A brief introduction to Epigenetics

Nutriepigenomics reveal how diet determine epigenetic modifications both histone and Non-coding RNAs of the human genome regulating both to health and disease. Histone modifications is the mechanism by which methylation and acetylation of histone tails regulates the epigenetic cellular system.

Each of the eight histone proteins make an octamer (see figure 1a & 1b), and a combination of post-translational modifications (methylation and acetylation) occur at sites on the nucleosol histone-core tails. Although other modifications occur, phosphorylation, Sumoylation, ubiquitylation(Ub), GlcNAcylation, citrullination, krotonilation, and isomerization. The later three are more recent discoveries, these modifications add or remove from histone amino acid residues via a set of enzymatic reactions.

Post-translational modifications (PTMs) of histone-tails have resultant changes in chromatin that may induce and increase or decrease in DNA-histone affinity (udali S, Guarini et al - 2013) an increase of DNA-histone affinity results in transcriptional repression the opposite results with relaxation of the DNA coils around the histone proteins for gene expression. Histone methylation normally is on arginine, lysine, and histone residues; the magnitude and location determines transcriptional activation or repression of gene expression (see figure 1a & 1b).

Figure 1a shows a graphical representation of the structural chromosomal chromatin with coiled DNA, the nucleosol DNA coils around the histone proteins to make a nucleosome that coil to make a chromatin fiber that coils to make a chromosome.

Figure 1a - the DNA coils around the octamer/nucleosome core complexes which are bound firmly with DNA for gene repression.

DNA double helix

Octamer

HI histone

N#cl#osme

300 nm

chromatin fibre

30 nm

250-nm-wicJe fiber

700 nm

1400 nm

Figure 1a shows a graphical representation of the structural chromosomal chromatin with coiled DNA, the nucleosol DNA coils around the histone proteins to make a nucleosome that coils to make a chromatin fiber that coils to make a chromosome.

The process of Acetylation unbinds the DNA loosely around the octamer so that gene expression can occur, the chromatin fiber consists of DNA wound around histone protein complexes that is the nucleosome coiled into the hairpin structure chromatin fiber; acetylation of histones effect how accessible the DNA is for repression or expression, that is for gene expression (see figure 1b).

Histone modifications

Histone modifications HTMs are diverse, including phosphorylation, methylation, acetylation, ubiquitylation and during meiotic spermatogenic cell division most haploid genome are misplaced by protamine, though not all some are retained so to transmit genetic information to the progeny. However, histone modifications are implicated with cell senescence, cancer, cardiovascular disease, obesity diabetes and many other epigenetic modifications.

Nucleosome

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Figure 1b shows graphical representation and x-ray diffraction analysis (front and side orientation) of the nucleosome and histone tails providing access for transcription, mostly controlled by histone proteins. the nucleosome consists of an octamer made of two subunits contain four histone proteins: H2A, H2B, H3, and H4. (With tails) that is a total of eight histone proteins, 2 tetramers (H2-H4) and 2 (H2A-H2B) dimers in the histone/octamer core complex. The ammo acid linker proteins - H1 etc.... functions to bind and stabilize inter-nucleosol DNA, the linker DNA joins octamer together to make the nucleosome; the histone proteins undergo post-translational (PTM) and post transcriptional modifications in different ways (some are salt dependent). Some histone modifications disrupt nucleosol DNA interactions, thereby the nucleosomes unwind or relax for gene expression.

Histone methylation can activate or suppress gene expression in accordance to different lysine dependent states (i.e. Mono-methyl, Di-methyl, or Tri-methyl states; the demethylated function is in reverse (relaxes the DNA coils) on the histone-tails during transcription. There are seven transcriptional regulatory core histone modifications on the H3 histone-tail that is:- 2 active promoters (H3K9acH3K4me3), 2 enhancer promoters (H3K4me1 (stem cell line), H3K27ac), 1 transcribed gene bodies (H3K36me3), 1 polycomb promoters (H3K27me3), 1 heterochromatin (H3K9me3) it is possible to define chromatin profile status (biomarkers) of the genome via the histone-tail modification epigenetic biomarker status (see figure, 1d & Appendix, I, II).

Other than Acetylation(Ac) and methylation(Me) there are other types of histone modifications have been discovered:- phosphorylation(P), sumoylation, ubiquitylation(Ub), GlcNAcylation, citrullination,

krotonilation, and isomerization the later three are more recent discoveries, all the above modifications add or remove from histone protein's amino acid residues via a set of enzymatic reactions (see figure 1c & 1d, and Appendix, I,

II).

Histone proteins are (H1 -linker protein, H3, H4, H2A, H2B) which are dependent on Post-Translational Modification (PTMs); PTMs normally are reversible and effect all chromatin remodeling and centromere formation. PMTs are classified as reader, writer and eraser and are either: Effectors(enhancers) or Presenters(promoters). Histone PTMs may alter the chromatin state making it active, inactive or poised state. PTM associations may occur with cis or trans events on same or nearby histone tails, within the same or neighboring nucleosome (Zang T et al - 2015).

Figure 1c - shows adapted graphical representation showing numbered Histone modifications with Histone-tails, showing the modifications are transactional epigenetic markers that undergo events via: Acetylation(Ac), methylation(Me), Phosphorylation(P), ubiquitylation(Ub) all are necessary to allow activity of the chromatin remodeling complex.

Methylation activates or represses gene expression depending on which residue is methylated; Methylation of histone methyltransferases (HMTs), of Lysine SET domain containing (histone tails) and Non-SET domain containing histone cores. All of the above modifications add or remove from histone proteins amino acid residues via a set of enzymatic reactions (see figure 1c & 1d, appendix, I, II)

Mechanisms of nutrition on epigenetics

Three epigenetic mechanisms: DNA methylation, histone modification, and non-coding RNA that is involved in gene silencing.

The nutritional variables that effect the function of the epigenome are biological molecules of vitamins, minerals and herbs that have epigenetic benefit diminishing the onset of illness; achieved via epigenetic enhancement during histone acetylation of the HAT enzymes occurs on the c-amino lysine residue. Histone acetyltransferase (HAT) inhibits gene expression, and the HDAC enzyme, histone deacetylase (HDAC) enables gene expression. Thus, HAT and HDAC are involved in control gene expression switching gene expression off (methyl-groups) or on (acetyl- groups) via structural histones and histone-tails that compress the DNA for repression and uncoil the DNA for gene expression. HAT and HDAC are reversible epigenetic modifications that nutritional molecules are effectors. Each histone octamer is wrapped by 147 bp of DNA to form a nucleosome, the spacing between each base-pair (bp) varies between 30 and 100 and can be modified by nucleosome repositioning complexes. Figure 1d (also see figure 1a, 1b & 1c) shows HAT & HDAC reversible histone modifications that are dependent biological molecules. Ref:(2013). Acetyltransferases (HAT) for Neurological Therapeutics. Neurotherapeutics: the journal of the American Society for Experimental Neuro Therapeutics)

DNA methylation

DNA methylation regulates gene expression via the addition of a methyl group on the 5' position on the pyrimidine ring of the nucleotide, this methylation occurs on the amino acid cytosine flanked by a guanine that yields a 5'-cytosinephosphate-guanine-3'(CpG) methylation. Also, methylation occurs on the cytosine neighboring other nucleotides for non-CpG methylation.

Approximately 5% of cytosines are methylated at the global level, with hypermethylation observed in areas of hetero-chromatin and hypo-methylation. High densities of CpG sites are localized to repetitive DNA, specifically the localization of methyl-cytosines in relation to the gene and the density of CpG islands.

DNA methylation occurs at CpG sites though most of the genome is CpG poor, there are segments of 300-3000 bp with a 65% observed to expected ratio of CpG sites that are called CpG islands (CGIs). The CpG islands are localized to the promoter region of 70% of human genes, including tissue-specific genes, and developmentally regulated genes vital for stem cells due to distinctive topology that is reprogrammed with the gametes. DNA methylation is regulated via DNA methyltransferases (DNMT) there is DNMT 1, DNMT 3a, DNMT 3b though DNMT 1 is predominant in humans (Duygu et al 2013 - also see Appendix, I, II).

DNA methylation function is to transfer a methyl group (CH3-) to 5' end of the DNA (cytosine) sequence via DNMTs and S-adenosyl methionine (SAM) as the methyl group donor, cytosine is adjoining to the guanine residue refired to as CpG inland. Gene sequencing is enriched at CpG and if present in the gene promoter region transcriptional repression will occur, however if present on the exon region transcriptional activation will occur (udali S, Guarini - 2013, Mazzio EA et al -2012).

DNA demethylation

There are various pathways for DNA demethylation and the passive removal of a methyl group (CH3) of 5-mC, during de-methylation 5-mC is demethylated for cellular division during mitosis for replication; however active de-methylation occurs with non-replicating neurons. DNA demethylation is the process of removal of a methyl group from cytosines. DNA demethylation can be passive or active. The passive process takes place in the absence of methylation of newly synthesized DNA strands by DNMT1 during several replication cycles.

DNA Hydroxy methylation

The ten-eleven transferase (TET) enzyme catalyzes an oxidation reaction that converts 5-methylcytosinein to 5-hydroxymethylcytosine before subsequent steps that ultimately yield an unmodified cytosine (see figure 1f). Regions of hydroxy methylated DNA are considered to be sites of active demethylation and have been associated with an increase in gene expression (Tammen et al., 2015). In the presence of a hydroxy-methyl group on the 5 position of cytosine in CpG dinucleotides is a biomarker, considered a transient step in active demethylation of DNA.

Figure 1f - shows - proposed mechanism of active demethylation by ten-eleven transferase (TET). The enzyme TET acts on a methylated cytosine to catalyze a series of reactions to yield transitions to hydroxy methyl cytosine, formyl methyl cytosine, and carboxyl cytosine. The enzyme DNA glycosylase catalyzes the final step to yield an unmethylated cytosine. DNMT, DNA methyltransferase; SAM, S-

adenosylmethionine. (Tammen, S.A., Friso, S., Choi, S.W., 2013. Epigenetics: the link between nature and nurture. Mol Asp Med 34(4), 753e764), see Glossary.