Questions tagged [cpg]
CpG refers to any cytosine nucleotide in DNA that neighbors a guanine. CpG site comes from "cytosine-phosphate-guanine site". These sites have the potential for a methyl (or other derivative) to be attached. Dense regions of CpG's are known as CpG islands.
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Are CpG sites always palindromic? If so how?
I'm having a bit of difficulty understanding why CpG sites are said to be palindromes. In what sense are they palindromes? Like they always have this shape CGGC? (for example)
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How do DNA methylation canyons/DNA methylation valleys/DMCs differ from CpG islands?
Are these just both regions of the genome that are undermethylated? Is the only difference that for something to be a CpG islands it needs a high level of CpG sites and DMCs don't?
So could a 3.5kb ...
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what kind of dinucleotides can be considered important from a mutational point of view other than CpG islands?
CpG islands are regions with an high frequency of CpG (Cytosine-phosphate-Guanine) sites. The usual formal definition is that of a region with at least 200 bp, a GC percentage greater than 50% and an ...
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Observed to Expected CpG
Observed to Expected CpG is calculated as below :
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) where N = length of sequence.
I also don't ...
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what is CpG coverage? DNA starting material?
referring to this quote from an article about predicting methylation states:
"Because of the small amounts of genomic DNA starting material per
cell, single-cell methylation analyses are ...
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How does CpG island methylation lead to gene silencing?
I see often the blanket statement that CpG island methylation can lead to gene silencing. However, I have been unable to find a straightforward explanation of the mechanism by this.
Is it a purely ...
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Why does the gc content deviate from 50% in prokaryotes
I have read quite some articles but I can't figure out the main reason for gc content deviation in prokaryotes. In eukaryotes I can understand it, because the genome isn't composed at random, like ...
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Gene silencing: relative or absolute number of methylated CpG sites?
CpG content varies a lot across the human genome. What does determine a promoter to be silenced through DNA methylation: the fraction of CpG sites that are methylated or the total number of methylated ...
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How correlated are proximally related CpG sites in human DNA?
Cytosine residues in DNA that can be methylated (i.e. CpG sites) are likely to be in the same methylation state if they are geographically (proximally) close together.
I can only find one paper that ...
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