Integral Consciousness Studies - M.Sc. program

Epigenetics: Story of Life:
You are more than your genes


by Edmond Cigale, Ph.D.



Copyright © 2025 by Rushmore University & Transpersonal Psychology Institute
All rights reserved.

Your Body's Amazing Storybook

  • Your body's DNA is a storybook holding all your cellular instructions. Epigenetics acts like "sticky notes" or "bookmarks," guiding each cell to read specific chapters and skip others, defining its function.
  • These "sticky notes" don't alter the DNA's words but control gene expression. Key mechanisms include DNA methylation (adding chemical tags to silence genes) and histone modifications (changing DNA winding for accessibility). This understanding is vital for life and future health improvements.

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The Storybook and Its Bookmarks

DNA: The Master Storybook

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.

Genes: Individual Stories

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.

Epigenome: The Bookmarks

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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Epigenetics Dancing

  • Key epigenetic mechanisms include DNA methylation (adding a chemical tag to DNA) and histone modification (changing proteins around which DNA is wound).
  • These chemical tags can turn genes on or off, or dial their activity up or down.
  • What's fascinating is that these epigenetic bookmarks can be influenced by environmental factors like diet, stress, exercise, and even exposure to toxins.
  • This means your experiences can leave marks on your epigenome that affect gene expression. In a few animal studies such marks are passed to offspring; whether this happens in humans is still debated.

Sources: Carey (2012), chs. 4 & 6.

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Rolling Down the Hill

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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Two Types of Sticky Notes

"Off Switches": DNA Methylation

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.

"Winding" Control: Histone Modifications

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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A Memory That Can Change

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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Real-Life Stories: A Preview

Identical Twins

  • Identical twins share the same DNA, yet they already differ epigenetically at birth, and the differences grow with age.
  • Chance events in early development and different environments may account for some of their different health outcomes.

Agouti Mice

  • When pregnant mothers were fed extra methyl donors, more of their genetically identical offspring were brown and lean rather than yellow and obese.
  • Diet shifted an epigenetic switch without changing the DNA.

Queen & Worker Bees

  • All female larvae share the same DNA; larvae kept on royal jelly become queens, the rest become workers.
  • Diet sets caste through changes in gene expression, including DNA methylation.

Tortoiseshell Cats

  • Their patches result from random X-chromosome inactivation (Lyonization): one X is silenced in each early cell, and all its descendant cells keep the same X silent.
  • This stable silencing is a classic epigenetic phenomenon.

Dutch Hunger Winter

  • Famine in early pregnancy was followed, decades later, by higher rates of obesity and other health problems in the children.
  • Some effects may extend to grandchildren, though the mechanism is still debated.

Childhood Trauma

  • Childhood abuse and neglect are linked to a higher risk of depression, self-harm, drug abuse and suicide in adulthood.
  • Animal studies and post-mortem human brain tissue point to lasting epigenetic changes in stress-response genes.

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

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Identical Twins Who Aren't Identical

  • If one identical twin develops schizophrenia, there's only a 50% chance their twin will too. Why not 100% if their DNA is identical?
  • Part of the answer may lie in epigenetics – changes to gene expression that don't involve alterations to the underlying DNA sequence.
  • Think of it like this: identical twins start with the same "recipe book" (DNA). However, epigenetics introduces "sticky notes" or "bookmarks" that can tell certain genes to be read more often, less often, or not at all.
  • Identical twins already differ epigenetically at birth, and these differences grow with age, especially in twins who have lived apart for a long time. Chance events in early development, as well as different environments, contribute.
  • Epigenetic differences may account for some of the differences in health between identical twins, but much of the evidence is still correlation rather than proven cause.

Sources: Carey (2012), Introduction & ch. 5.

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The Agouti Mice Mystery: A Paradigm of Epigenetics

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:

  • The Lean, Brown, and Resilient: These mice have a brownish, near-normal coat, stay lean and healthy, and on average live longer. In them, the inserted DNA element next to the agouti gene is heavily methylated and silent.
  • The Obese, Yellow, and Vulnerable: These siblings have yellow fur, become obese and diabetic, are more susceptible to cancer, and on average live shorter lives. In them, the inserted element is unmethylated and keeps the agouti gene switched on.

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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  • Normally the agouti gene switches on only briefly in each hair-growth cycle, producing a yellow band in an otherwise dark hair. In viable yellow (Avy) mice, a retrotransposon (an IAP 'jumping gene') inserted just upstream of agouti keeps the gene switched on all the time, in almost every tissue. The result is yellow fur together with obesity, high insulin and diabetes.
  • The key discovery was that a mother's diet could move this switch. When pregnant mothers were fed extra methyl donors (folic acid, vitamin B12, choline and betaine), a larger share of their genetically identical offspring had brown, mottled-to-agouti coats and fewer were fully yellow.
  • The extra methylation silenced the retrotransposon in more embryos, without any change to the DNA sequence. The effect was a shift in proportions, not a guarantee for each pup, and in these experiments the diet effect was not passed on to the following generation.

Sources: Carey (2012), chs. 5–6; Wolff et al. (1998), Introduction & Results (Table 4); Waterland & Jirtle (2003), Abstract.

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The Queen Bee's Secret

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.

Royal Jelly 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.

Becomes Queen

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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Regular Diet

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.

Becomes Worker

These larvae become worker bees, characterized by:

  • Smaller size and underdeveloped (sterile) ovaries.
  • Specialized structures for foraging and hive work, such as pollen baskets.
  • A much shorter lifespan: on average 15–38 days in summer and 150–200 days in winter.

Sources: Carey (2012), ch. 14; Remolina & Hughes (2008), p. 178.

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The Tortoiseshell Cat Map

  • Every tortoiseshell cat is a vivid example of epigenetics. These cats are almost always female, because the orange/black coat-colour gene sits on the X chromosome and a cat needs two X chromosomes to carry both colours. X-inactivation then turns those two colours into a patchwork. These stunning felines are almost exclusively female, thanks to a fascinating biological process called X-inactivation.
  • The coat-colour gene for orange or black fur sits on the X chromosome. A female (XX) can carry the orange version on one X and the black version on the other. A normal male (XY) has only one X, so he can be orange or black, but not both.
  • During early development, each cell randomly "shuts down" one of its two X chromosomes. This means some cell patches express the orange fur gene, while others express the black fur gene.
  • The result is the distinctive, beautiful mosaic pattern of a tortoiseshell cat, a direct, visible outcome of random X-inactivation.


Sources: Carey (2012), ch. 9.

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Epigenetics made visible

  • The orange and black patches of tortoiseshell cats are a direct result of X-inactivation: each patch grows from cells that switched off the same X chromosome.
  • This "cellular roulette" beautifully demonstrates epigenetics: how gene expression can be altered without changing the underlying DNA sequence.
  • Male tortoiseshells are rare. Most that have been examined carry an extra X chromosome (an XXY make-up, comparable to Klinefelter syndrome in humans), and almost all of them are sterile.

Sources: Carey (2012), ch. 9; Centerwall & Benirschke (1975), Abstract.

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The Dutch Hunger Winter: Epigenetics in Action

  • Near the end of World War II, from November 1944 to May 1945, a German blockade caused severe famine in the occupied western Netherlands. At times people had only about 30 per cent of normal daily calories, and more than 20,000 died.
  • Excellent Dutch medical records allowed researchers to follow, for decades, children who were in the womb during the famine. What mattered was not only that the famine happened, but when in pregnancy it happened:

Sources: Carey (2012), Introduction & ch. 5.

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1

Starvation in Last 3 Months

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.

2

Starvation in First 3 Months

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.

3

Epigenetic Echo: The Next Generation

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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Developmental programming

  • Researchers propose that famine in early pregnancy 'programmed' the developing baby's metabolism for scarcity. One influential explanation for such links is the 'thrifty phenotype' hypothesis: poor nutrition early in life produces permanent changes in how the body handles glucose and insulin.
  • When these children later lived with plenty of food, that early programming may have raised their risk of obesity and metabolic disease. Studies of famine survivors have found changes in DNA methylation at key metabolic genes, but these findings show correlation, not proven cause.

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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Love Leaves Its Mark

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.

Well-Cared-For Pups

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-Groomed Pups

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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Maternal care: epigenetic program?

  • This work suggests that maternal care acts as biological information, not only affection: during a short window after birth it sets how strongly the brain will respond to stress for the rest of the animal's life.
  • These changes alter how genes are expressed without changing the DNA sequence. Post-mortem studies of human brain tissue have found a similar pattern, with more methylation of the cortisol receptor gene in people who suffered abuse or neglect in childhood. This is a correlation, not yet proof of cause.

Sources: Carey (2012), ch. 12.

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How Plants Remember Winter: The Epigenetic Clock

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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Before Winter: The Flowering Brake is On

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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During Winter: The Epigenetic Clock Ticks

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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After Winter: Brake Released, Flowering Unleashed

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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The Rules of Life

The Cloned Toad

  • In 1962, John Gurdon transferred nuclei from intestinal cells of feeding tadpoles of the African clawed toad (Xenopus laevis) into eggs whose own nucleus had been destroyed.
  • Some of these eggs developed into normal tadpoles, and later into fertile adult frogs.

Sources: Carey (2012), ch. 1; Gurdon (2006), p. 3.

Genomic Imprinting: Why You Need Mom and Dad

  • Genomic imprinting means some genes are active only from the mother or father due to epigenetic "stickers."
  • One parent's gene copy is expressed while the other is silenced, which is crucial for proper development.

Inheriting Memories

  • The Dutch Hunger Winter and other historical cohorts suggest that some effects of a grandparent's environment may reach later generations.
  • In animal studies, a few epigenetic marks clearly pass from parent to offspring; in humans the evidence is suggestive, not settled.

Sources: Carey (2012), chs. 6–7.

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Inheriting Memories? Inter- vs Transgenerational

  • Why grandchildren are not yet proof: A female fetus already carries the egg cells that will become her own children, so a famine during pregnancy reaches three generations at once. Most human studies therefore show inter-generational effects, not trans-generational inheritance, which would require an effect in a generation that was never exposed. Grandchildren of prenatally exposed fathers were heavier, which is harder to explain without sperm, but this is not yet proof.
  • In Överkalix, an isolated region of northern Sweden, records of good and bad harvests were linked to the health of later generations. When food was plentiful during a man's 'slow growth period' before puberty, his grandsons had a higher risk of dying from diabetes. When food was scarce during a father's slow growth period, his sons had a lower risk of dying from cardiovascular disease.
  • Because this pattern passed down the male line, it is unlikely to be explained by the womb, which makes an epigenetic explanation attractive, but it remains a hypothesis.
  • The findings come with caveats: they rely on old historical records, and some of the effects were small. Animal studies of over-fed or under-fed fathers point in the same direction.

Sources: Carey (2012), ch. 6; Heard & Martienssen (2014); Veenendaal et al. (2013), Abstract.

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Genomic Imprinting: Why You Need Mom and Dad

  • These 'stickers' are vital for proper fetal development, especially for regulating growth, brain function, and metabolism.
  • A healthy baby needs a balanced set of instructions from both parents. If a child inherits two active copies of a paternally expressed imprinted gene, or two inactive copies of a maternally expressed one, it can lead to severe developmental disorders.
  • Conditions like Prader-Willi syndrome and Angelman syndrome are classic examples of what happens when these delicate epigenetic tags go awry, often due to an imbalance or error in the parental origin of these crucial imprinted genes.

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The Cloned Toad

  • This experiment showed that specialised cells still contain all the genetic information needed to make a whole animal. Later, nuclei from adult skin cells also produced swimming tadpoles.
  • It was initially believed that as cells differentiated, they permanently lost or switched off genes they no longer needed. Gurdon's work demonstrated that the "storybook" of life, the full set of genetic instructions, remains intact in all body cells.
  • It also showed that the epigenetic marks that keep a cell specialised can be largely erased and rewritten by the egg. The process is inefficient: hundreds of transfers were needed for each success, and cloned animals often have abnormalities, probably because the reset is incomplete.

Sources: Carey (2012), chs. 1 & 7; Gurdon (2006), pp. 3–4.

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You Are More Than Your Genes!

  • For too long, genetic determinism suggested our DNA was an immutable, fixed blueprint—our destiny written in stone from conception. This view presented a fatalistic outlook, where the script of our lives was entirely pre-written.
  • But our understanding of biology revealed a revolutionary truth: our genes are not the sole arbiters of our fate. We discovered the epigenome, a dynamic, responsive layer "above" the genome that orchestrates how our genes are expressed—which ones are turned on, which are turned off, and how strongly they influence our cellular functions. It's about changing how the DNA code is read, not the code itself.

The epigenome is a responsive layer linking our genes to our development and environment.

(Author's summary.)

  • This dynamic interplay makes our biological narrative far more flexible. Acting like a complex dimmer switch, the epigenome responds to internal and external cues. Mechanisms like DNA methylation add chemical tags to silence genes, while histone modification can make genes more or less accessible. These crucial epigenetic marks influence cell differentiation, tissue development, and our ongoing adaptation to life.

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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You Are More Than Your Genes!

The profound lesson that we are not prisoners of our genetic destiny is echoed in a fascinating array of biological phenomena:

  • The Cloned Toad: John Gurdon showed that a specialised cell's nucleus keeps all its genes and can be reprogrammed by an egg.
  • Identical Twins: Despite identical DNA, twins differ epigenetically from birth, and the differences grow with age.
  • Bees: Genetically identical queens and workers differ because of diet; royal jelly acts at least partly through DNA methylation.
  • Cats: Tortoiseshell (calico) cats' distinct fur patterns arise from random X-chromosome inactivation, an epigenetic process that silences one X chromosome in each cell, expressing different color genes.
  • The Dutch Famine: Famine early in pregnancy was followed by higher obesity rates in adult children, with possible effects in grandchildren.
  • Maternal Nurturing in Rats: A mother's licking and grooming in the first week of life sets the pup's adult stress response through methylation of the cortisol receptor gene.

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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The story of possibilities

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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References

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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