Epigenetics: Answers Beyond Our Genes.

Consider the fact that our cells contain the same DNA, but different cell types exist in our body; neurons, skin cells, liver cells, and others. How is this possible? Why are monozygotic twins, not actually identical? Why could a genetics experiment yield an inconclusive result?

The answer; epigenetics.

What is Epigenetics?

The term ‘epi’ means ‘above’, hence epigenetics translates to ‘above’ genetics. Precisely, it is the study of characteristics that do not involve changes to the DNA sequence, but rather, external heritable modifications that alter gene expression. These signatures can determine if the gene should be ‘switched on’ or ‘switched off’, and are of prime importance during cell differentiation, morphogenesis, variability, and adaptability of an organism.

Epigenetic Modifications

Over the past decade, there has been expansive study of epigenetics to characterize diseases that could not be explained just by genetic factors or the environment. With the advent of molecular techniques such as massively parallel signature sequencing (MPSS), chromatin immunoprecipitation microarray analysis (ChIP-chip), protein binding microarrays and more, researchers are able to delineate the epigenetic modifications in gene regulation and phenotypic severity.

The three best characterized epigenetic modifications are;

1. DNA Methylation: The addition of methyl group at 5’ end of the cytosine base (to form 5-methylcytosine), is mediated by DNA methyltransferase enzymes such as DNMT1, DNMT3a, and DNMT3b. These marks are usually repressive, and may inhibit gene transcription, switching the gene ‘off’. Cytosines may exist as a dinucleotide, CpG, most of which are methylated. However, unmethylated or hypomethylated dinucleotides cluster together to form a CpG island, and may exist at promoter regions of exons (60%), in order to allow gene transcription (Figure 1 and Figure 2).
2. Histone Modification: The DNA wraps around clusters of histone proteins to form chromatin. Protruding histone N-terminal tails, are subject to enzyme mediated modifications. Some modifications include, methylation, acetylation, phosphorylation, at lysine and arginine residues. Unlike DNA methylation, these marks will either repress or activate gene transcription by chromatin remodelling. Most active marks such as acetylation mediated by histone acetyl transferase enable heterochromatin to form euchromatin, less compact and open to gene transcription (Figure 1 and Figure 2). Repressive marks can cause the opposite.
3. Non coding RNA: MicroRNAs (miRNAs), are ~17 to 25 nucleotides long and are a member of the non-coding RNAs, mediating 60% of protein-coding genes in humans by attachment and repression of mRNA function (Figure 2). These miRNA’s are epigenetically controlled by DNA methylation in CpG islands, histone modifications or both.

Figure 1: Chromatin remodelling and transcription control (Asansi-Fabado et al., 2016).

Figure 2: The interplay of key epigenetic players; DNA methylation, histone post-translational alterations, and miRNAs, to rearrange chromatin into areas such as euchromatin, heterochromatin, and transcription regulation (Honda et al., 2018).

Lifestyle and the Environment; It’s not all in our DNA.

Epigenetic modifications can fluctuate with environmental factors such as diet, lifestyle (exercise, stress, alcohol intake, smoking), toxicity and drugs, and this in turn may regulate gene expression (Moosavi and Ardekani, 2016; Alegría-Torres et al., 2011). A few findings are listed below.

Diet: The Dutch Famine during the second world war and the repercussions on the foetus’ inside the womb during the famine, have been extensively studied. These children developed higher susceptibility to a subset of diseases, including schizophrenia, stress sensitivity, and obesity, in contrast to children conceived after the famine. Thus, this could mean early development is a sensitive time period, and the correlation of ‘the food we eat, and our child someday’, remains an esoteric research prospective. Additionally, reduction in dietary folate (a methyl donor), may enhance colorectal carcinogenesis through hypomethylation of DNA.

Changes in the mouse coat colour from yellow to brown were directly associated to supplementation of the pregnant mother’s diet with high soy, vitamin B12, folic acid, choline, and betaine. The coat colour changes were linked to alterations in DNA methylation for the respective gene (Figure 3).

Figure 3: Maternal diet supplementation components altered DNA methylation, that were reflected in offspring coat colour changes (Weinhold, 2006).

Exercise: LINE-1 elements are repetitive and are usually repressed in the human genome, and physical activity is associated with hypermethylation in these regions. Elderly individuals with LINE-1 hypermethylation have shown to be associated with lower mortality from ischemic heart disease and stroke.

Exposure: Black carbon exhaust exposure has been linked with decreased LINE-1 methylation. As this change has been found in patients with cancer and cardiovascular disease, air pollution might be another factor for modulation of epigenetic processes. Additionally, studies on children exposed to stress in utero, have higher risks of predisposition to psychiatric disorders due to the increased epigenetic promoter activity of glucocorticoid receptor. In studies assessing nursing methods of pups including licking and grooming that mother rats used, affected the long-term behaviour of the offspring such that epigenetic changes were observed in the glucocorticoid receptor in the pup’s hippocampus. This finding reveals nurturing in addition to nature could play a role in determining gene expression.

Smoking: Condensate of cigarette smoke has been linked to respiratory epithelial cells demonstrating certain reduction in histone modifications such as H4K16 acetylation and H4K20 trimethylation. Interestingly, these alterations were similar to findings witnessed in lung cancer tissues, which is usually mediated by DNA methylation.

Epigenetics; A culprit in human disease

Aberrant methylation patterns have been correlated with different cancers, autoimmune, neurological and imprinting disorders.

Additionally, the inheritance from a trait becomes more complicated, when DNA methylation patterns are different on the maternal and paternal alleles. One copy is active, while the other remains silent. If the paternal chromosome is faulty, there might be inheritance of two inactive genes, with no functional copy as is the case with Angelmann syndrome, and vice versa for Prader-Willi syndrome. These are known as imprinting disorders.

In cancer, there is hypermethylation of promoter regions in tumour suppressor genes, inactivating their function. There is also global hypomethylation at usually methylated repetitive sequences, which may act in conjunction with non-coding RNA, causing genomic instability. (Figure 4).

Figure 4: Aberrant DNA methylation patterns in human cancer (Lopez-Serra and Esteller, 2011).

The future for epigenetic therapy

To date, epigenetic therapies are few in number. However, inhibitors of DNA methylation, have the potential to re-activate silenced genes, especially in cancer. Two drugs approved by the FDA of this nature include, 5-azacytidine (for leukemia) and 5-aza-2′-deoxycytidine. These drugs inhibit DNA methyltransferase activity, which re-activates the genes.

Drugs targeting histone modifications include histone deacetylase (HDAC) inhibitors (phenylbutyric acid, SAHA, depsipeptide, and valproic acid); which may enable gene expression.

Future therapies used in combination would prove effective (demethylating agents and HDAC inhibitors), in addition to conventional chemotherapy which could re-sensitize drug resistant tumour cells to standard therapies (Rodenhiser, 2006).

Hype or Harm?

We can begin to conceptualise that we control most of the ways our genes are expressed. Efforts to understand the correlation of ‘the food we eat today, and our child someday’, the effects of heritability and avoiding our faulty genes has prompted expansive research over the years with untapped opportunity; ‘The Hype’.

However, there are still gaps between the fantasy and the facts; so much is still unknown in the complexities of gene regulation and inheritance; ‘The Harm’.

Collectively, the understanding of the interplay between epigenetics, the environment and our genes, is yet in its infancy. Further research prompts biomarker discovery, molecular diagnosis and potent therapeutic outcomes; which certainly seems promising.

Additional Insight: Massive Open Online Course (MOOC) in Epigenetics offered by the University of Melbourne on the Coursera site.

References

1. Weinhold, B. (2006). Epigenetics: The Science of Change. Environmental Health Perspectives, 114(3). doi: 10.1289/ehp.114-a160
2. Alegría-Torres, J., Baccarelli, A., & Bollati, V. (2011). Epigenetics and lifestyle. Epigenomics, 3(3), 267–277. doi: 10.2217/epi.11.22
3. Moosavi, A., & Motevalizadeh Ardekani, A. (2016). Role of Epigenetics in Biology and Human Diseases. Iranian biomedical journal, 20(5), 246–258. doi: 10.22045/ibj.2016.01
4. Rodenhiser, D. (2006). Epigenetics and human disease: translating basic biology into clinical applications. Canadian Medical Association Journal, 174(3), 341–348. doi: 10.1503/cmaj.050774
5. Lopez-Serra, P., & Esteller, M. (2011). DNA methylation-associated silencing of tumor-suppressor microRNAs in cancer. Oncogene, 31(13), 1609–1622. doi: 10.1038/onc.2011.354
6. Asensi-Fabado, M., Amtmann, A. and Perrella, G., 2017. Plant responses to abiotic stress: The chromatin context of transcriptional regulation. Biochimica et Biophysica Acta (BBA) — Gene Regulatory Mechanisms, 1860(1), pp.106–122. doi:
7. Honda M., Nakashima K., Katada S. (2018) Epigenetic Regulation of Human Neural Stem Cell Differentiation. In: Buzanska L. (eds) Human Neural Stem Cells. Results and Problems in Cell Differentiation, 66. doi: 10.1007/978–3–319–93485–3_5