG islands, and often serve as ...