Mohit Aspal ’21 and Tom Lawley ’20

Introduction: The Magic Pill

Imagine telling people that there is a magic health pill that if they take once a day, they could be the most physically and mentally healthiest version of themselves. They could toss aside their sleeping pills, diet supplements, plans for liposuction, nootropics, and even some prescription medicines for blood pressure, cholesterol, and vascular health. In addition to these physiological benefits, this magic pill would also help improve cognitive function, be one of the best preventative measures for diseases, and improve overall longevity and mental well-being. Now, imagine telling people that this pill is free and has essentially no side effects. People would be lining outside the door for days without hesitation waiting to purchase this pill!

Surprisingly, doctors and health professionals have been prescribing this pill since biblical times: physical exercise. We often hear the catchphrase “exercise is the best medicine” thrown around in the media and we think that this is probably just another tactic to motivate people to hit the gym. However, this substantial claim actually holds much validity. The physiological benefits of exercise have been extensively studied and are quite well-established. There has been mounting evidence of exercise improving heart function and blood glucose levels, and also being an effective preventive measure against heart disease, stroke, type II diabetes, and breast and colon cancers 4. However, physical exercise also has many cognitive and psychological benefits that often go overlooked, possibly since these mechanisms have not been well-studied until recently.

“Breaking Down” the Neuroepigenetics

Interestingly, many of these cognitive changes are rooted in the emerging field of neuroepigenetics. This field explores how structural changes at the molecular level of genes can have functional implications in the nervous system—especially in the brain. Oftentimes, people associate exercise with having direct changes in their physical appearance. Yet, when we think of the genes in our brain, we never consider the effect of environmental conditions. However, as we will discover, physical exercise is one of these important environmental factors that can directly impact how specific genes in the brain are expressed, and in turn, how our brain functions.

This new knowledge allows us to leverage exercise to improve our general cognitive functioning, including our memory and productivity throughout the workday6. Also, by understanding how physical exercise can help change our brain cognition, memory, and other crucial functions, we can apply this knowledge to treatments or protection against neurodegeneration or pathologies such as Alzheimer’s disease that affect cognitive functioning. Oftentimes, uncovering these mechanisms opens doors to better understanding how environmental factors exactly target specific genes, helping design more effective clinical solutions for treating these disorders. Just as we care about the how’s and why’s of specific drug mechanisms, it is important to understand how exercise can distinctly change our bodies.

In the nucleus of all non-dividing cells in our body, we have DNA-protein complexes where DNA is wrapped tightly around proteins known as histones, which protect the DNA from unravelling and getting damaged. However, in this native state, RNA polymerase, which transcribes the DNA, cannot get proper access to the DNA, resulting in transcriptional repression and lowered gene expression. Think of this as a yo-yo, with the DNA as the string and the histones as the outer yo-yo shell. DNA wrapping tightly around histones is similar to the yo-yo string being tightly wrapped to its core. In this situation, the string is too condensed to play with. However, it is possible to unravel this string and slowly loosen it enough so that the yo-yo can be used for its intended function.

Similarly, in our bodies, during development or due to environmental factors, epigenetic modifications can occur, which alter some properties of this DNA-protein complex to change the expression of certain genes. It’s easy to visualize these epigenetic mechanisms as a simple seesaw. Imagine there is a seesaw for every specific function that a brain performs; for example, a seesaw for memory, a seesaw for cognitive ability, one for spatial awareness, and so on. Now, for each seesaw, imagine there are genes sitting on each end, with one end of the seesaw corresponding to repressive genes and the other one corresponding to activating genes. Epigenetic modifications can shift this seesaw so that one side lifts up, promoting transcription of either the repressive genes that decrease function or the activating genes that increase it.

For example, if we were looking at the brain’s ability to control memory and neural plasticity, we would have a seesaw with the protein phosphatase 1 gene (PP1) on the repressive seat of the seesaw and the brain-derived neurotrophic factor (BDNF) gene on the activating seat. Exercise (or the lack of it) could then cause specific epigenetic modifications that shift this seesaw to either express the BDNF gene that helps with memory and plasticity or express the PP1 gene that represses memory. In this way, environmental factors—such as physical exercise—can change the level of gene expression, which in turn controls how the brain functions. For example, research has shown that physical exercise can generate new neurons, form new neural connections, and promote other development in brain regions such as the hippocampus and neocortex6. Exercise can also cause molecular changes in our brains, for example by affecting levels of serotonin and insulin growth factors6.

Protein Phosphatase 1 (PP1) Gene

So, what exactly do these epigenetic modifications consist of? Let’s start by taking a closer look at the PP1 gene. As mentioned before, past research studies have shown PP1 to be an important memory suppressor gene. Therefore, since we know that exercise helps improve memory ability, we would want epigenetic changes that push this repressive side of the seesaw down. In other words, there should be epigenetic modifications that decrease expression of PP1. Indeed, this is exactly what research studies have found. One study examined hippocampal function by comparing PP1 protein levels in exercising and sedentary mice1. The researchers set up an experiment with three groups of aged, male rats: a control group of sedentary rats, an experimental group with voluntary treadmill exercise rats, and another experimental group with involuntary treadmill exercise rats1. In both exercise groups, from a period of 5 to 23 months, there was a significant decrease in measured PP1 protein levels1.

How did exercise decrease PP1 expression? Another study found a link between environmental-stimulated memory consolidation and an increase in methylated PP17. This brings us to our first important mode of epigenetic modification: DNA methylation. Let’s return to our yo-yo analogy. Imagine that currently our yo-yo is unraveled, and the string is completely visible. If in this case the string represents our PP1 gene, it means that the PP1 gene will be available for us to “play with” and express. However, imagine a person coming up and re-wrapping the PP1 yo-yo so it becomes compacted again. Now, we can’t play with the yo-yo anymore– in other words, PP1 gets shut off. This is essentially what DNA methylation does on the molecular level inside our bodies. It condenses our DNA so PP1 expression lowers. DNA methylation usually occurs at a special nucleotide site called CpG sites, so this is sometimes known as CpG methylation too.

Based on this logic, since memory consolidation was associated with an increase in PP1 methylation, we expect transcriptional silencing of this PP1 gene. Indeed, the authors of this study found that the experimental group of rats that underwent neuronal stimulation (in this case, this was a fear conditioning response), had increased memory consolidation, which corresponded to increased methylated PP1 and decreased PP1 mRNA in the hippocampus7. It might be convincing to say that exercise, too, improves memory consolidation via this increased PP1 methylation. However, since this study did not specifically test the neuronal stimulation of physical exercise, no concrete conclusions can be made yet about this particular epigenetic modification. Yet, it does provide a foundation for future studies to test whether exercise directly decreases PP1 expression.

Brain-Derived Neurotrophic Factor (BDNF) Gene

Next, let’s take a look at the molecule on the other side of this epigenetic seesaw, BDNF, or brain-derived neurotrophic factor. BDNF has been shown in various studies to play an indispensable role in both cognitive development and maintenance. Strengthened neural connections8, as well as increased neuron formation10 are just two of the many beneficial effects that BDNF enacts on your brain, and these effects ultimately influence one’s ability to learn and memorize12. For these reasons, BDNF, specifically in the hippocampus, has been a popular topic of study to understand the relationship between physical exercise and cognitive function. Therefore, as we move to the other side of the seesaw, we now expect epigenetic changes that push BDNF up, resulting in increased BDNF expression. Again, this is exactly what we see in research studies. In one such study, researchers used RT-PCR (which is a technique to essentially measure RNA) of extracted mice hippocampal tissue to analyze this effect. They found that mice who underwent four weeks of aerobic exercise expressed a roughly 25% increase in BDNF mRNA compared to sedentary control mice5.

To understand the epigenetic mechanisms underlying these changes in mRNA, these researchers next looked at the hippocampal levels of two enzymes called histone acetyltransferases (HATs) and histone deacetylases (HDACs). This brings us to our second important mode of epigenetic modification: histone acetylation. Returning to our yo-yo analogy, think of our BDNF yo-yo as being wrapped relatively tightly in its normal state. There is still a little bit of string available to play with the yo-yo, but not too much. However, we can change some properties of the yo-yo so the BDNF “string” becomes a little bit more unraveled and easier to play with. Acetylation is one way to do this. Just as methylation is the person who wraps the string tightly, acetylation is the person who unravels it. HATs and HDACs are the remodeling enzymes that cause this wrapping and unwrapping. Since HATs perform acetylation, they “unwrap” genes and increase expression. HDACs perform deacetylation, so they “tighten” genes and decrease expression.

When exercise is involved, these HATs begin to work harder to unravel the BDNF yo-yo. At the same time, remember that methylation is working to wind up the PP1 yo-yo. Thus, we see our memory seesaw shift up towards the side of BDNF expression. Quantitative measurements of these proteins showed that the ratio of HATs to HDACs significantly increased in the experimental mice that underwent the aerobic exercise regimen3,5. Since this was also accompanied by an increase in BDNF expression, it is likely that physical exercise increases transcription of the BDNF gene via this increased histone acetylation5. Another study further supported this possibility, as experimental exercise rats were found to have an almost two-fold increase in acetylation of a specific BDNF histone when compared to the sedentary rats3. To test the cognitive effects of this increase in BDNF expression, the mice were subject to the novel-object recognition test. In this test, mice are exposed to two objects and are given time to get familiarized with them. The next day, one of the objects is replaced with a novel item and the time spent analyzing the novel item is measured. In theory, mice with better memory should spend more time studying the novel item as they already recognize the old item. In this study, the experimental exercise mice spent a significantly greater time with the novel item, demonstrating the positive effects of BDNF on memory.

A deeper dive into the mechanism behind physical exercise increasing BDNF was conducted in a study where rats were caged with or without an exercise wheel for one week3. In this study, we return to the epigenetic mechanism of DNA methylation. Here, researchers analyzed the CpG methylation patterns within the BDNF gene. One week of physical exercise was sufficient to reduce methylation from 59.2% in the control mice to only 18.4% in the experimental mice. As we talked about before, methylation wraps the string of DNA tightly around the yo-yo, so based on this logic, a reduction in methylation would have the opposite effect. Indeed, demethylation helped shift our memory seesaw towards BDNF expression, and amazingly, it only took one week of moderate exercise to do so.

Future Implications

So, why is all this important? What exactly are the broader implications of these studies for humans? Well, by understanding these neuroepigenetic links between physical exercise and improvements in brain function, we can apply this knowledge to start shifting the “seesaws” in our own brains by ourselves, helping treat and reduce the risk of cognitive disorders. By uncovering these mechanisms, researchers have begun to unravel some potential treatments for age-associated cognitive impairments, particularly by creating epigenetic changes in the hippocampus of mice9. In this study, cognitive decline was associated with decreased expression of several memory genes in the hippocampus, which also correlated to lower acetylation levels9. However, when the researchers added HATs to restore acetylation, there was a significant revival in memory consolidation9. In humans, there have also been preliminary studies done exploring the neurocognitive benefits of exercise in cognitive disorders. Specifically, exercise as a treatment for pathologies such as Parkinson’s and Alzheimer’s has been a prominent area of research. In one study, incorporating a 6-month physical exercise program, with both aerobic and muscle resistance components, in older subjects with Parkinson’s disease showed improved executive functioning, including components such as decision making, planning, and carrying out tasks11. This training regimen also showed increases in both maximum oxygen consumption (VO2) and BDNF levels in the exercising participants11. In the future, these findings could possibly be applied to designing drugs that positively target these mechanisms, helping neurodegenerative patients who are immobile or cannot exercise. Maybe we could design an actual “magic pill.”


  1. Chen, W. Q., Viidik, A., Skalicky, M., Höger, H., & Lubec, G. (2007). Hippocampal signaling cascades are modulated in voluntary and treadmill exercise rats. Electrophoresis, 28(23), 4392-4400.
  2. Fernandes, J., Arida, R. M., & Gomez-Pinilla, F. (2017). Physical exercise as an epigenetic modulator of brain plasticity and cognition. Neuroscience & Biobehavioral Reviews, 80, 443-456.
  3. Gomez-Pinilla, F., Y. Zhuang, J. Feng, Z. Ying, and G. Fan. “Exercise Impacts Brain-Derived Neurotrophic Factor Plasticity by Engaging Mechanisms of Epigenetic Regulation.” European Journal of Neuroscience 33, no. 3 (2010): 383–90.
  4. Harvard Health. (n.d.). Is exercise really medicine? Harvard Health. Retrieved March 23, 2020, from
  5. Li, Xiang, Takahiro Inoue, Masataka Hayashi, and Hiroshi Maejima. “Exercise Enhances the Expression of Brain-Derived Neurotrophic Factor in the Hippocampus Accompanied by Epigenetic Alterations in Senescence-Accelerated Mice Prone 8.” Neuroscience Letters 706 (2019): 176–81.
  6. Mandolesi, L., Polverino, A., Montuori, S., Foti, F., Ferraioli, G., Sorrentino, P., & Sorrentino, G. (2018). Effects of physical exercise on cognitive functioning and wellbeing: biological and psychological benefits. Frontiers in psychology, 9, 509.
  7. Miller, C. A., & Sweatt, J. D. (2007). Covalent modification of DNA regulates memory formation. Neuron, 53(6), 857-869.
  8. Pang, Petti T., and Bai Lu. “Regulation of Late-Phase LTP and Long-Term Memory in Normal and Aging Hippocampus: Role of Secreted Proteins TPA and BDNF.” Ageing Research Reviews 3, no. 4 (2004): 407–30.
  9. Peleg, S., Sananbenesi, F., Zovoilis, A., Burkhardt, S., Bahari-Javan, S., Agis-Balboa, R. C., … & Salinas-Riester, G. (2010). Altered histone acetylation is associated with age-dependent memory impairment in mice. science, 328(5979), 753-756.
  10. Rossi, Chiara, Andrea Angelucci, Laura Costantin, Chiara Braschi, Mario Mazzantini, Francesco Babbini, Maria Elena Fabbri, et al. “Brain-Derived Neurotrophic Factor (BDNF) Is Required for the Enhancement of Hippocampal Neurogenesis Following Environmental Enrichment.” European Journal of Neuroscience 24, no. 7 (2006): 1850–56.
  11. Tanaka, K., de Quadros Jr, A. C., Santos, R. F., Stella, F., Gobbi, L. T. B., & Gobbi, S. (2009). Benefits of physical exercise on executive functions in older people with Parkinson’s disease. Brain and cognition, 69(2), 435-441.
  12. Vaynman, Shoshanna, Zhe Ying, and Fernando Gómez-Pinilla. “Hippocampal BDNF Mediates the Efficacy of Exercise on Synaptic Plasticity and Cognition.” European Journal of Neuroscience 20, no. 10 (2004): 2580–90.

Leave a Reply