Answers.Body: <p>If I'm understanding you correctly, by "types of DNA methylation" you mean "nucleotide contexts where DNA methylation occurs".
  This is going to be a function of the methyltransferase proteins involved in the methylation process, and this largely depends on the organism, and even cell type being studied.</p>
  
  <p>Generally, what has been observed is:</p>
  
  <ol>
  <li>The phenomenon of DNA methylation (methyl group addition to <code>A</code>/<code>C</code> nucleotides) has been observed in both eukaryotes and prokaryotes</li>
  <li>The nucleotide context of DNA methylation differs between the organism, and even the cell type being studied, due to the methyltransferase proteins involved in the methylation process</li>
  <li>Methylation of RNA, predominantly in N6 position <code>A</code>s</li>
  </ol>
  
  <p>In humans:</p>
  
  <ul>
  <li>The <em>DNMT1</em> methyltransferase is referred to as the "maintenance" methyltransferase, due to its observation of binding to hemi-methylated <code>CpG</code> sites (methylated <code>C</code> on one strand and not the other)</li>
  <li>The <em>DNMT3A/B</em> methyltransferases are referred to as the "<em>de novo</em>" methyltransferases for their affinity of binding to naked DNA</li>
  <li>These proteins almost exclusively methylate <code>CpG</code> dinucleotides in human cells</li>
  <li>There are cases of non-negligible methylation of cytosines in <code>CHG</code> and <code>CHH</code> nucleotide contexts (brain tissues, for example)</li>
  </ul>
  
  <p>The proteins and their effects on DNA methylation are similar for mice, as well.
  Plants tend to have similar nucleotide contexts of methylation, but have much more <code>CHG</code> and <code>CHH</code> methylation than mammals.</p>
  
  <p>In prokaryotes, again, the nucleotide context is dependent on the proteins.
  Like you mentioned, we have that:</p>
  
  <ul>
  <li>The Dam methyltransferase methylates the N6 position of the <code>A</code> in <code>GATC</code></li>
  <li>The Dcm methyltransferase methylates the C5 position of the second <code>C</code> in <code>CCAGG</code> and <code>CCTGG</code></li>
  <li>The EcoKI methyltransferase methylates <code>A</code>s in <code>AACNNNNNNGTGC</code> and <code>GCACNNNNNNGTT</code></li>
  </ul>
  
  <p>NEB has a good <a href="https://international.neb.com/tools-and-resources/selection-charts/dam-dcm-and-cpg-methylation" rel="noreferrer">list of its restriciton enzymes</a>, and how DNA methylation affects their binding/cutting, which also gives some info on the type of methylation in cells.</p>
  
  <p>As for a "comprehensive list", you'll likely have to find some relevant review papers in your organism(s) of interest and compile on yourself.</p>
  
  <p>But also think about how you're phrasing your question.</p>
  
  <blockquote>
    <p>Is there a comprehensive list of which sequences of base pairs <em><strong>allow</strong></em> methylations to occur?</p>
  </blockquote>
  
  <p>I don't think that many papers studying DNA methylation think of the nucleotide context <strong>allowing</strong> methylation to occur so much as <strong>observing</strong> the context in which methylation occurs and how it relates to proteins in those organisms.</p>
  
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Answers.Text: Yes, I was referring to nucleotide context where methylation occurs. Thanks for the great response and explaining differences between organisms/cells, but my original question remains unanswered (i.e. in approximately how many contexts have methylations been found across species?). Five to ten, or possibly hundreds? I seem to only see the above 3-5 ever mentioned. Is that because this is still an active area of research? Are these discovered through experimentation with the above restrictive enzymes?
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Answers.UserDisplayName: James Hawley
Body: <p>My current understanding is:</p>
  
  <ul>
  <li>bases <code>A</code> or <code>C</code> can become methylated due to interaction with a methyltransferase</li>
  <li>these methylations only occur if the <code>A</code> or <code>C</code> is surrounded by a specific sequence of base pairs</li>
  <li>different types of DNA methylations occur in different species at different rates</li>
  </ul>
  
  <p>Is there a comprehensive list of which sequences of base pairs allow methylations to occur? </p>
  
  <p>I'm currently aware of:</p>
  
  <ul>
  <li>dcm-methylation: <code>CCAGG</code> or <code>CCTGG</code></li>
  <li>dam-methylation: <code>GATC</code></li>
  <li>EcoKI methylation: <code>AACNNNNNNGTGC</code> or <code>GCACNNNNNNGTT</code></li>
  <li>CpG methylation: <code>CG</code> (or <code>CHG</code> or <code>CHH</code>)</li>
  </ul>
  
Tags: <phylogenetics><methylation>
Title: How many types of DNA methylation are there?
ThreadText: # How many types of DNA methylation are there?
  
  (Asked by: username_0 on 2019-10-10)
  
  My current understanding is:
  
  * bases `A` or `C` can become methylated due to interaction with a methyltransferase
  * these methylations only occur if the `A` or `C` is surrounded by a specific sequence of base pairs
  * different types of DNA methylations occur in different species at different rates
  
  Is there a comprehensive list of which sequences of base pairs allow methylations to occur?
  
  I'm currently aware of:
  
  * dcm-methylation: `CCAGG` or `CCTGG`
  * dam-methylation: `GATC`
  * EcoKI methylation: `AACNNNNNNGTGC` or `GCACNNNNNNGTT`
  * CpG methylation: `CG` (or `CHG` or `CHH`)
  
  **Tags:** phylogenetics, methylation
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-10-11. Score: 5 | Accepted answer
  
  If I'm understanding you correctly, by "types of DNA methylation" you mean "nucleotide contexts where DNA methylation occurs".
  This is going to be a function of the methyltransferase proteins involved in the methylation process, and this largely depends on the organism, and even cell type being studied.
  
  Generally, what has been observed is:
  
  1. The phenomenon of DNA methylation (methyl group addition to `A`/`C` nucleotides) has been observed in both eukaryotes and prokaryotes
  2. The nucleotide context of DNA methylation differs between the organism, and even the cell type being studied, due to the methyltransferase proteins involved in the methylation process
  3. Methylation of RNA, predominantly in N6 position `A`s
  
  In humans:
  
  * The *DNMT1* methyltransferase is referred to as the "maintenance" methyltransferase, due to its observation of binding to hemi-methylated `CpG` sites (methylated `C` on one strand and not the other)
  * The *DNMT3A/B* methyltransferases are referred to as the "*de novo*" methyltransferases for their affinity of binding to naked DNA
  * These proteins almost exclusively methylate `CpG` dinucleotides in human cells
  * There are cases of non-negligible methylation of cytosines in `CHG` and `CHH` nucleotide contexts (brain tissues, for example)
  
  The proteins and their effects on DNA methylation are similar for mice, as well.
  Plants tend to have similar nucleotide contexts of methylation, but have much more `CHG` and `CHH` methylation than mammals.
  
  In prokaryotes, again, the nucleotide context is dependent on the proteins.
  Like you mentioned, we have that:
  
  * The Dam methyltransferase methylates the N6 position of the `A` in `GATC`
  * The Dcm methyltransferase methylates the C5 position of the second `C` in `CCAGG` and `CCTGG`
  * The EcoKI methyltransferase methylates `A`s in `AACNNNNNNGTGC` and `GCACNNNNNNGTT`
  
  NEB has a good [list of its restriciton enzymes](https://international.neb.com/tools-and-resources/selection-charts/dam-dcm-and-cpg-methylation), and how DNA methylation affects their binding/cutting, which also gives some info on the type of methylation in cells.
  
  As for a "comprehensive list", you'll likely have to find some relevant review papers in your organism(s) of interest and compile on yourself.
  
  But also think about how you're phrasing your question.
  
  > Is there a comprehensive list of which sequences of base pairs ***allow*** methylations to occur?
  
  I don't think that many papers studying DNA methylation think of the nucleotide context **allowing** methylation to occur so much as **observing** the context in which methylation occurs and how it relates to proteins in those organisms.
  
  > **Comments:**
  > **username_0**: Yes, I was referring to nucleotide context where methylation occurs. Thanks for the great response and explaining differences between organisms/cells, but my original question remains unanswered (i.e. in approximately how many contexts have methylations been found across species?). Five to ten, or possibly hundreds? I seem to only see the above 3-5 ever mentioned. Is that because this is still an active area of research? Are these discovered through experimentation with the above restrictive enzymes?  
  
  ---
  
  