What Are Epigenetic Tags/Factors Made Of?

[icakeov]

Hello
I am curious about whether:
- epigenetic tags/factor compounds are coded by genes? Or are they "external" compounds?
- are epigenetic factors/tags usually monomers? Or can they be polymers?
- Is there a comprehensive list somewhere of all epigenetic tags/factors?
(I have been attempting to use google to find info above to no avail, I don't know if I am using the wrong terminology)
Thanks for any feedback!

 

[BillTre]

- epigenetic tags/factor compounds are coded by genes? Or are they "external" compounds?

The tags are usually small molecules that are either:
added to DNA in certain places
or added to proteins (like histones) associated with the DNA which seem to preserve and replicate their location with respect to DNA sequence when the DNA is replicated.
There are genes that code for multi-protein systems that generate and maintain genetic tags biochemically.
The tags are made indirectly through reactions controlled by proteins encoded in the genome.
Therefore, tags are not external compounds.

 

[jim mcnamara]

Two examples: methylation of DNA - methyl groups added, histones added (as @BillTre mentioned).
See the "candy example" of the chemistry of epigenetics in this video:

 

[pinball1970]

Hello
- Is there a comprehensive list somewhere of all epigenetic tags/factors?
(I have been attempting to use google to find info above to no avail, I don't know if I am using the wrong terminology)
Thanks for any feedback!

Nessa Carey has written a couple of books that will give you an overview. Junk DNA and the epigenetic revolution. They are not textbooks but give lots of examples and ref papers, studies

 

[Ygggdrasil]

A note on terminology. Many people refer to DNA modification and histone modifications as epigenetic tags (because they are acting as an extra layer of information on top of the genome). This definition is problematic because of confusion with other definitions of the term epigenetic, particular those surrounding cell states that are heritable across cell divisions without underlying changes in DNA sequence (see https://www.sciencedirect.com/science/article/pii/S096098220701007X for more discussion). While DNA methylation is certainly heritable and epigenetic, there is much debate as to the extent to which histone modifications are heritable and epigenetic (for example, see http://science.sciencemag.org/content/361/6397/33.long for a discussion).

So, just because many people refer to histone modifications as "epigenetic," do not assume that they are necessarily behind some "epigenetic" phenomena during cell differentiation and development (this is one complaint I have with the otherwise excellent Nessa Carey video above)!

- epigenetic tags/factor compounds are coded by genes? Or are they "external" compounds?

The enzymes that deposit DNA and histone modifications are encoded by genes in the human genome. External factors can affect the activity of these enzymes, but the enzymes themselves as well as the source of the tags are synthesized in the body (for example, methylation comes from the compound S-adenosylmethionine which is synthesized in the body via folate metabolism).

- are epigenetic factors/tags usually monomers? Or can they be polymers?

The tags are generally monomeric, though in the case of histone methylation, multiple methyl groups can be appended to a single amino acid side chain. For example, lysine 27 of the histone H3 protein (referred to as H3K27) can have either one, two or three methyl groups attached and the different methylation states are associated with different biological functions.

One type of histone post-translational modification called ubiquitinylation can be polymeric, though poly-ubiquitinylation is generally associated with protein degratation while mono-ubiquitinylation can act as a regulatory tag on histone proteins.

- Is there a comprehensive list somewhere of all epigenetic tags/factors?

Many molecular biology and cell biology textbooks would have a good discusison of the topic. The answer also depends on the organism being studied. Bacteria have a very different types of DNA methylation than humans and lack histone proteins. Plants have multiple different types of DNA methylation machinery that functions in different ways than in humans. Various species of animals (e.g. fruit flies, a common model organism in genetics research), have negligible amounts of DNA methylation compared to humans.

Here is a good review discussing histone modifications: https://www.annualreviews.org/doi/abs/10.1146/annurev.genet.032608.103928

 

[pinball1970]

I didn't realize that was her in the video! I'll watch it now I think!

 

[pinball1970]

Two examples: methylation of DNA - methyl groups added, histones added (as @BillTre mentioned).
See the "candy example" of the chemistry of epigenetics in this video:

She cites both books at the end too, it was 39 minutes so I didn't bother. I have now so now I think i will read junk DNA again