by Edmond Cigale, Ph.D.
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At the core of every cell, DNA is a magnificent double helix containing all the genetic instructions for building and operating an organism. This comprehensive manual dictates everything from your physical traits to how your organs develop and immune system responds.
Within the vast DNA storybook, individual genes are like specific chapters. Each gene is a distinct segment of DNA carrying instructions for a particular function or characteristic, such as building a muscle fiber or digesting food. When 'expressed,' these instructions are read to produce functional molecules, usually proteins, that perform the body's work.
If DNA is the master storybook, the epigenome acts as a dynamic system of "sticky notes" or "bookmarks" on top of the DNA. These bookmarks don't alter the genetic code but decide which genes are read aloud, whispered, or skipped. This allows different cells, despite having identical DNA, to perform vastly different functions.


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Sources: Carey (2012), chs. 4 & 6.
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Scientist Conrad Waddington imagined cells as balls rolling down a sandy hill carved with valleys. Once a ball enters a valley, it's hard to jump out—it keeps rolling to the bottom.
This metaphor illustrates how cells specialize: a cell rolling into the "skin cell" valley becomes skin, while one in the "brain cell" valley becomes brain.
The epigenome is the "master sculptor" that carves these valleys. It does this by dynamically adding and removing molecular "sand barriers" and "grooves" on the DNA. These epigenetic modifications don't change the genetic code itself, but they dictate which genes are actively read and which remain silent, defining the unique path of each cell.



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DNA methylation adds a tiny chemical tag (a methyl group) to specific cytosine bases on the DNA sequence. This "Do Not Read" tag physically blocks the cell's reading machinery, preventing genes from being copied and translated into proteins. It's a powerful, long-lasting way to silence genes.
DNA wraps around protein spools called histones. Histone modifications involve adding or removing chemical tags to these histones, controlling how tightly the DNA is wound. Tags like acetyl groups loosen the DNA, making genes accessible, while other tags tighten it, hiding genes. This flexible method allows for quick responses to cellular needs, affecting gene expression on demand.


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When cells divide, they pass on not just DNA but also epigenetic 'sticky notes', so the daughters of a skin cell remain skin cells.
These marks differ in how easily they change. DNA methylation is very stable and is removed only under specific circumstances. Most histone modifications are far more plastic: they can be added and removed in response to signals such as hormones, nutrients and drugs. Through them, the environment can alter gene expression without changing the DNA sequence.
Sources: Carey (2012), ch. 4.


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Sources: Carey (2012), Introduction, chs. 5–6, 9, 12, 14.


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Sources: Carey (2012), Introduction & ch. 5.
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Agouti mice are a compelling example of epigenetics: genetically identical mice can look and age very differently, depending on how one gene is switched.
Genetically identical agouti mice range along a spectrum between two extremes:
Mice with in-between methylation have mottled coats. The methylation level works like a dimmer switch.
Sources: Carey (2012), ch. 5; Wolff et al. (1998), Abstract & Discussion.



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Sources: Carey (2012), chs. 5–6; Wolff et al. (1998), Introduction & Results (Table 4); Waterland & Jirtle (2003), Abstract.
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Genetically identical female larvae develop into either sterile workers or fertile queens, not through DNA changes but through differences in gene expression. The key factor is their diet.
For their first three days all larvae are fed royal jelly. Larvae destined to become queens go on being fed royal jelly throughout development. Experimentally switching off the DNA-methylating enzyme Dnmt3 in larvae has the same effect as royal jelly: most become queens. This suggests royal jelly acts at least partly through DNA methylation, although whether it inhibits Dnmt3 directly has not been shown.
Queens have a much larger body with fully developed ovaries, lay up to about 2,000 eggs a day, and on average live 1–2 years. Their role centres on reproduction.
Sources: Carey (2012), ch. 14; Remolina & Hughes (2008), p. 178.


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After day three, larvae destined to be workers are switched to a diet of pollen and nectar. Their brains end up with a different pattern of DNA methylation from queens' brains.
These larvae become worker bees, characterized by:
Sources: Carey (2012), ch. 14; Remolina & Hughes (2008), p. 178.


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Sources: Carey (2012), ch. 9.


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Sources: Carey (2012), ch. 9; Centerwall & Benirschke (1975), Abstract.
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Sources: Carey (2012), Introduction & ch. 5.
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Mothers malnourished only in the final months of pregnancy had babies who were born small, stayed small throughout life, and had lower obesity rates than the general population.
Mothers malnourished only in the first three months had babies of normal birth weight. As adults, these children had higher obesity rates than normal and more of some other health problems, including schizophrenia. Not every exposed child became obese: the famine raised the risk, it did not decide each outcome.
Some effects may reach the next generation. Daughters exposed early in the womb later had first-born babies who tended to be heavier than those in control groups. Whether this is true epigenetic inheritance is still open: the mother's womb environment or the contents of her egg could also explain it.
Sources: Carey (2012), chs. 5–6.
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The Dutch Hunger Winter is a landmark case for developmental programming: the idea that conditions in the womb can shape health for decades.
Sources: Carey (2012), ch. 5; Hales & Barker (2001), Abstract.
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Rat mothers naturally differ in how much they lick and groom their pups in the first week of life. Scientists compared pups raised by high- and low-licking mothers. Early care shaped the pups' adult stress responses through epigenetic changes to the glucocorticoid (cortisol) receptor gene in the hippocampus.
Plenty of licking and grooming led to less DNA methylation on the cortisol receptor gene, so more receptor was made. As adults, these rats stayed calm under mild stress and had lower levels of stress hormones.
Less licking and grooming left more methylation on the gene, so less receptor was made. As adults, these rats reacted strongly even to mild stress, with higher stress hormones. Cross-fostering showed that the care received, not the birth mother, decided the outcome.
Sources: Carey (2012), ch. 12.


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Sources: Carey (2012), ch. 12.
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Many plants rely on 'vernalization' – a period of prolonged cold – to accurately time their flowering. This prevents them from blooming too early in mild autumns, ensuring they wait for the consistent warmth of spring.
Plants achieve this 'memory' through epigenetic changes to the chromatin of a key flowering gene, not to the DNA sequence itself. In crops such as wheat, warmer winters are expected to change vernalization requirements, with consequences for flowering time and grain yield.
Sources: Carey (2012), ch. 15; Afshari-Behbahanizadeh et al. (2024), Abstract.


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Prior to the cold season, a key gene, often referred to as the Flowering Locus C (FLC) in model plants like *Arabidopsis thaliana*, is highly active.
This gene acts as a molecular "brake," producing proteins that actively suppress the genes responsible for initiating flowering. It's the plant's way of saying, 'Hold on, it's not spring yet!'
This active FLC ensures the plant conserves energy for vegetative growth – growing leaves and roots – rather than risking premature flowering.


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Cold weather switches on a protein called VIN3 and a long non-coding RNA called COLDAIR. Together they bring an enzyme to the FLC gene that adds a repressive mark, methylation of lysine 27 on histone H3 (H3K27me3). During the cold this mark builds up gradually at FLC, and the longer the cold lasts, the more stable the silencing of FLC becomes.
Sources: Carey (2012), ch. 15; Angel et al. (2011), Abstract.


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Once a sufficient and sustained period of cold has passed, and enough epigenetic marks have accumulated, the FLC gene becomes almost completely silenced. Its expression is switched off, and the molecular 'brake' on flowering is released.
With FLC no longer inhibiting flowering, the plant is free to respond to the increasing warmth and longer days of spring. Other flowering genes, previously suppressed, are now activated, triggering the development of flowers and eventually seeds.
This epigenetic memory ensures that the plant blooms only when conditions are optimally favorable for reproduction.
The memory does not pass to the next generation. When the plant makes seeds, the repressive marks on FLC are removed, so each new plant must experience its own winter before it flowers.
Sources: Carey (2012), ch. 15.


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Sources: Carey (2012), ch. 1; Gurdon (2006), p. 3.
Sources: Carey (2012), chs. 6–7.


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Sources: Carey (2012), ch. 6; Heard & Martienssen (2014); Veenendaal et al. (2013), Abstract.
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Sources: Carey (2012), chs. 1 & 7; Gurdon (2006), pp. 3–4.
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The epigenome is a responsive layer linking our genes to our development and environment.
(Author's summary.)
Genes still matter. Carey cautions that the field risks swinging too far away from DNA: genetics and epigenetics work together.
Sources: Carey (2012), Introduction & ch. 3.
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The profound lesson that we are not prisoners of our genetic destiny is echoed in a fascinating array of biological phenomena:
The epigenome links nature and nurture. Our genes are not a fixed destiny, but they are not irrelevant either: environment, diet, stress and relationships influence how they are used, within limits set by the DNA itself.
Sources: Carey (2012), chs. 1, 3, 5, 9, 12, 14.
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Epigenetics is a story of flexibility, as our cells adapt; of memory, as some experiences leave lasting molecular marks; and of realistic hope, because some of those marks respond to how we live.
This ongoing dialogue between our genes and our lives does not make us authors of every outcome. Even genetically identical animals in identical conditions differ by chance, but sound habits still improve the odds of good health.
Sources: Carey (2012), chs. 5–6.
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Afshari-Behbahanizadeh, S., Puglisi, D., Esposito, S., & De Vita, P. (2024). Allelic variations in vernalization (Vrn) genes in Triticum spp. Genes, 15(2), 251. https://doi.org/10.3390/genes15020251
Angel, A., Song, J., Dean, C., & Howard, M. (2011). A Polycomb-based switch underlying quantitative epigenetic memory. Nature, 476(7358), 105–108. https://doi.org/10.1038/nature10241
Carey, N. (2012). The epigenetics revolution: How modern biology is rewriting our understanding of genetics, disease, and inheritance. Columbia University Press.
Centerwall, W. R., & Benirschke, K. (1975). An animal model for the XXY Klinefelter's syndrome in man: Tortoiseshell and calico male cats. American Journal of Veterinary Research, 36(9), 1275–1280.
Gurdon, J. B. (2006). From nuclear transfer to nuclear reprogramming: The reversal of cell differentiation. Annual Review of Cell and Developmental Biology, 22, 1–22. https://doi.org/10.1146/annurev.cellbio.22.090805.140144
Hales, C. N., & Barker, D. J. P. (2001). The thrifty phenotype hypothesis. British Medical Bulletin, 60(1), 5–20. https://doi.org/10.1093/bmb/60.1.5
Heard, E., & Martienssen, R. A. (2014). Transgenerational epigenetic inheritance: Myths and mechanisms. Cell, 157(1), 95–109. https://doi.org/10.1016/j.cell.2014.02.045
Remolina, S. C., & Hughes, K. A. (2008). Evolution and mechanisms of long life and high fertility in queen honey bees. Age, 30(2–3), 177–185. https://doi.org/10.1007/s11357-008-9061-4
Veenendaal, M. V. E., Painter, R. C., de Rooij, S. R., Bossuyt, P. M. M., van der Post, J. A. M., Gluckman, P. D., Hanson, M. A., & Roseboom, T. J. (2013). Transgenerational effects of prenatal exposure to the 1944–45 Dutch famine. BJOG, 120(5), 548–553. https://doi.org/10.1111/1471-0528.12136
Waterland, R. A., & Jirtle, R. L. (2003). Transposable elements: Targets for early nutritional effects on epigenetic gene regulation. Molecular and Cellular Biology, 23(15), 5293–5300. https://doi.org/10.1128/MCB.23.15.5293-5300.2003
Wolff, G. L., Kodell, R. L., Moore, S. R., & Cooney, C. A. (1998). Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice. FASEB Journal, 12(11), 949–957. https://doi.org/10.1096/fasebj.12.11.949


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Integral Consciousness Studies - M.Sc. program