Histones, Acetylation, Methylation, HDAC, DNA and mRNA

Long time members of this forum have seen me go on about HDAC inhibition and I have been asked to write a post to explain what this is about. I think it is probably best to do something with a bit of detail. I may not get everything right, but if anything is wrong please tell me and I will set out to edit this OP.

The Genome is the entirety of the DNA in cells. In short what happens is that DNA is transcribed into messenger RNA (Ribonucleic Acid) - mRNA. The mRNA then goes to the Ribosome and proteins are created from it through a process called translation.

I have a hypothesis that a large part of the difficulties that result from Aging (age based diseases) arises from failures with these two processes.

When everything is working properly the DNA is wrapped around a structure called the Histone. This is a mixture of a number of proteins and about 146 base pairs of DNA are wrapped around each set of histone proteins.

There is arguably an evoluntionary advantage to this as a structure as it means that the DNA is to some extent protected from harm by being held in a relatively compact structure. Hence wandering reactive molecules may not get to the DNA as readily.

However, because of this wrapping up of the DNA, there are difficulties creating mRNA from the DNA.

The main enzyme that is used to transcribe DNA into mRNA is called RNA Polymerase II (aka RNAPII, RNA pol II).

This reacts with the DNA to produce mRNA (not as a precise copy, but as a copy with the same meanings, uracil being used instead of thymine).

However, the DNA is wrapped tightly around the histone. This makes transcription difficult (it may be impossible, I don’t know).

There are various changes that can be made to the histone. One of the most common is for it to be acetylated. An acetyl group is added to one of the lysines neutralising the positive charge so the negative DNA drifts away from the histone.

In essence, therefore, the acetylation of the histone enables the opening up of DNA so that RNA Pol II can transcribe it.

RNA Pol II is in fact a complex of enzymes and it drags along with it a Histone Acetyl Transferase. This processes the histone and uses a substrate of acetyl-CoA and it adds the acetyl group to one of the lysines on the histone.

This only happens on each set of the histones so for about every 146 base pairs a molecule of acetyl-CoA is needed for the DNA to be transcribed. This is a useful energy control as at a cellular level the concentration of acetyl-CoA in the cytosol indicates the energy availability to make proteins.

Once the DNA has been transcribed then there is a Histone Deacetylase (HDAC) enzyme which can close down the DNA again so it is safer from damage.

There are HDAC inhibitors (there are lots of these) and they react with the HDACs to prevent some of them from closing down the histone.

There is at this point quite a bit that is not entirely clear. It is clear that RNA Pol II stalls from time to time. I think that is from a shortage of acetyl-CoA.

It is also clear that when there is a shortage of acetyl-CoA, RNA Pol II can terminate before finishing off the gene. That is called a splice. Some splices are welcomed by the cells, but other splices (called aberrant splices) can cause negative consequences (such as growth of the prostate).

We also know that at times methyl groups are added to the DNA (not the histone, but the DNA) and that this can discourage transcription.

We know that HDAC inhibitors affect transcription.

Hence I have a thought experiment. If you have RNA Pol II stuck at a particular histone because of a shortage of acetyl-CoA and then a HDAC comes around and deacetylates the histone. What happens? Is that the event which creates the alternative splice?

We know that HDAC inhibition can be helpful. This can be seen by the way in which the queen bee is quite different to a worker bee although their DNA is the same. The Worker Bee is allowed about 3 days of Royal Jelly whereas the Queen eats RJ all her life. One of the main ingredients in RJ is an HDAC inhibitor called (E)-10-hydroxy-2-decenoic acid (10HDA) which is about 5% of RJ.

The Queen lives a lot longer than worker bees as well.

Hence if one of the problems of aging is the failure to produce particularly the longer proteins then HDAC inhibition (a small amount of it, a large amount can cause ATP depletion) is something which would act to improve the situation.

This does seem to fit with the observed facts.

I think there are energy issues with translation, but that is a separate issue.

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https://academic.oup.com/geronj/article-abstract/3/1/9/548317?redirectedFrom=fulltext

In experiments conducted with drosophila melanogaster, Dr. Gardner noted that biotin had no effect upon the life span, but both pyridoxine and sodium yeast nucleate lengthened it. These three substances in combination materially extended the span of life, and with the addition of pantothenic acid a substantial increase was demonstrated.

summary

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John, great post! Helps me understand your theory. Not sure how the second post relates to the first. Did some research on HDAC inhibitors and now understand that better. Couple of questions:
Under normal functioning, “In essence, therefore, the acetylation of the histone enables the opening up of DNA so that RNA Pol II can transcribe it.”
Then, “Once the DNA has been transcribed then there is a Histone Deacetylase (HDAC) enzyme which can close down the DNA again so it is safer from damage.
There are HDAC inhibitors (there are lots of these) and they react with the HDACs to prevent some of them from closing down the histone.”
Do they prevent some of them from closing down because of a shortage of acetyl-CoA? So, that creates a splice? What causes some splices to be good and some to be aberrant?
" If you have RNA Pol II stuck at a particular histone because of a shortage of acetyl-CoA and then a HDAC comes around and deacetylates the histone. What happens?" So, is this a malfunction of the system where an HDAC inhibitor should have prevented the deacetylation of the histone because the process was stalled? So, more HDAC inhibition should mean fewer splices? But what about the splices that are welcomed by the cells?
And how does supplementation with citrates affect this process?
I used these 3 Wikipedia entries for background:
https://en.wikipedia.org/wiki/Histone_deacetylase_inhibitor
https://en.wikipedia.org/wiki/Acetyl-CoA
https://en.wikipedia.org/wiki/Citric_acid_cycle

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Think that there is this enzyme (HAT) which needs acetyl-CoA to turn up, a bit like a bus turning up a a bus stop. Until the acetyl-CoA molecule turns up it cannot do its thing (which is to put an acetyl group on the histone.)

It is possible for RNA Pol II to be terminated whilst waiting for the bus.

The removal of the acetyl group can occur any time after it has been added.

The question as to which splices are good and bad is really dependent on the effect of the resultant protein.

Supplementation with citrates increases the amount of acetyl-CoA,

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Interesting theory and another reason to eat low carbs and run on ketones:

Ketone bodies, particularly β-hydroxybutyrate (β-HB), have been shown to have HDAC inhibitory activity, which contributes to their regulatory effects on gene expression and potential health benefits. β-Hydroxybutyrate is one of the primary ketone bodies produced during ketosis, a metabolic state induced by fasting, prolonged exercise, or a ketogenic diet.

Do you know how they compare to other HDAC inhibitors?

β-HB primarily inhibits class I HDACs, offering a degree of specificity. However, as a naturally occurring metabolite, its role in HDAC inhibition is just one aspect of its functions in the body.
[…]
Ketone bodies like β-HB offer a more physiological and potentially broader approach to leveraging HDAC inhibition’s benefits,

Butyrate also is an HDACi. HDACis vary as what concentration is needed to have a given strength and which types (claases) of HDAC they affect. However, I don’t have a useful answer.

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John,

Have you (or anyone else here) tried Valproic acid for HDAC inhibition activity?

I haven’t. Off the top of my head I think it is a much more powerful HDAC inhibitor running in the nanomolar range rather than the micromolar range. I like the substances that are known to be HDAC inhibitors which there is a long track record of people eating (such as curcumin, pterostilbene, quercetin, berberine). That is because we would be pretty certain to know of any side effects at any dosage.

My approach is to use a number of HDAC inhibitors simultaneously with a view to accumulating an HDAC inhibition whilst minimising side effects.

If you do too much HDAC inhibition you can cause ATP depletion in a cell. (all the focus goes onto transcription leaving insufficient energy for translation).

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Worth knowing that pterostilbene increases LDL cholesterol.

Hi John, thank you for a very interesting and well presented theory. I have been looking into “sodium yeast nucleate”. Where can it be sourced? Does it have a more typical name in the supplement realm?
:pray: :slight_smile:

I think it is RNA extract.

I buy this:
https://www.amazon.co.uk/gp/product/B07YFS5XXW/

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I keep an eye on my overall LDL position and overall ApoB position. I am content with these values.

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Thank you @John_Hemming :star_struck:

I believe commercial sources of yeast extract include “Vegemite” and “Promite” in Australia and “Marmite” in the UK.

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HDAC1/2 inhibitor therapy improves multiple organ systems in aged mice

Aging increases the risk of age-related diseases, imposing substantial healthcare and personal costs. Targeting fundamental aging mechanisms pharmacologically can promote healthy aging and reduce this disease susceptibility. In this work, we employed transcriptome-based drug screening to identify compounds emulating transcriptional signatures of long-lived genetic interventions. We discovered compound 60 (Cmpd60), a selective histone deacetylase 1 and 2 (HDAC1/2) inhibitor, mimicking diverse longevity interventions. In extensive molecular, phenotypic, and bioinformatic assessments using various cell and aged mouse models, we found Cmpd60 treatment to improve age-related phenotypes in multiple organs. Cmpd60 reduces renal epithelial-mesenchymal transition and fibrosis in kidney, diminishes dementia-related gene expression in brain, and enhances cardiac contractility and relaxation for the heart. In sum, our two-week HDAC1/2 inhibitor treatment in aged mice establishes a multi-tissue, healthy aging intervention in mammals, holding promise for therapeutic translation to promote healthy aging in humans.

https://www.cell.com/iscience/fulltext/S2589-0042(23)02758-X

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Looks like a definite candidate for the ITP.
I’d like to get hold of some. 1 Mg/kg pulsed 1 month on, one off.
Pity it’s probably like “Unobtainium”.

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Here are some good reviews on Histone acetylation / deacetylation for anyone interested.

A short guide to histone deacetylases including recent progress on class II enzymes | Experimental & Molecular Medicine.

Histone acetylation: molecular mnemonics on the chromatin

https://www.nature.com/articles/nrn3427

Recent developments of HDAC inhibitors: Emergingindications and novel molecules
https://bpspubs.onlinelibrary.wiley.com/doi/epdf/10.1111/bcp.14889

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In the end it is the transcription process that needs intervention

For the life of me IDK why these labs don’t keep a cohort of mice alive and monitor their survival curve. They can still publish the data from the euthanised mice.
If the survivors outlive controls they can publish that, too.

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