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 undermethylated region of the genome be considered a DMC even though there are not many methylatable CpG sites there?



1 Answer 1


The level of methylation does not play a role in defining a CpG island, whereas it is central to defining canyons/valleys.

CpG islands are areas of the genome that are >200bp in length and which contain an observed-to-expected number of CGs > 0.6, and a CG% > 50%.

A methylation canyon or valley is instead an area that is >3.5kb in length and contains < 10% average methlation at any given CpG.

  • $\begingroup$ This looks like a helpful answer, but it would be improved by citations or links to supporting materials. $\endgroup$ Jan 19, 2023 at 20:20
  • $\begingroup$ @Risk, Do you have any references to back up those numbers? I found that it sort of matches the definition of CpG island in a paper: "annotates the segment as a CpG island if it satisfies the following criteria: (1) G + C content >50%, (2) length >200, and (3) the ratio of observed to expected number of CpG dinucleotides (“CpG O/E”) >0.6". But in a paper the methylation valley is longer "> 5kb" and notes that most contain few CpG islands. $\endgroup$
    – llrs
    Feb 14, 2023 at 14:31
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    $\begingroup$ @llrs The CpG definition is taken from UCSC genomics institute here: link The definition for valley/canyon came from here: [link[(ncbi.nlm.nih.gov/pmc/articles/PMC4719427/#B1). $\endgroup$ Feb 14, 2023 at 18:56
  • $\begingroup$ @Risk many thanks! I'm not sure about the second link: In the paper "Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells", (first reference from the second link) under the section "Identification of DNA Methylation Valleys" it says "These DMVs range in size from 5 kb to 68 kb and are much larger than the CGIs in these regions ". Did you meant to link a different paper? $\endgroup$
    – llrs
    Feb 15, 2023 at 8:47
  • $\begingroup$ @IIrs - Sorry I must've messed up the link. If you look in the introduction of that paper, 4th paragraph: "identified around 1,000 larger (>3.5-kb) genomic domains with low average methylation levels, termed DNA methylation valleys or DNA methylation canyons (1, 15). These elements remained unmethylated during differentiation and were often associated with developmental genes". One of those papers is the paper you're referring to, the other one is the one I tried to link to. $\endgroup$ Feb 16, 2023 at 4:57

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