Introduction to Epigenetics

Why can identical twins, with exactly the same genetic makeup, follow such different paths in health and disease? How does the air we breathe, the food we eat, or the stress we endure leave marks not just on us, but potentially on our children and grandchildren? How does nurture manifest itself in biology in the context of the nature vs nurture debate? These are the questions that drive the field of epigenetics, seeking to understand the nuanced dialogue between our genes and our environment.

Epigenetics introduces a layer of complexity above the genome, it’s literally what it means. The prefix epi- means “over” in Greek. It’s a layer of information added “on top of” the genome itself.¹ Epigenetics is organization of the genome. If the genome, the DNA is the raw data stored in the hard drive of biology, the part that stores all the raw information . The epigenome is the operating system that can run applications pulling information from multiple data points from the hard drive. An adaptable system that responds to stimuli to control a cell’s functions and molecular processes. These responses, influenced by lifestyle, environmental exposures, and even psychological states, can turn genes on or off, effectively shaping an individual’s development, health, disease risk and guess what, aging.

In this 4 part expert series we will discuss epigenetics; what it is, how it’s maintained, what happens to it during aging, what we can do about it today and possibly in the future. But, before diving into all of it one must understand what epigenetics is and how it plays into cellular and physiological function.

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This article is part one of a four-part series on epigenetics.

1. Introduction to Epigenetics
2. Epigenetics and Gene Expression
3. Epigenetics and Aging
4. Coming Soon

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A brief introduction

Epigenetics is increasingly becoming a buzzword in the realms of science and health, often mentioned in discussions ranging from groundbreaking research to everyday health advice. The definitions and explanations that people give when talking about epigenetics doesn’t do justice to the importance and magnitude of the role it plays in biology. A common way people describe epigenetics is only through DNA methylation, only one of the several modifications epigenetics uses. Described as “chemical tags added to DNA which can turn genes on or off”.² While this definition captures a core mechanism of epigenetics it fails to highlight the profound effect it can have when deregulated or fixed. Epigenetics is arguably one of the strongest pathways for interventions for disease and aging. In this article we’ll talk about what epigenetics is, how it plays a role in maintaining and propagating biological information, how it gets specified during development and some tools we can use to remodel the entire epigenome (the entire epigenetic state of a cell).

A primer into biological information

All complex systems require some way of storing information. They rely on this information to maintain themselves and control responses to different stimuli. The primary 2 ways biology does this is through genetics and epigenetics.³ Genetics store information in the form of deoxyribonucleic acid, better known as DNA. Deoxyribonucleic acid is composed of deoxyribonucleotides, the building blocks of DNA. Each nucleotide includes one of four bases: adenine (A), thymine (T), cytosine (C), or guanine (G). These nucleotides are chemically connected to each other to form large stretches of DNA which maintain their information. The information required to make a human stretches for ~3.1 billion nucleotides across 23 chromosomes (24 for males).⁴ But most cells present in our bodies contain 2 copies of each chromosome so the total length doubles to approximately ~6.2 billion base pairs. Now this long stretch of DNA contains the recipes of how to make proteins. The recipe is then copied into small molecules called ribonucleic acids aka RNAs (which use the same language as DNA). These RNA molecules are then used as the template by the molecular machinery of the cell to make proteins. Proteins are pretty much the only way a cell does anything. They’re the functional units, the workers, the builders, the demolishers. Proteins, like DNA, are formed by the combination of their own building blocks, amino acids. Instead of 4 options like in DNA the number of blocks grows to 20. Each protein is made by connecting these blocks in an orderly fashion. Their sequence governs other properties such as 3D structure and what modifications they acquire which effects and determines their function. This process is called the central dogma and is at the center of life as we know it.⁵

The central dogma illustrates the flow of information from genetics coded in DNA to functional proteins. Yet, without regulation, the simultaneous activation of all genes would lead to chaos rather than coordinated biological processes. There has to be order, there are proteins that work with other proteins to form complexes that carry out specialized functions which necessitates a precise timing and sequence of protein production. The unique expression of proteins is what differentiates the over 200 cell types in the human body. And what determines which parts of the genome are opened and used to make protein? What ensures coordinated expression of proteins that gives order to the central dogma that allows complex life to exist? Epigenetics.

What is epigenetics?

Epigenetics is a field that extends our understanding of genetics by focusing on how gene expression is regulated beyond the “digital” information encoded within our DNA. Digital in the sense that DNA is a set of ordered molecules that can take one of four values. It’s a quaternary system similar to the binary system of computers. However, epigenetics introduces an “analog” dimension to this framework, where the expression of genes can be modulated in degrees of expression which allows responding dynamically to the environment.

The genetic content present in the 200+ cell types present in the human body is essentially the same. They differ in their epigenetics. Which parts of the genome they express. There are around 20,000 protein coding genes in the human genome. Although a good majority of these genes can be detected across cell types the number of genes that are highly expressed in a cell are around 3 to 4 thousand. And these differ from cell to cell. Thus what allows cells to have drastically different characteristics. Take for example a nerve cell and a skin cell. They contain the same genetic material but the part that codes the enzyme responsible for making the neurotransmitter dopamine is open and being expressed in nerve cells while it isn’t in skin cells. The entirety of the genes being transcribed is called the transcriptome of that cell. It’s what epigenetic ultimately manipulates and is a term you’ll hear more often as you read on. 

This sophisticated layer of biological regulation ensures that, despite having a constant genetic code, cells can exhibit a wide range of behaviors and functions by fine-tuning how genes are turned on or off. Through the complex interplay of various epigenetic mechanisms (which we’ll get into in the second article), cells are able to maintain an organized and coordinated gene expression profile that is specific to their type and current environmental conditions. Essentially, epigenetics bridges the gap between the static genetic code and the dynamic needs of an organism. 

While it takes millennia and hundreds of generations for the genetic code to change meaningfully, epigenetics offers a more immediate, adaptable response to the environment within a single organism’s lifetime or that of its offspring. However, one might wonder, can epigenetic alterations indeed be inherited by subsequent generations?

Epigenetics Inheritance

The definition of epigenetics often mentions the word “heritable”. If a thing is heritable it means its capable of being passed on from generation to generation. This happens with epigenetics both on a cellular level and an organismal level. At the cellular level, the process is relatively straightforward: when a skin cell divides, its progeny remain skin cells, preserving their identity through cell division despite the compaction of chromosomes and disintegration of the nucleus. This retention of epigenetic information is critical for maintaining cellular function and identity but is an area of research that remains underexplored. On an organismal level, epigenetic inheritance becomes even more fascinating.

One of the most popular examples of epigenetic inheritance in humans shows through the effects of famine on children. Perhaps the most popular study is the widely cited Dutch famine study. This landmark research highlighted how environmental stressors, like severe malnutrition, can leave epigenetic marks that are passed down to subsequent generations. Specifically, individuals who were in utero during the Dutch famine towards the end of World War II, a period marked by the Nazis cutting off food supplies, exhibited an increased susceptibility to metabolic diseases later in life. In another study the findings showed that children whose fathers that started smoking before the age of 11 (the study was conducted with adult fathers in 1992) were more overweight.⁶ These epigenetic changes, transcending generations, highlight the dynamic nature of inheritance, where environmental experiences directly influence genetic regulation and disease susceptibility across descendants. This understanding prompts further investigation into how aging might affect the stability of these epigenetic markers, potentially altering their influence over time.

Biological information and aging

Now that we have a foundational grasp of biological information and how epigenetics plays into it we can talk about why this is important in the context of aging. The debate on what aging is isn’t still agreed upon, among the definitions that attempt at elucidating aging there are ones that do so through explaining its causes and others that do through its results. The latter definitions have broader consensus. Most aging researchers would agree that aging results in a progressive decline of cellular and bodily function. Among the hotly debated definitions that try to explain aging through its causes is one that is extremely relevant to epigenetics and that is the information theory of aging. This theory states that aging is driven through the progressive loss of biological information (mainly epigenetic). The biological information required for normal functions are established during development and over time, through aging, cell divisions and external damage the gradual loss of information leads to disruptions in these functions that eventually leads to progressive decline in function of the organism. Resulting in higher incidence of disease and disorders and decreased regeneration and repair capacity. But luckily there are hints of evidence that this information loss is reversible.³ But before getting into how this epigenetic erosion happens during aging we must understand how its established in the first place and tools to manipulate it. Perhaps the magnum opus of evolution is the ability of a single cell to form an adult human and guess what epigenetics is the main player.

Differentiation

We mentioned that the difference between all cell types is their epigenomes, while their genetic material remains identical. But how does this happen? Tens of trillions of cells, hundreds of cell types; each knows their function and carries it out in harmony with other cells to form a fully functioning adult human being.⁷ It all starts with a single cell, the zygote. The zygote is what we call the cell that arises when a sperm fertilizes an egg. The DNA that forms when that happens is entirely unique, different from any of the 117 billion humans that have ever existed.⁸ Then, the zygote begins to divide, 2 cells, 4 cells, 8, 16, until it reaches 1000 cells in a matter of days. Through every division, the cells start to stray from each other, not only physically in space but epigenetically and in terms of their potential roles in the body.

The zygote is totipotent, meaning it can give rise to an entire organism, which is evident every single time a mammal is born. But the cells in the embryo a few divisions after are also totipotent.⁹ In fact, if one of those cells separates early enough, you get identical twins. However, as the number of total divisions grows, the cells lose their potencies. They first become pluripotent, these cells being capable of giving rise to any cell type in the body. During the differentiation process, some of these pluripotent cells will go on to make nerve cells while others may become muscle cells, depending on the signals they receive and the epigenetic changes that occur within them. As development continues, they become multipotent, referring to cells that are able to generate a couple of different cell types, and finally, they become unipotent, the terminally differentiated cells that make up most of the adult human body.¹⁰

This process of the incremental and orderly specification of the epigenomes of every single cell is called differentiation. Where cells progressively specialize to perform specific functions. In fact it is through the study of this very process with which epigenetics was first discovered. Conrad Waddington first used the word epigenetics in the 1940s. In fact in his paper he proposes the name “epigenotype” which didn’t stick on for some unfortunate reason. He summarizes the discovery of epigenetics beautifully in his own words.

“…between genotype and phenotype lies a whole complex of development processes, for which Dr. Waddington proposes the name ‘epigenotype.”¹¹

Waddington’s insights into the developmental processes that shape an organism’s phenotype laid the groundwork for a deeper exploration of how environmental factors and genetic makeup interact to determine cellular fate. Later he modeled the differentiation process through a metaphorical landscape that remains relevant to this day. Waddington’s epigenetic landscape illustrates a series of valleys that branch and are separated by hills. At the very top of the valley sits a ball representing the undifferentiated cell that has many possible paths it can take when rolling down. As it does the paths become more specific just like a cell becoming more specialized. Each valley represents a different terminal cell type. As the ball goes down further the valleys become deeper, becoming more and more difficult to move to adjacent valleys.¹² This metaphorical journey down the hill happens billions of times throughout development, imaging the ball divides and divides in the end to form trillions of specialized cells in their own valley. When Waddington first proposed the landscape the idea of a ball climbing back up the hill, or a cell reverting to a more primitive, undifferentiated state, was largely inconceivable. The ball always rolled towards the path of least resistance, down the hill. That’s how things were. It remained that way for decades until the birth of a sheep, Dolly.¹³

Somatic Cell Nuclear Transfer (SCNT)

The first cloned organism wasn’t actually Dolly, it was a frog cloned by John Gurdon and colleagues in 1962.¹⁵ Dolly was the most popular cloned organism that got the most publicity. Although John Gurdon was the first to produce sexually mature adult organisms through cloning, the idea reaches further back. Hans Spemann, a renowned German embryologist first mentioned the idea of cloning.¹⁶ Then Briggs & King set the ground for the field by conducting the first actual experiment of transferring somatic cell nuclei into eggs. They observed frogs developing until the tadpole stage.¹⁷ Fast forward to today the same experiment has been conducted in a wide variety of animals ranging all the way from ferrets to primates.¹⁸

The actual process of somatic cell nuclear transfer is actually a somewhat similar concept. As the same suggests the nucleus of a somatic cell is transferred into an egg whose nucleus is removed. Like we’ve gone over the genetic content of somatic cells are identical to the content conceived in the zygote. They differ in their epigenetics. When the nucleus of a somatic cell is removed and placed into an egg whose nucleus was removed. The proteins present in the egg remodel the entire epigenome to start development from scratch and an organism is formed.¹⁷

One question that comes to mind is what happens to the lifespan of cloned organisms. This question was especially pushed to the forefront for Dolly. The birth of Dolly was big news, her birth and life were tracked by many and when she died prematurely it raised important questions about the health of cloned organisms.¹⁹ The normal lifespan of a Finn Dorset sheep is around 11-12 years. Dolly died at 6.5 due to a form of lung cancer which is a common disease among sheep caused by the retrovirus JSRV. What was interesting was that the flock that she was raised with (which weren’t cloned) also died of the same disease. In 2016, the 20th anniversary of Dolly’s birth, scientists released a report on sheep that were generated from the same genetic material as Dolly. In this report the author’s assessed the long term health of 13 cloned sheep (genetically identical to Dolly) and reported no signs of accelerated aging or disease when compared with normal animals.²⁰

Cellular Reprogramming

The SCNT experiments, in essence, shows that the proteins and/or mRNA present in the egg cytoplasm can reprogram the epigenome of a somatic cell to create an entirely new organism. Leveraging this information a brilliant scientist named Shinya Yamanaka asked the question: which proteins? In 2006 he released a paper where he tested the ability of combinations of proteins to effectively do the same thing that SCNT does, reversing the cellular state of a somatic cell to a more developmentally primitive one.²¹ And through his testing he discovered 4 transcription factors (proteins that affect transcription) that, when expressed in somatic cells were able to induce the formation of pluripotent stem cells and named them induced pluripotent stem cells (iPSCs). 

With the mere expression of proteins he was not able to make the cells as developmentally immature as SCNT does. Although iPSCs are able to differentiate into any cell type present in the body they are not able to form an organism by themselves. In fact this still is a very active research area today. Hundreds of papers are published each year to contribute to the effort of producing more and more developmentally immature cells artificially. 

After the groundbreaking discovery of Yamanaka and colleagues, cellular reprogramming became a dedicated area of research in and of itself. People worked on improving the process, understanding it. They worked on the generation of different cell types differentiated from the generated iPSCs. They’ve even discovered ways to directly reprogram the cells from a cell type to another (e.g. from fibroblast to myocyte) and termed it direct reprogramming.²² Remember the epigenetic landscape Waddington proposed. This discovery gave us the ability to move balls out of valleys, over hills, into other valleys and up the hill it once rolled down. This triggered the start of research that improves the control we have over the epigenome. Each day we are learning how to better manipulate it, only a matter of time until we have precise control over all its aspects.

As a result of the growing knowledge about epigenetic manipulation, fast forward to 2016, 4 years after Yamanaka was awarded the Nobel prize for his discovery (along with John Gurdon) Ocampo et al. used cellular reprogramming to extend the lifespan of mice with an accelerated aging syndrome.^{23 24}Cellular reprogramming is a complex process that can take anywhere from 2 to 8 weeks. Through each stage the cells progressively lose their somatic cell identity and begin to acquire their pluripotent identities. The “cellular age” of pluripotent stem cells is theoretically zero, because they differentiate and are no longer present in the body, which is when we start to add age numbers (traditionally).  Ocampo and colleagues reasoned that the cellular reprogramming process can be applied incompletely. The cells would have decreased cellular ages but not lose their identities which are required for them to carry out their vital tasks in the body. They would effectively be rejuvenated. Which is what happened, the mice that were partially reprogrammed had almost ~50% increased lifespans. And thus another field of research ignited partial reprogramming. Now there are dozens of papers and some startups that have and are working on applying partial reprogramming as an aging intervention which we’ll dive into later in the series.

Conclusion

We’ve gone through the basics in this article. By now you hopefully have a good understanding of the following: what biological information is, what role epigenetics plays in it, a theoretical understanding of what epigenetics is and differentiation and de-differentiation. In the next article we’ll be building upon the concepts introduced in this article, diving into the molecular mechanisms that make up the epigenome.

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1. What is epigenetics?: MedlinePlus Genetics. https://medlineplus.gov/genetics/understanding/howgeneswork/epigenome/.
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2. Henriques, M. Can the legacy of trauma be passed down the generations? https://www.bbc.com/future/article/20190326-what-is-epigenetics. ↩︎
3. Lu, Y. R., Tian, X. & Sinclair, D. A. The Information Theory of Aging. Nat. Aging 3, 1486–1499 (2023). ↩︎
4. Homo sapiens genome assembly T2T-CHM13v2.0. NCBI https://www.ncbi.nlm.nih.gov/data-hub/assembly/GCF_009914755.1/. ↩︎
5. Crick, F. Central Dogma of Molecular Biology. Nature 227, 561–563 (1970). ↩︎
6. Northstone, K., Golding, J., Davey Smith, G., Miller, L. L. & Pembrey, M. Prepubertal start of father’s smoking and increased body fat in his sons: further characterisation of paternal transgenerational responses. Eur. J. Hum. Genet. 22, 1382–1386 (2014). ↩︎
7. Alberts, B. Molecular Biology of the Cell. (Garland Science, 2017). ↩︎
8. How Many People Have Ever Lived on Earth? PRB https://www.prb.org/articles/how-many-people-have-ever-lived-on-earth/. ↩︎
9. Lu, F. & Zhang, Y. Cell totipotency: molecular features, induction, and maintenance. Natl. Sci. Rev. 2, 217–225 (2015). ↩︎
10. Mahla, R. S. Stem Cells Applications in Regenerative Medicine and Disease Therapeutics. Int. J. Cell Biol. 2016, 6940283 (2016). ↩︎
11. Waddington, C. H. The epigenotype. 1942. Int. J. Epidemiol. 41, 10–13 (2012). ↩︎
12. Waddington, C. H. The Strategy of the Genes. (Routledge, 2014). ↩︎
13. Wilmut, I., Schnieke, A. E., McWhir, J., Kind, A. J. & Campbell, K. H. S. Viable offspring derived from fetal and adult mammalian cells. Nature 385, 810–813 (1997). ↩︎
14. Goldberg, A. D., Allis, C. D. & Bernstein, E. Epigenetics: A Landscape Takes Shape. Cell 128, 635–638 (2007). ↩︎
15. Gurdon, J. B. The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpoles. J. Embryol. Exp. Morphol. 10, 622–640 (1962). ↩︎
16. Spemann, H. & Mangold, H. Induction of embryonic primordia by implantation of organizers from a different species. 1923. Int. J. Dev. Biol. 45, 13–38 (2001). ↩︎
17. Briggs, R. & King, T. J. Transplantation of Living Nuclei From Blastula Cells into Enucleated Frogs’ Eggs. Proc. Natl. Acad. Sci. U. S. A. 38, 455–463 (1952). ↩︎
18. Matoba, S. & Zhang, Y. Somatic Cell Nuclear Transfer Reprogramming: Mechanisms and Applications. Cell Stem Cell 23, 471–485 (2018). ↩︎
19. Dolly the sheep clone dies young. http://news.bbc.co.uk/2/hi/science/nature/2764039.stm (2003). ↩︎
20. Sinclair, K. D. et al. Healthy ageing of cloned sheep. Nat. Commun. 7, 12359 (2016). ↩︎
21. Takahashi, K. & Yamanaka, S. Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell 126, 663–676 (2006). ↩︎
22. Wang, H., Yang, Y., Liu, J. & Qian, L. Direct cell reprogramming: approaches, mechanisms and progress. Nat. Rev. Mol. Cell Biol. 22, 410–424 (2021). ↩︎
23. The Nobel Prize in Physiology or Medicine 2012. NobelPrize.org https://www.nobelprize.org/prizes/medicine/2012/summary/. ↩︎
24. Ocampo, A. et al. In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming. Cell 167, 1719-1733.e12 (2016). ↩︎