Acetylation vs Methylation?

[Plutocracy]

Hi all, I'm wondering why there are more scientific papers published on methylation over acetylation. On PubMed, there are 50k results when I type in "DNA methylation", but only 12k results when I type in "histone acetylation". Is there any clear reason why? Methylation being easier to assay, having more clinical importance, or being discovered earlier? Please let me know .

Edited August 20, 2015 by Plutocracy

[CPG]

I'll offer up a disclaimer that this is not my area of expertise, but it's a good question worth addressing so I'll give it a shot

 

The common thread here is that both epigenetic mechanisms affect what portions of the genome are accessible for transcription, but they tell you different things. I think there are a variety of reasons for the discrepancy you noted on Pubmed, but as you suggested the available assays and what they they tell you certainly play a role. The history of when epigenetic markers were discovered, and how useful they are would also factor in. Sometimes what is "trending" and gaining interest can factor in. (Suggestion: Try your Pubmed search again and look at the histogram that appears to the right which shows publications by year that match your query.) Eventually some assays gain enough momentum to become widespread lab techniques. This particular field that you are inquiring about is in a state where there are some well-established assays and others that are constantly changing with fancy new technology. DNA methylation assays would be in the former category.

 

Assays of methylation can tell you precise information about exactly which base pairs are methylated in a given sample. Our capabilities with genomic sequencing are becoming more advanced and cheaper all the time. The situation is much like Moore's Law for biotechnology in that respect. One common technique to do this uses the fact that methylation often occurs at Cytosine residues that are next to Guanine, so-called "CpG" sites. If you're familiar with PCR, it requires a little extra step where you treat the DNA sample with sodium bisulfite. If the Cytosine is not methylated, it will be converted to Uracil. If it is methylated (5-methylCytosine), it is not going to be converted. Then you're able to amplify your bisulfite-treated DNA using PCR and sequence it. Once you have that sequence, you can align your bisulfite-treated sample with a reference genome or untreated sample and you can see exactly which sites were converted and which were not converted. By inference, you now have very specific information about the epigenetic markers' position and can begin to interpret more about how that impacts gene expression at that locus. In a way, it gives you a nice clear "snapshot" of the state of DNA. I have never performed this technique myself, but my impression is that it is easier and cheaper than a lot of histone modification assays.

 

When dealing with histone modifications (such as acetylation), you are dealing with chromatin and have to deal with more macromolecular complexes that are important and ultimately can affect the accessibility of large portions of the genome for transcription. The 3D structure of this lends itself to a more difficult interpretation than the linear base pair approach as in classical genetics. Notice that you can look at DNA methylation from this perspective.

 

I think as a result, there tend to be other assays people often run first that don't zero in on histone acetylation per se. A common approach to identifying regions of the genome that are made either more or less accessible by the state of the chromatin would be something like chromatin immunoprecipitation (ChIP) which may not necessarily tell you specifically about acetylation. There can be many other chemical modifications involved (palmitoylation, methylation, sumoylation...) that may not be resolved by this method. Essentially, here is the basis for this assay: because histones are proteins that interact with DNA they can be chemically cross-linked so that they stay bound together. You would then be able to use enzymes to digest the exposed portions. Then using antibodies against histones, you precipitate out the regions that are undigested and pull down the undigested DNA along with the antibodies. At this point, you can determine which portions of the genome have been made inaccessible by chromatin modifications and which were exposed to enzymatic degradation.

 

 

If you're interested specifically in histone acetylation you would then proceed accordingly from there, but off the top of my head I'm afraid I'm not able to be a competent guide through this portion. Another broad route to go would be to look for expression of the enzymes responsible (Histone acetyltransferases / histone deacetylases). This alone could indicate their presence or absence but would not be very helpful in telling you where throughout the genome they are acting.

 

 

The technology for this stuff is rapidly advancing so I am pretty sure my knowledge is lagging behind the times. I may ask a friend and colleague who does this stuff for a living to offer her two cents if she has the time.

Edited August 21, 2015 by CPG

[Plutocracy]

Thank you a ton for your response! The histogram shows that methylation was discovered around the same time as acetylation, but the papers on DNA methylation were published at a much faster rate. I didn't know that bisulfite sequencing and ChIP were used as assays; I just assumed the ones were gel electrophoresis and RNA extraction.