Epigenetics is the study of how cells control gene activity without changing the DNA sequence."Epi-" means on or above in Greek, and "epigenetic" describes factors beyond the genetic code. Epigenetic changes are modifications to DNA that regulate whether genes are turned on or off. These modifications are attached to DNA and do not change the sequence of DNA building blocks. Within the complete set of DNA in a cell (genome), all of the modifications that regulate the activity (expression) of the genes is known as the epigenome.

Because epigenetic changes help determine whether genes are turned on or off, they influence the production of proteins in cells. This regulation helps ensure that each cell produces only proteins that are necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Patterns of epigenetic modification vary among individuals, in different tissues within an individual, and even in different cells within a tissue. Environmental influences, such as a person’s diet and exposure to pollutants, can impact the epigenome. Epigenetic modifications can be maintained from cell to cell as cells divide and, in some cases, can be inherited through the generations.

A common type of epigenetic modification is called DNA methylation. DNA methylation involves the attachment of small chemical groups called methyl groups (each consisting of one carbon atom and three hydrogen atoms) to DNA building blocks. When methyl groups are present on a gene, that gene is turned off or silenced, and no protein is produced from that gene.

Another common epigenetic change is histone modification. Histones are structural proteins in the cell nucleus. DNA wraps around histones, giving chromosomes their shape. Histones can be modified by the addition or removal of chemical groups, such as methyl groups or acetyl groups (each consisting of two carbon, three hydrogen, and one oxygen atoms). The chemical groups influence how tightly the DNA is wrapped around histones, which affects whether a gene can be turned on or off.

Errors in the epigenetic process, such as modification of the wrong gene or failure to add a chemical group to a particular gene or histone, can lead to abnormal gene activity or inactivity. Altered gene activity, including that caused by epigenetic errors, is a common cause of genetic disorders. Conditions such as cancers, metabolic disorders, and degenerative disorders have been found to be related to epigenetic errors.

Scientists continue to explore the relationship between the genome and the chemical compounds that modify it. In particular, they are studying the effects that epigenetic modifications and errors have on gene function, protein production, and human health.

Epigenetic changes affect gene expression in different ways. Types of epigenetic changes include:

DNA Methylation

DNA methylation works by adding a chemical group to DNA. Typically, this group is added to specific places on the DNA, where it blocks the proteins that attach to DNA to “read” the gene. This chemical group can be removed through a process called demethylation. Typically, methylation turns genes “off” and demethylation turns genes “on.”

Histone modification

DNA wraps around proteins called histones. When histones are tightly packed together, proteins that ‘read’ the gene cannot access the DNA as easily, so the gene is turned “off.” When histones are loosely packed, more DNA is exposed or not wrapped around a histone and can be accessed by proteins that ‘read’ the gene, so the gene is turned “on.” Chemical groups can be added or removed from histones to make the histones more tightly or loosely packed, turning genes “off” or “on.”

Non-coding RNA

Your DNA is used as instructions for making coding and non-coding RNA. Coding RNA is used to make proteins. Non-coding RNA helps control gene expression by attaching to coding RNA, along with certain proteins, to break down the coding RNA so that it cannot be used to make proteins. Non-coding RNA may also recruit proteins to modify histones to turn genes “on” or “off.”

Each cell expresses, or turns on, only a fraction of its genes. The rest of the genes are repressed, or turned off. The process of turning genes on and off is known as gene regulation. Gene regulation is an important part of normal development. Genes are turned on and off in different patterns during development to make a brain cell look and act different from a liver cell or a muscle cell, for example. Gene regulation also allows cells to react quickly to changes in their environments. Although we know that the regulation of genes is critical for life, this complex process is not yet fully understood.

Gene regulation can occur at any point during gene expression, but most commonly occurs at the level of transcription (when the information in a gene’s DNA is transferred to mRNA). Signals from the environment or from other cells activate proteins called transcription factors. These proteins bind to regulatory regions of a gene and increase or decrease the level of transcription. By controlling the level of transcription, this process can determine the amount of protein product that is made by a gene at any given time.

Your epigenetics change as you age, both as part of normal development and aging and in response to your behaviors and environment.

Epigenetics and Development

Epigenetic changes begin before you are born. All your cells have the same genes but look and act differently. As you grow and develop, epigenetics helps determine which function a cell will have, for example, whether it will become a heart cell, nerve cell, or skin cell.

Example: Nerve cell vs. Muscle cell

Your muscle cells and nerve cells have the same DNA but work differently. A nerve cell transports information to other cells in your body. A muscle cell has a structure that aids in your body’s ability to move. Epigenetics allows the muscle cell to turn “on” genes to make proteins important for its job and turn “off” genes important for a nerve cell’s job.

Epigenetics and Age

Your epigenetics change throughout your life. Your epigenetics at birth is not the same as your epigenetics during childhood or adulthood.

Example: Study of newborn vs. 26-year-old vs. 103-year-old

DNA methylation at millions of sites were measured in a newborn, 26-year-old, and 103-year-old. The level of DNA methylation decreases with age. A newborn had the highest DNA methylation, the 103-year-old had the lowest DNA methylation, and the 26-year-old had a DNA methylation level between the newborn and 103-year-old (1).

Epigenetics and Reversibility

Not all epigenetic changes are permanent. Some epigenetic changes can be added or removed in response to changes in behavior or environment.

Example: Smokers vs. non-smokers vs. former smokers

Smoking can result in epigenetic changes. For example, at certain parts of the AHRR gene, smokers tend to have less DNA methylation than non-smokers. The difference is greater for heavy smokers and long-term smokers. After quitting smoking, former smokers can begin to have increased DNA methylation at this gene. Eventually, they can reach levels similar to those of non-smokers. In some cases, this can happen in under a year, but the length of time depends on how long and how much someone smoked before quitting.

Epigenetic changes can affect your health in different ways:

Infections

Germs can change your epigenetics to weaken your immune system. This helps the germ survive.

Example: Mycobacterium tuberculosis

Mycobacterium tuberculosis causes tuberculosis. Infections with these germs can cause changes to histones in some of your immune cells that result in turning “off” the IL-12B gene. Turning “off” the IL-12B gene weakens your immune system and improves the survival of Mycobacterium tuberculosis.

Cancer

Certain mutations make you more likely to develop cancer. Likewise, some epigenetic changes increase your cancer risk. For example, having a mutation in the BRCA1 gene that prevents it from working properly makes you more likely to get breast and other cancers. Similarly, increased DNA methylation that results in decreased BRCA1 gene expression raises your risk for breast and other cancers.While cancer cells have increased DNA methylation at certain genes, overall DNA methylation levels are lower in cancer cells compared with normal cells. Different types of cancer that look alike can have different DNA methylation patterns. Epigenetics can be used to help determine which type of cancer a person has or can help to find hard to detect cancers earlier. Epigenetics alone cannot diagnose cancer, and cancers would need to be confirmed with further screening tests.

Example: Colorectal Cancer

Colorectal cancers have abnormal methylation at DNA regions near certain genes, which affects expression of these genes. Some commercial colorectal cancer screening tests use stool samples to look for abnormal DNA methylation levels at one or more of these DNA regions. It is important to know that if the test result is positive or abnormal, a colonoscopy test is needed to complete the screening process.

Nutrition During Pregnancy

A pregnant woman’s environment and behavior during pregnancy, such as whether she eats healthy food, can change the baby’s epigenetics. Some of these changes can remain for decades and might make the child more likely to get certain diseases.

Example: Dutch Hunger Winter Famine (1944-1945)

People whose mothers were pregnant with them during the famine were more likely to develop certain diseases such as heart disease, schizophrenia, and type 2 diabetes. Around 60 years after the famine, researchers looked at methylation levels in people whose mothers were pregnant with them during the famine. These people had increased methylation at some genes and decreased methylation at other genes compared with their siblings who were not exposed to famine before their birth. These differences in methylation could help explain why these people had an increased likelihood for certain diseases later in life.

Did you know that just knowing the genome sequence of an organism only reveals part of the story - and that it is also important to determine how that organism interprets its genome and uses that information to build and operate itself accordingly? Less than 2 percent of the human genome corresponds to "genes," but we know other parts are important for regulating and translating the genome as well as responding to environmental influences. Even still, the job of large parts of the genome remains a bit of a mystery!

When scientists started the Human Genome Project, they didn't even know how many genes were in the human genome. It then came as a big surprise to learn that human beings only require roughly 20,000 genes! Those 20,000 or so genes are encoded by less than 2 percent of our genome. What is the rest of it doing? And how does each cell read and interpret its genome?

How Your Cells Use the Genome

Although it's appealing to think of the genome sequence as the "book of life" for an organism - one that contains all of the biological instructions to develop and operate that organism - we now know that the DNA bases are only the starting point.

It can be useful to think of a genome and how it works by a set of maps. Some maps are very simple; they may represent basic information such as the locations and intersections of roads. Such a simple map would be like the sequence of a genome: it would reflect the structure of the road, but would not give information about how it's used. As genomic technology improved, more complicated maps could be developed, adding many features and layers of information to a simple genome map. For instance, we learned that the basic sequence of a genome has stop signs and start signs added to it, just like roads do, and that these additions direct the "traffic" of proteins that bind to DNA and allow the cell use the genome. Other technologies also became available to map traffic patterns, revealing the presence of high- versus low-traffic area. In a genome, a high-traffic area might be a place where many genes are turned on by proteins binding to the DNA. These areas call for multiple layers of regulation, just like in a city where you might have high-rise buildings on top of a busy street with a subway underneath. In low-traffic areas, a genome can have deserts of hundreds of thousands of bases with no genes, with little sign of proteins binding the DNA. In the 15 years since the completion of the Human Genome Project, scientists have developed better and better methods for constructing three-dimensional "satellite" maps of genomes, where we can see what proteins bind to what DNA sequences in a single cell and at a specific time. It is the different patterns of "on" and "off" genes that helps produce the different types of cells that makes you, you.

Some of the stop and start signals that direct our cells to translate the map of our genomes are called "epigenomic modifications." Epigenomic modifications are often chemical groups that are added or subtracted from DNA bases or proteins that bind to DNA that change the way genes are read. Such modifications can be passed on as cells divide, even though they are not strictly changes in the DNA itself. One of these epigenomic modifications is called methylation. As a human is developing, some early cells start to become brain cells. Specific small chemicals (called methyl groups) are added onto the DNA in front of genes that won't be needed for brain cells. Here, the methyl groups act like stop signs: in all future brain cells, the methyl groups will make sure the genes that aren't needed stay turned off. This and other cellular tools in your cells are how the body makes sure its roughly 20,000 genes are used correctly by each cell type. Did you know that your cells were so smart?

Although methyl groups are not changes in the sequence of the DNA bases, epigenomic modifications like these can act like mutations by directing if the bases are read or not.. For example, in cancer cells, methyl groups are often inappropriately added at specific places in the genome. Now the cells grow out of control because the "stop" signs have been added in front of genes that would keep the cell in check. Some cancer therapies are drugs designed to stop these methyl groups from being added where they should not be, like the medicine azacitidine which is used in some blood cancers.

How Epigenomics Affects You

In the last 15 years, we have learned how the environment influences how the genome works through epigenomics. Here's one example: in the winter of 1944-1945, Germany had blocked the food supply to the Netherlands, and the population suffered a terrible famine. The effects of the "Dutch Hunger Winter" could be seen in the children born from women who were pregnant during the famine. The babies from mothers who were malnourished only in the beginning of their pregnancy, but then had normal levels of food later, had a greater frequency of obesity throughout their lifetimes; they also had higher risks of chronic diseases like diabetes when compared to their siblings who were born before or after the famine. In a striking finding, the children of these babies were also found to have higher risks for the same chronic diseases. So it seemed like something could be passed down through generations, but not changes to the DNA sequence itself. Sure enough, research has shown that the methylation patterns in the DNA were altered in these children, and the altered patterns were inherited by their own children, changing their health outcomes.

We know that diet directly affects methylation because nutrients in our food provide the methyl groups themselves. This means that the diet of either parent can affect their children and grandchildren. But it's not just diet - there is strong evidence shows that smoking can change methylation patterns as well. Epigenomic patterns can also be altered by drinking alcohol during pregnancy, leading in extreme cases to fetal alcohol syndrome. While not everything is controlled through epigenomics, these modifications to our DNA play a central role in how the genome carries out its work. But they aren't the only controls we've learned about through the Human Genome Project.

What the Rest Of the Genome Does

If only 2 percent of the genome's bases are used to encode proteins, what is the other 98 percent doing? Some of the genome's bases help determine its structure. There are areas like the telomeres, the ends of each chromosome, that are very important. Just like the caps on the end of your shoelaces, telomeres keep the ends of your chromosomes from fraying. Some of the other parts of your genome position the genes in the right places to be read by the cell's machinery. So, although those bases might not encode proteins, the genome cannot function without their presence.

dark matter" or "junk DNA," we are learning that the 98 percent has all kinds of important roles. Some parts called "ultraconserved elements" have kept the exact same sequence for millions of years in mammals, even though they don't contain genes. Why would that be? Recent studies suggest that deleting these elements causes brain changes and could lead to some neurological diseases like Alzheimer disease, although we are still learning why.

Here's another fact that might be a little creepy: up to 45 percent of your genome is actually leftover DNA from viruses that infected mammals over millions of years. We haven't yet worked out what much of that old viral DNA is doing, but we know it's contributed to at least one very important mammalian trait: exchanging nutrients between mother and baby through the placenta. The rest of the genome includes regulatory elements, including areas that influence genes to be expressed at the same time in response to the environment; transcribed sequences that the cell reads but does not use for making protein; and material which acts as a hotspot for your chromosomes to exchange information with each other.

Mendelian randomization studies examine how certain behaviors, environments, or other factors lead to specific health outcomes by looking at genetic differences that affect the way people’s bodies react to the behavior, environment, or other factor.

Why use Mendelian Randomization?

An important part of public health research is looking at whether behaviors, environments, and other factors, which can sometimes be changed, make people more likely to get certain diseases. However, showing that these factors cause a specific disease presents challenges.

In some studies, researchers compare people with and without a certain disease to look for behaviors, environments, and other factors that are linked to disease. In other studies, researchers compare health outcomes in people with and without a specific behavior, environment, or other factor to see if one group is more or less likely to develop a disease. The researchers are not able to control who has which behavior, environment, or other factor. Accurately measuring some behaviors, such as how much a person smokes or uses alcohol, can be difficult. In some cases, one factor is linked to other factors, and figuring out which one is the cause can be hard. For example, people who have higher alcohol use also tend to smoke more, so a link found between alcohol use and a health outcome might actually be due to smoking causing the outcome. Some factors can be present because of the disease itself, meaning that they are caused by the disease rather than leading to it. For example, as people get sick, they might tend to smoke less, so that decreased smoking might be associated with worsening of disease, even though in reality the decrease in smoking does not make the disease worse. These issues can mean that findings from one study are not repeated in later studies or that different studies can have findings that do not agree.

The gold standard for studying whether behavioral, environmental, or other factors cause disease is randomized controlled trials (RCTs). RCTs involve randomly assigning participants to one of two or more groups that differ by one factor. For example, those in a group either do or do not perform a certain behavior, are or are not exposed to a specific environmental factor, or do or do not receive a treatment. However, RCTs are costly, take a long time, and are not always possible due to ethical or other concerns, such as those related to assigning a group of people to perform an unhealthy behavior. RCTs are often used to confirm findings from other studies, and due to the cost of conducting RCTs, it is important to have the best evidence available from other study designs prior to starting an RCT. Mendelian randomization studies can help provide this evidence.

EXAMPLE: Mendelian Randomization Supports the Role of High Cholesterol and Heart Disease

Scientists observed that people with higher blood levels of low-density lipoprotein (LDL) cholesterol are more likely to have coronary artery disease. While this suggested that high blood LDL levels could lead to coronary artery disease, other explanations were possible.

For example, an unknown factor could cause both high LDL levels and make people more likely to develop coronary artery disease. This would make it seem like high LDL cholesterol levels caused coronary artery disease when the unknown factor was the actual cause.

Using a Mendelian randomization approach, scientists could look at genetic differences that affect LDL cholesterol levels to see if these variants make people more likely to develop coronary artery disease. The unknown factor would not influence which genetic difference is inherited.

For example, people with familial hypercholesterolemia have genetic changes that increase their blood levels of LDL cholesterol. These genetic changes are linked to an increased risk of coronary artery disease, which provides evidence that high LDL levels can cause heart disease.

These genetic changes are present from birth, before the development of coronary artery disease, providing evidence that high LDL levels lead to coronary artery disease, rather than coronary artery disease leading to high LDL.

How does Mendelian Randomization work?

“Mendelian randomization” is based on the fact that every person randomly inherits one of the two versions of every gene that each of their parents has. Each genetic difference is inherited independently, meaning that one genetic difference a person inherits does not influence which other genetic differences they inherit. Mendelian randomization studies take advantage of this fact to look for links between health outcomes and genetic differences that have a similar effect as the randomly assigned behaviors, environments, or other factors in RCTs but are not subject to the influence of other factors. For example, a Mendelian randomization study could look at genetic differences that affect how people’s bodies break down a toxin that is thought to be linked to a disease. If people with the genetic difference that makes their bodies less able to break down the toxin show higher rates of disease, this provides evidence that the toxin causes the disease. This effect would only be seen for people exposed to the toxin, and the genetic difference would have no effect on disease risk in those not exposed to the toxin. Mendelian randomization can be used to look at whether levels of a substance found naturally in a person’s body is linked to disease. Measuring the levels themselves can be a problem because the levels can change in response to other factors that could be related to the disease, such as diet, smoking, or alcohol use. However, if genetic differences that affect the levels are linked to the disease, that provides evidence that the substance is related to the disease, as shown in the example for high cholesterol and heart disease (see textbox).

Mendelian Randomization and Public Health

Mendelian randomization is one of many examples of how genetic approaches can help increase our understanding of the causes of disease. This approach has not been fully utilized in public health so far and finding genetic differences that result in effects similar to behaviors, environments, or other factors of interest can be challenging. In addition, showing that the genetic difference results in the health outcome through its effect on the behavior, environment, or other factor, not through a different pathway, can be challenging. Nonetheless, Mendelian randomization promises to be a helpful tool for future public health research.

Epigenomics is a field in which researchers chart the locations and understand the functions of all the chemical tags that mark the genome.

What is the epigenome?

The epigenome is a multitude of chemical compounds that can tell the genome what to do. The human genome is the complete assembly of DNA (deoxyribonucleic acid)-about 3 billion base pairs - that makes each individual unique. DNA holds the instructions for building the proteins that carry out a variety of functions in a cell. The epigenome is made up of chemical compounds and proteins that can attach to DNA and direct such actions as turning genes on or off, controlling the production of proteins in particular cells.When epigenomic compounds attach to DNA and modify its function, they are said to have "marked" the genome. These marks do not change the sequence of the DNA. Rather, they change the way cells use the DNA's instructions. The marks are sometimes passed on from cell to cell as cells divide. They also can be passed down from one generation to the next.

What does the epigenome do?

A human being has trillions of cells, specialized for different functions in muscles, bones and the brain, and each of these cells carries essentially the same genome in its nucleus. The differences among cells are determined by how and when different sets of genes are turned on or off in various kinds of cells. Specialized cells in the eye turn on genes that make proteins that can detect light, while specialized cells in red blood cells make proteins that carry oxygen from the air to the rest of the body. The epigenome controls many of these changes to the genome.

What makes up the epigenome?

The epigenome is the set of chemical modifications to the DNA and DNA-associated proteins in the cell, which alter gene expression, and are heritable (via meiosis and mitosis). The modifications occur as a natural process of development and tissue differentiation, and can be altered in response to environmental exposures or disease.

The first type of mark, called DNA methylation, directly affects the DNA in a genome. In this process, proteins attach chemical tags called methyl groups to the bases of the DNA molecule in specific places. The methyl groups turn genes on or off by affecting interactions between the DNA and other proteins. In this way, cells can remember which genes are on or off.The second kind of mark, called histone modification, affects DNA indirectly. DNA in cells is wrapped around histone proteins, which form spool-like structures that enable DNA's very long molecules to be wound up neatly into chromosomes inside the cell nucleus. Proteins can attach a variety of chemical tags to histones. Other proteins in cells can detect these tags and determine whether that region of DNA should be used or ignored in that cell.

Is the epigenome inherited?

The genome is passed from parents to their offspring and from cells, when they divide, to their next generation. Much of the epigenome is reset when parents pass their genomes to their offspring; however, under some circumstances, some of the chemical tags on the DNA and histones of eggs and sperm may be passed on to the next generation. When cells divide, often much of the epigenome is passed on to the next generation of cells, helping the cells remain specialized.

What is imprinting?

The human genome contains two copies of every gene-one copy inherited from the mother and one from the father. For a small number of genes, only the copy from the mother gets switched on; for others, only the copy from the father is turned on. This pattern is called imprinting. The epigenome distinguishes between the two copies of an imprinted gene and determines which is switched on.Some diseases are caused by abnormal imprinting. They include Beckwith-Wiedemann syndrome, a disorder associated with body overgrowth and increased risk of cancer; Prader-Willi syndrome, associated with poor muscle tone and constant hunger, leading to obesity; and Angelman syndrome, which leads to intellectual disability, as well motion difficulties.

Can the epigenome change?

Although all cells in the body contain essentially the same genome, the DNA marked by chemical tags on the DNA and histones gets rearranged when cells become specialized. The epigenome can also change throughout a person's lifetime.

What makes the epigenome change?

Lifestyle and environmental factors (such as smoking, diet and infectious disease) can expose a person to pressures that prompt chemical responses. These responses, in turn, often lead to changes in the epigenome, some of which can be damaging. However, the ability of the epigenome to adjust to the pressures of life appears to be required for normal human health. Some human diseases are caused by malfunctions in the proteins that "read" and "write" epigenomic marks.

How do changes in the epigenome contribute to cancer?

Cancers are caused by changes in the genome, the epigenome, or both. Changes in the epigenome can switch on or off genes involved in cell growth or the immune response. These changes can lead to uncontrolled growth, a hallmark of cancer, or to a failure of the immune system to destroy tumors.

In a type of brain tumor called glioblastoma, doctors have had some success in treating patients with the drug temozolomide, which kills cancer cells by adding methyl groups to DNA. In some cases, methylation has a welcome secondary effect: it blocks a gene that counteracts temozolomide. Glioblastoma patients whose tumors have such methylated genes are far more likely to respond to temozolomide than those with unmethylated genes.

Changes in the epigenome also can activate growth-promoting genes in stomach cancer, colon cancer and the most common type of kidney cancer. In some other cancers, changes in the epigenome silence genes that normally serve to keep cell growth in check.

To compile a complete list of possible epigenomic changes that can lead to cancer, researchers in The Cancer Genome Atlas (TCGA) Network, which is supported by the National Institutes of Health (NIH), are comparing the genomes and epigenomes of normal cells with those of cancer cells. Among other things, they are looking for changes in the DNA sequence and changes in the number of methyl groups on the DNA.Understanding all the changes that turn a normal cell into a cancer cell will speed efforts to develop new and better ways of diagnosing, treating and preventing cancer.

How are researchers exploring the epigenome?

In a field of study known as epigenomics, researchers are trying to chart the locations and understand the functions of all the chemical tags that mark the genome.

Until recently, scientists thought that human diseases were caused mainly by changes in DNA sequence, infectious agents such as bacteria and viruses, or environmental agents. Now, however, researchers have demonstrated that changes in the epigenome also can cause, or result from, disease. Epigenomics, thus, has become a vital part of efforts to better understand the human body and to improve human health. Epigenomic maps may someday enable doctors to determine an individual's health status and tailor a patient's response to therapies.

As part of the ENCODE (ENCyclopedia Of DNA Elements) project-which aims to catalog the working parts of the genome-the National Human Genome Research Institute is funding researchers to make epigenomic maps of various cell types. Other NIH-supported investigators have developed a number of epigenomic maps from several human organs and tissues. These NIH projects are part of an international effort to understand how epigenomics could lead to better prevention, diagnosis and treatment of disease.