What is epigenetics?

Laboratory News investigates how this mechanism produces a diverse range of effects in mammals

Epigenetics is a relatively new area of research that is currently attracting a high level of interest. The term epigenetics describes heritable changes in genome function that occur without a change in the DNA nucleotide sequence. The basis of epigenetics lies in the control of gene expression.

The existence of epigenetic mechanisms is not a new discovery. For many years, certain examples of non-Mendelian inheritance have been attributed to epigenetic events, such as position effect variegation in Drosophila. In this instance, expression of an eye colour gene is prevented when a chromosomal rearrangement moves the gene near to an area of heterochromatin, resulting in a variegated eye colour phenotype.

Today, scientists are uncovering evidence suggesting that epigenetic mechanisms, very different to those that occur in the Drosophila example, are key to a diverse range of biological processes in mammals. Interest in the subject has been raised further as new data emerges showing that epigenetic dysfunction plays a central role in the cause of many human diseases including cancer and birth defects.

A number of tools are available to scientists working in this rapidly expanding area. Cambridge BioScience has an extensive range of products from several manufacturers to make life easier for epigenetics researchers.

A new outlook on heredity
The nucleotide sequence of DNA was once regarded as the only mechanism by which genetic information could be transmitted between generations. According to this view, phenotypic variation occurred as a result of recombination or genetic mutation. This long established concept is now undergoing radical modification as evidence builds to support the idea that factors that alter the chromatin structure of DNA, rather than the nucleotide sequence itself, are closely associated with heritable changes in gene function.

Recent research indicates that exposure to specific nutrients, toxins, certain behavioural patterns or other types of environmental factors can all influence gene expression, without altering the genetic code at all. Furthermore, such influences can be transmitted to subsequent generations.

Protein expression can be controlled essentially by two main mechanisms, either by changing the chromatin structure of DNA or through DNA methylation:

Methylation of cytosine in the DNA of mammals occurs by the enzymatic addition of a methyl group to the carbon-5 position of cytosine1. The majority of 5'-methylcytosine in mammalian DNA is present in cytosine–guanine (CpG) dinucleotides2. These CpG dinucleotides are not uniformly distributed throughout the human genome. In 98% of the genome, CpGs are present approximately once per 80 dinucleotides. In contrast, areas known as CpG islands, which comprise 1-2% of the genome, have a frequency of CpGs approximately five times greater than the genome as a whole3, 4.

The promoter regions of many genes are rich in CpG dinucleotides. Methylation at CpG islands is usually associated with transcriptional repression. Nutrients such as folate, choline and methionine play an important role in this process as major dietary sources of methyl groups. DNA methylation is a normal part of embryonic cell differentiation; its influence persists through the life of the cell and can also be passed on during cell replication5, 6.

Histones are the proteins involved in the folding of DNA into chromatin. Several different chemical reactions can modify histones and change the chromatin structure, such modifications regulate many processes including the transcriptional activation or silencing of genes. For example, acetylation reduces the adhesiveness of DNA to histones by increasing the repulsive force between the DNA and the histone core. This relaxes the chromatin structure and permits access to other DNA binding factors5. Many histone modifications are stably maintained during cell division, but this mechanism for epigenetic inheritance is not yet fully understood7.

Both DNA methylation and histone modification play a role in allele-specific gene expression, also known as genomic imprinting. Around 100 to 200 genes in our genome are thought to be subject to genomic imprinting8. Such epigenetic control allows a functional haploidy - silencing one allele to allow expression by a single active copy. Gene expression in these circumstances becomes a direct consequence of the providing parent’s sex.

This type of epigenetic regulation is vital for normal embryogenesis. One well-studied example is the insulin-like growth factor II gene (Igf2). Igf2 is silenced by methylation on the maternal chromosomes, so that only the paternal copy is expressed. In some cases, where this control is lost and Igf2 is biallelically expressed, babies are born with the rare Beckwith-Wiedemann syndrome disorder.

The role of epigenetics in embryonic development
Current findings suggest that many important epigenetic interactions between the genome and the environment, whether caused by nutrients or other factors, often occur during embryonic development. In 2003 Waterland and Jirtle published a key paper underlining the importance of epigenetics in embryonic development9. Their breakthrough research also served to greatly increase the level of scientific interest in epigenetics, highlighting that epigenetic mechanisms could be much more important in human disease than previously realised.

Waterland and Jirtle conducted their research with the yellow agouti mouse. This mouse typically has yellow fur and exhibits a tendency towards obesity. They showed that when normal mice were fed before and during pregnancy on a diet of methyl rich donors, such as folic acid and vitamin B12, the agouti gene could be silenced and the offspring would have brown fur (the agouti gene controls coat colour, producing a horizontal yellow stripe just below the tip of each hair). It was also observed that suppression of the agouti gene reduced the adult offspring’s susceptibility to diabetes, cancer and obesity.

Although this experiment was conducted with mice, these remarkable findings have direct relevance to humans. Waterman and Jirtle showed that adding a supplement such as folic acid to a mother’s diet could permanently affect the offspring’s DNA methylation at epigenetically susceptible sites. Folic acid has long been recommended for human mothers as it has been shown to reduce the incidence of neural tube defects in babies. But these data raise the question of whether the introduction of methyl donors could also have unintended effects on epigenetic mechanisms in humans.

Epigenetics and disease
It was once considered that mutant genes were responsible for the majority of diseases. But the dramatic increase in developed countries of rates of obesity, heart disease and diabetes for example, suggest that a different cause is likely. Many now think that these disorders could arise from epigenetic dysfunction. Indeed, with as much as 35-45% of the human genome consisting of methyl-rich transposons9, 10, the potential for epigenetic modification by methylation alone is huge, with major implications for human health11.

Below are a just a few examples of links between epigenetics and human disorders:
Abnormal levels of methylation can cause serious problems - too little can result in the activation of oncogenes, too much and tumour suppressesor genes may be silenced. A combination of descriptive studies and manipulative experiments has offered hints of mechanisms for epigenetic silencing of tumour suppressor genes in cancer cells12.

Other diseases that may have an epigenetic aetiology may be linked to parental-specific gene expression. From an evolutionary viewpoint, genomic imprinting associated with parental specific expression seems to place an individual at a disadvantage - by removing the protection against recessive mutations that is normally provided in diploid organisms. Also, the complex mechanisms involved in epigenetic control of imprinted genes are susceptible to dysregulation. Research indicates that areas of the genome where imprinted regions occur are associated with a number of developmental disorders and diseases.

There are further implications on human health when we consider assisted reproductive technology (ART). ART is a widely used therapy for infertility but there are now concerns that removing and handling the germline may disrupt normal epigenetic processes. An association between ART and epigenetic defects is supported by experimental studies with mouse embryo culture and through the incidence of ‘large offspring syndrome’ seen in the animal husbandry industry13.

Conclusion
Recent research in the field of epigenetics indicates that an individual’s susceptibility to a wide range of diseases over the course of their lifetime could be determined during embryonic development. It also seems likely that the epigenetic events that control this susceptibility can be passed on to subsequent progeny.

Much of the data that has emerged so far places a major emphasis on the importance of maternal nutrition, but some of the very latest findings – published in the European Journal of Human Genetics - suggest that the behaviour or environment of prepubescent boys could influence the phenotype of their sons and grandsons14.

While there is still much to learn in this rapidly developing field, epigenetics looks set to have a major impact on public health.

By Emma Greatorex, molecular biology product manager at Cambridge BioScience

Products for epigenetics research are as wide ranging as the subject itself and include:
DNA modification: Kits for bisulphite modification and isolation of small amounts of methylated DNA
Protein-DNA interaction: Chromatin immunoprecipitation kits – compatible with all DNA amplification-based approaches
Methylation: Non-isotopic DNA/histone methyltransferase assay kits
Acetylation/Deacetylation: HDAC activity and inhibitor assay kits
Antibodies: for epigenetics research
To keep up to date with the latest epigenetics products, visit www.bioscience.co.uk/epigen  

References
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4. Bird AP. Nature 1986;321:209-213
5. Cho KS, Elizondo LI, Boerkoel CF. Curr Opin Gen Dev 2004;14(3):308-315
6. Dennis C Nature 2003;421(6924):686-688
7. Pray LA. The Scientist 2004;18(13)
8. Murphy SK, Jirtle RL. BioEssays 2003;25:577-588
9. Waterland RA, Jirtle RL. Mol Cell Biol 2003;23(15):5293-5300
10. Waterland RA, Jirtle RL. Nutrition 2004;20(1):63-68
11. Johnson-Zeiger A. GlycoScience 2004; 3(5)
12. Tycko B. J Clin Invest 2000; 105(4):401-407
13. Niemitz EL, Feinberg AP. Am J Hum Genet 2004;74:599-609
14. Pembrey M, Bygren LO, Kaati GP et al. Eur J Hum Genet 2006;14:159-166