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I am looking for a reference to help me understand what is meant by acronyms such as : H3K9me1, H3K9me2, and H3K9Ac.

I know that these are all histone proteins, but is there a general nomenclature algorithm for all cellular proteins? Are H3K9me1 and H3K9me2 just different proteins that methylate the same region? What is meant by H3K? Etc.

Thanks!

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For H3K9me1:

  • H3: name of the histone
  • K9: amino acid and position (K = lysine, position 9) of modification
  • me1: modification (me = methylation, ac = Acetylation), and number of modifications

So H3K9me1 means that the 9th residue (lysine) of histone H3 was monomethylated. Similarly H3K9Ac means that same residue was acetylated.

Wikipedia gives a decent explanation of the nomenclature of histone modifications, and there is also a more detailed table in Nature Structural & Molecular Biology.

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  • $\begingroup$ Thanks! This is great, now when we say H3K9me1 vs. H3K9me2, is there a different protein that performs this single vs. double methylation, or can chIp-Seq or western blotting techniques somehow differentiate between when the same protein adds one or two methyl groups? $\endgroup$ – NaiveHalmos Sep 16 '15 at 16:16
  • $\begingroup$ @NaiveHalmos I don't know offhand but there are a number of histone methyltransferases (see en.wikipedia.org/wiki/Histone_methyltransferase). It looks like there are a number of methods to differentiate between different modifications, e.g. see ncbi.nlm.nih.gov/pubmed/22130888 $\endgroup$ – Harry Vervet Sep 16 '15 at 16:36
  • $\begingroup$ There is also a cool table at Cell Signaling Technology's website that lists all the known or suspected histone modifications, the modifying enzymes (again, if known), and known or suspected functions. $\endgroup$ – MattDMo Sep 17 '15 at 1:21
  • $\begingroup$ @NaiveHalmos if an appropriate reagent is available, yes you can differentiate between mono-, di-, and tri-methylation by Western or ChIP/ChIP-Seq. My lab uses a lot of CST's stuff, so I know they have a bunch of specific antibodies, but I'm sure other vendors do as well. $\endgroup$ – MattDMo Sep 17 '15 at 1:24

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