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Histones & Epigenetics
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> Documentation [name=MrDr.Staffan]
###### tags: `page`, `histones`, `epigenetics`

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### Table of Contents
[TOC]
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[Top](#Table-of-Contents)

**Why this page?**
Histones & Epigenetics largely novel field expanding rapidly. Correlation to metabolism?

Bacteria do not have histones. More prone to mutation? https://en.m.wikipedia.org/wiki/Histone

[ My idea of methylation being a snapshot of the currently open pathways]

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# Epigenetics and metabolism
[Nature 2020](https://sci-hub.53yu.com/10.1038/s41576-020-0270-8) The evolving metabolic landscape of chromatin biology and epigenetics

[2020 Protein Cell](https://sci-hub.53yu.com/10.1007/s13238-020-00722-w) Non-enzymatic covalent modifications: a new
link between metabolism and epigenetics


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[See PTMs protein methylation](https://hackmd.io/@sholmqvist/BJpKurTBB/%2FArIdX3sNQNmpB7okZDFLBQ#Modification-by-Methylation--CH3)

**Arginine** can get me1 me2
**Lysine** can get me1, me2, me3

Tet1 Ten-eleven translocation (TET) enzymes
Tet2
Tet3

[Not expressed in astro?]

Tets are inhibited by Hypoxia, meaning without/before oxygen, methylation remain.

SAM levels are regulated by the level of methionine that is an essential amino acid in one-carbon metabolism, and methionine deficiency reduces liver SAM levels and H3K4 trimethylation drastically [76]. 1C units can be generated from serine by cytosolic or mitochondrial folate metabolism, and the loss of mitochondrial pathway renders cells dependent on extracellular serine to make 1C units [77].

Histone lysine methyltransferases are mostly specific towards one methylation state. Trimethylation of K is catalyzed by the SET domain-containing proteins, the SUV39 family, the MLL family, and the non-SET methyltransferase DOT1L

# Histone acidic patch. (Negative-Glu, Asp)
Likely Glutamic acids are modified by

Synthesis of dna/RNA also produce net water.(polymer formation)

But strand separation consumes water (de polymerization)

# Histone lysine (positively charged, Histidine, aspargine)

Lysin's terminal nitrogen is positive if saturated.

If a terminal nitrogen gets methylated it becomes a caged positive. I.e. Acting as a divalent ion?

# Epigenetics and mitochondria
[2022. Cells. An Epigenetic Role of Mitochondria in Cancer](https://doi.org/10.3390%2Fcells11162518)


# Epigenetics, methylation, DNA
Efficient deamination of 5-methylcytosines in DNA by human APOBEC3A, but not by AID or APOBEC3G
https://doi.org/10.1093/nar/gks685

The AID/APOBEC family of enzymes in higher vertebrates converts cytosines in DNA or RNA to uracil. They play a role in antibody maturation and innate immunity against viruses, and have also been implicated in the demethylation of DNA during early embryogenesis

5mC marks are placed on genomic DNA via DNA methyltransferases (DNMTs). There are 5 DNMTs in humans: DNMT1, DNMT2, DNMT3A, DNMT3B, and DNMT3L, and in algae and fungi 3 more are present (DNMT4, DNMT5, and DNMT6). [ref](https://doi.org/10.1093%2Fmolbev%2Fmsi098)
Bisulfite sequencing

In cancer, DNA can become both overly methylated, termed **hypermethylation**, and under-methylated, termed **hypomethylation**


# Methylation clock And age
https://www.nature.com/articles/s43587-023-00463-5

# Phosphatidyl -ethanolamine -> -choline
See Choline

See CBT CTH

*phosphatidylethanolamine*: a major lipid component of cellular membranes in a wide range of organisms
![](https://hackmd.io/_uploads/Sy4YFiVk3.png "ethanolamine" =100x)

Pemt // Phosphatidylethanolamine N-Methyltransferase

![](https://hackmd.io/_uploads/r1vTb78lh.png "choline" =100x)

SAM methylates PE into PC. (by PEMT)
This way PC fromation goes up (is in balance with) methylation of RNA, DNA, Lipid, Protein.

Estrogen boosts PEMT activity in the liver

[Towards understanding methyllysine readout](https://sci-hub.hkvisa.net/10.1016/j.bbagrm.2014.04.001)

## As a biomarker of aging
"Epigenetic age" refers to the connection between chronological age and levels of DNA methylation in the genome.
https://doi.org/10.1038%2Fs41576-018-0004-3

Coupling the levels of DNA methylation, in specific sets of CpGs called "clock CpGs", with algorithms that regress the typical levels of collective genome-wide methylation at a given chronological age, allow for epigenetic age prediction

Youth (0–20 years old), rate in DNA methylation faster as development and growth progresses,
and the changes begin to **slow down at older ages**.

[Multiple epigenetic age estimators exist. Horvath's clock measures a multi-tissue set of **353 CpGs**, half of which positively correlate with age, and the other half negatively, to estimate the epigenetic age](https://doi.org/10.1186%2Fgb-2013-14-10-r115)

Hannum's clock utilizes adult blood samples to calculate age based on an orthogonal basis of **71 CpGs**.
Levine's clock, known as DNAm PhenoAge, depends on **513 CpGs** and surpasses the other age estimators in predicting **mortality and lifespan**, yet displays bias with non-blood tissues.

[Methylation of ELOVL2 gene as a new epigenetic marker of age](https://doi.org/10.1111%2Facel.12005)
reports of age estimators with the methylation state of only **one CpG** in the gene ELOVL2.

"we identified 3 regions, the CpG islands of ELOVL2, FHL2, and PENK genes, whose methylation level strongly correlates with age. "

[HackMD:Lipids III FA metabolism:ELOVL2:](https://hackmd.io/@sholmqvist/BJpKurTBB/%2FFTG3zDLIRjOQtrWE2DD6gg#Elovl2) (C20- and C22-PUFA), acting specifically toward polyunsaturated acyl-CoA with the higher activity toward C20:4(n-6) acyl-CoA

# Epigenetics and One-Carbon Metabolism
See MHF

[2019. One-Carbon Metabolism: Linking Nutritional Biochemistry to Epigenetic Programming of Long-Term Development. **Annual Review of Animal Biosciences**](https://www.annualreviews.org/doi/10.1146/annurev-animal-020518-115206?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub++0pubmed)

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# Acetylation vs succinylation

Acetylation removes the positive charge of lysine -> relax neg. charged chromatin.

Succinylation introduce Negative charge to lysine(+) -> super-relax neg. chromatin.
"Found at initiation sites"
https://onlinelibrary.wiley.com/doi/full/10.1111/jcmm.16676

[**Open question?**
Are succinylation sites and acetylation sites the same?]
[Answer - Yes](https://www.cell.com/cell-reports/fulltext/S2211-1247(13)00386-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124713003860%3Fshowall%3Dtrue)


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# General

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**Also See**
[Also See Slc25a1 epigenetics reference](https://hackmd.io/@sholmqvist/BJpKurTBB/%2FXHmVBY6pTCWnwr1AA9xOkA#Mitochondrial-SLCs-and-epigenetics) Citrate?
[Also See Slc25a26 epigenetics reference](https://hackmd.io/@sholmqvist/BJpKurTBB/%2FXHmVBY6pTCWnwr1AA9xOkA#Mitochondrial-SLCs-and-epigenetics)
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**References**
Ulrey, C. L., Liu, L., Andrews, L. G. & Tollefsbol, T. O. The impact of metabolism on DNA methylation. Hum. Mol. Genet. 14, R139–R147 (2005). 10.1093/hmg/ddi100

![](https://i.imgur.com/o09kx9Y.png "metabolic effects (Supplement, KOs etc.) on DNA methylation" =200x)
**metabolic effects (Supplement, KOs etc.) on DNA methylation**

2019 - Mini review - The Impact of One Carbon Metabolism on Histone Methylation.
https://www.frontiersin.org/articles/10.3389/fgene.2019.00764/full

![](https://i.imgur.com/ycjsqyK.png "metabolites effect on methylation" =200x)
**metabolites effect on methylation - different models**

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# Epigenetic regulation of astro- neuro-genesis
NFIA, an inhibitor of Dnmt1 activity.
Nuclear Factor I A

Diseases associated with NFIA include Brain Malformations With Or Without Urinary Tract Defects and Cleft Palate, Isolated
[](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5201129/#:~:text=Astrocytic%20domains%20have%20been%20proposed,to%20be%20determined%20(21).)

# Histones

[Also See Redox](https://hackmd.io/@sholmqvist/BJpKurTBB/https%3A%2F%2Fhackmd.io%2FSfqcAU4uTK-tBuX41qqFrg)
[2020 The secret life of histones. Copper reductases](The secret life of histones. Copper reductases)

The crystal structure of the nucleosome core particle consisting of H2A , H2B , H3 and H4 core histones, and DNA. The view is from the top through the superhelical axis.

Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1/H5 are known as the linker histones.

## Linker Histones
Mm H1f0 H1f7 H1f8 H1f10
H1f1 H1f5 H1f2 H1f3 H1f4 H1f6

Hs
H1-0 H1-7 H1-8 H1-10
H1-1 H1-5 H1-2 H1-3 H1-6

H1F0 // H1-0 Mm H1f0
H1FNT // H1-7 Mm H1f7 // H1fnt
H1FOO // H1-8 Mm H1f8
H1FX // H1-10 Mm H1f10 // H1fx

HIST1H1A // H1-1 Mm H1f1
B // H1-5 Mm H1f5
C // H1-2 Mm H1f2
D // H1-3 Mm H1f3
HIST1H1E // H1-4 Mm H1f4
T // H1-6 Mm H1f6
## Histone regulation and turnover

[](https://www.frontiersin.org/articles/10.3389/fmolb.2022.990006/full)
**Nucleosome proteostasis and histone turnover**

During DNA replication (i.e., S phase of the cell cycle), cells must duplicate the entire genome, and as a result must contain approximately **twice the number of histone proteins** present in a non-dividing cell (Gunesdogan et al., 2014).

As discussed above, uncontrolled interactions of histones with DNA or other proteins can be geno- and proteotoxic and can result in genomic instability (Gunjan and Verreault, 2003; Singh et al., 2010).

Such catastrophic interactions are avoided during DNA replication by an orchestrated balance between histone synthesis, histone degradation, and histone chaperone activity, which cooperate to maintain nucleosome dynamics

in proliferating cultures of the yeast Saccharomyces cerevisiae, histone synthesis undergoes sub scaling during cell growth i.e., synthesis of histones is matched to DNA content and phase of the cell cycle, rather than cell size (Marzluff et al., 2008; Swaffer et al., 2021)

At the post-transcriptional level, the transcripts encoding replication-dependent histones exhibit a short half-life due to the lack of a stabilizing poly-A tail. However, they are stabilized and trafficked to the translational machinery during S phase by histone stem-loop-binding protein (SLBP), which binds to the 3’ untranslated region of these transcripts and is degraded at the end of S phase in the cell cycle (Zheng et al., 2003).

# Histone methylation
https://en.wikipedia.org/wiki/Histone_methylation

Histone methylation is a process by which methyl groups are transferred to amino acids of histone proteins

Addition of methyl groups to histones by **histone methyltransferases**

Methylation of histones can either increase or decrease transcription of genes, depending on which amino acids in the histones are methylated

associated with stimulation of neural pathways known to be important for formation of long-term memories and learning

Methylation of some lysine (K) and arginine (R) residues of histones results in transcriptional activation
> Examples include methylation of lysine 4 of histone 3 (H3K4me1), and arginine (R) residues on H3 and H4

**Histone methyltransferases** are enzymes which transfer methyl groups from S-Adenosyl methionine (SAM) onto the lysine or arginine residues of the H3 and H4 histones

The histone methyltransferases are specific to either lysine or arginine.

methyltransferases can add 1-3 methyls on the target residues

uman genes encoding proteins with histone methyltransferase activity include:

ASH1L
DOT1L
EHMT1, EHMT2, EZH1, EZH2
MLL, MLL2, MLL3, MLL4, MLL5
NSD1
PRDM2
SET, SETBP1, SETD1A, SETD1B, SETD2, SETD3, SETD4, SETD5, SETD6, SETD7, SETD8, SETD9, SETDB1, SETDB2
SETMAR, SMYD1, SMYD2, SMYD3, SMYD4, SMYD5, SUV39H1, SUV39H2, SUV420H1, SUV420H2

ash1l dot1l ehmt1, ehmt2, ezh1, ezh2 kmt2a kmt2b kmt2c kmt2d kmt2e


set, setbp1, setd1a, setd1b, setd2, setd3, setd4, setd5, setd6, setd7,


setd8, setdb1, setdb2 setmar, smyd1, smyd2, smyd3, smyd4, smyd5, suv39h1,


suv39h2, suv420h1, suv420h2

Couldnt find setd9

# Lysine modification

lysine monomethylation and lysine trimethylation of histone H3K4 respectively mark enhancers and promoters of active genes
https://www.nature.com/articles/nchembio.1497

## Trimethylated lysine
What is the difference between H3K9me2 and H3K9me3?
Unlike H3K9me3 domains, which are transcriptionally silent, H3K9me2 domains are transcriptionally active

2015 Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins [**too detailed**]
https://www.nature.com/articles/ncomms9911

2014 Where Does Nε-Trimethyllysine for the Carnitine Biosynthesis in Mammals Come from? [**vegtables? PLOS one**]
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084589

2020 Trimethyllysine: From Carnitine Biosynthesis to Epigenetics. Int J Mol Sci.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7764450/

2022 Trimethyllysine, a trimethylamine N-oxide precursor, predicts the presence, severity, and prognosis of heart failure [cardiac]
https://www.frontiersin.org/articles/10.3389/fcvm.2022.907997/full

# Histone acetylation
https://en.wikipedia.org/wiki/Histone_acetylation_and_deacetylation

Histone acetylation and deacetylation are essential parts of gene regulation

Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation

Catalysed by enzymes with "histone acetyltransferase" (HAT) or "histone deacetylase" (HDAC) activity.

type of epigenetic marker within chromatin

Acetylation removes the positive charge on the histones, thereby decreasing the interaction of the N termini of histones with the negatively charged phosphate groups of DNA

condensed chromatin is transformed into a more relaxed structure


## Histone acetyltransferase (HATs)

In addition to the core histones, certain HATs acetylate a number of other cellular proteins including transcriptional activators, basal transcription factors, structural proteins, polyamines, and proteins involved in nuclear import

**GNAT family **(Gcn5-related N-acetyltransferase)
includes Gcn5, PCAF, Hat1, Elp3, Hpa2, Hpa3, ATF-2, and Nut1

Kat2a // Gcn5
kat2b // Pcaf

Hpa2 // Hpse2
Hpa3 // Itga2b
Nut1 // ? cant find

**MYST family**

**p300/CBP family**

**Other.**

Clock Elp3 Gtf3c4 Hat1 Jmjd1c Kat5 Kat6a Kat2a Kat2b Kat6b
Kat7 Kat8 Ncoa1 Ncoa2 Ncoa3

## Histone deacetylase (HDACs)
**& SIRTS!** See Sirtuins

hdac1 hdac2 hdac3 hdac4 hdac5 hdac6 hdac7 hdac8 hdac9 hdac10

**Class I contains HDACs 1, 2, 3 and 8**

HDAC1 &

HDAC2 (HsAstro Barres)

HDAC3
HDAC8

**Class IIa contains HDACs 4, 5, 7 and 9**
Hdac4 (HsAstro Barres)

**Class IIb contains HDACs 6 and 10**

**Class III contains the sirtuins (SIRT1-7)**
[Also see Sirts in FA metabolism](https://hackmd.io/@sholmqvist/BJpKurTBB/%2FLviQI1LDRae6qatO08KKLQ#Sirts-Sirtuins)
Sirt2 - Oligo mice
Sirt2 - HsBarres Oligo+Astro


**Class IV contains only HDAC11**

HDAC11


Classes I, II and IV use Zn+ as a co-factor, whereas catalysis by Class III enzymes requires NAD+ as a co-factor, and members of this subfamily have ADP-ribosylase activity in addition to protein deacetylase function

HDACs have more general protein deacetylase activity, being able to deacetylate lysine residues in non-histone proteins [3] such as microtubules [9], the hsp90 chaperone [12] and the tumour suppressor p53 [15]

## Histone acetylation & BET-family proteins

brd1 brd2 brd3 Brd4 brdt

See powerpoint "BBOX_Creb_BRAF_BET"



# Methodological

Use either antibodies against acetylated forms of a protein.
Will detect a specific site acetylation.

Look at global HAT & HDAC acitvity. Changes in e.g. mRNA levels.

Immunohistochemical analysis of H3Ac, H4Ac and H3K18Ac
E.g. https://ar.iiarjournals.org/content/36/8/3961.long
histone H3 pan-acetylation (H3Ac; dilution 1:2500; #06-599)
histone H3 lysine 18 acetylation (H3K18Ac; 1:2500; #07-354)
histone H4 pan-acetylation (H4Ac; 1:2500; #06-866)