Epigenetics
Related Terms
Acetyl, bisulfite sequencing, cancer, chemical modification, chromatin immunoprecipitation, chromosome, cloning, disease, DNA, DNA methylation, expression, functional/structural genomics, heterochromatin, histone, immunohistochemistry, imprinting, methyl, PCR, polymerase chain reaction, RNA interference, Western blotting.
Background
Epigenetics is a field of biological research that focuses on changes to DNA (deoxyribonucleic acid) or chromosomal proteins that affect the amount produced of a particular gene. The amount of a gene produced by a cell is referred to as the expression level. Whereas the field of genetics commonly focuses on how changes in the DNA sequence affect gene activity, epigenetics focuses on changes to the DNA that do not involve changes in the sequence.
DNA is located in a compartment of the cell called the nucleus and is packaged in structures called chromosomes. In addition to DNA, chromosomes also contain proteins, such as histones, which help package the DNA in an orderly way. DNA also contains four different chemical compounds called bases: cytosine, thymine, guanine, and adenine. In any given individual, these bases are found in a particular order along the chromosomes, and it is the order, or sequence, of these bases that stores information for making genes.
Chromosomes contain hundreds of genes, which provide the instructions for making proteins. Chromosomes also contain many other regulatory sequences that control how much of a gene will be made, when it will be made, and where in the body it will be made.
The level of gene expression can be regulated by cells through chemical modification of DNA or the histone proteins. By adding specific chemical groups to or removing them from the DNA or histone proteins, more or less of a gene can be produced. Several chemical groups, such as acetyl or methyl groups, that affect gene expression levels have been identified. These chemical groups recruit other proteins that are able to regulate the expression of genes. Either the amount of a specific chemical modification or the location on the DNA sequence or chromosome where the modification is made can influence the level of gene expression.
Epigenetic control of gene expression is relevant to many biological processes, such as development or cell growth. Also, defects in epigenetic modifications may lead to certain diseases, such as cancer. When genes are not properly modified epigenetically, they may be produced at abnormally high or low levels. This may cause the cell cycle to become deregulated, which in turn, may lead to cancer. It is important to note that epigenetic changes can be inherited, or passed on from one generation to another, just like changes in DNA sequence. For these reasons, epigenetics is an active field of research with far-ranging implications.
Methods
Most epigenetics research focuses on measuring the amount of a specific chemical modification on DNA or on histone proteins. To measure chemical modifications, there are a variety of techniques that researchers may use.
Antibodies: Antibodies are commonly used in techniques that measure chemical modifications. Antibodies are a type of protein normally made in the body by immune system cells to fight off foreign invaders, such as viruses or bacteria. Because they have the ability to bind to specific proteins, however, antibodies may be used to detect specific chemical epigenetic modifications, for example, a modification on a histone protein.
Western blotting: Western blotting is a method that researchers may use to detect specific proteins from a biological sample. In Western blotting, researchers extract proteins from cells or tissues, separate the proteins on a gel using electrical charges, and then transfer the proteins onto a membrane. Researchers may then look for a certain protein on the membrane using an antibody that is able to detect that specific type of protein. For example, if a researcher is interested in knowing whether a histone protein has become attached to an acetyl group, an antibody that detects acetylated histone can be used to probe the membrane.
Immunohistochemistry: Immunohistochemistry is another method researchers may use to detect a specific protein in a biological sample with an antibody. With immunohistochemistry, researchers may use antibodies to study the level of a specific protein without extracting the proteins from cells. In this process, researchers apply an antibody directly to cells and observe whether the antibody is able to detect the protein of interest. Researchers commonly use a fluorescent detection system when performing immunohistochemistry so that antibody binding can be detected by the emission of colored light. A fluorescent microscope capable of detecting fluorescent light is needed to observe the results.
Chromatin immunoprecipitation: Chromatin immunoprecipitation is a method used to determine whether specific regions of DNA have undergone an epigenetic modification. An epigenetic modification is the addition or removal of a chemical group to DNA. To perform chromatin immunoprecipitation, researchers first extract DNA from cells and then cut it into small pieces using high-energy sound waves. Then an antibody that can detect a specific epigenetic modification is used to isolate all of the pieces of DNA that contain that epigenetic modification. Finally, a technique called polymerase chain reaction (PCR), which can amplify DNA containing a sequence targeted for study, is used to check for a DNA region of interest. PCR is a method that uses enzymes called DNA polymerases to amplify and detect pieces of DNA.
For example, if researchers are interested in whether a specific gene is highly acetylated, meaning that the DNA for the gene of interest contains a high number of acetyl groups, they would first use antibodies that can detect acetylated histones to isolate the DNA for all genes that are acetylated. Then they would perform PCR to check whether the sequence of the gene they are interested in was isolated by the antibody.
Bisulfite sequencing: Bisulfite sequencing is a method by which researchers treat DNA with a chemical called bisulfite to detect methylation of DNA. In some cases epigenetic modifications may occur directly on the DNA and not on histone proteins, which interact with and help organize DNA in a cell. When epigenetic modifications occur directly on the DNA, antibodies are not useful for detecting them, so bisulfite sequencing is commonly used to detect methylation directly on the DNA. Bisulfite causes areas of DNA that have not undergone DNA methylation to mutate, or change in sequence. However, areas of DNA that have undergone DNA methylation are not affected by the bisulfite. Therefore, by comparing the sequences of bisulfite-treated DNA with untreated, researchers may be able to infer which regions are epigenetically modified.
Research
Gene expression: Researchers who study epigenetics attempt to better understand how different chemical modifications on DNA or histone proteins can influence the expression of genes. Some types of chemical modification appear to cause genes to be expressed at higher levels, whereas other types cause genes to be expressed at lower levels.
For example, histone proteins that are methylated at specific positions appear to cause genes to be expressed at lower levels. Researchers have studied why this specific epigenetic modification influences gene expression. They found that a protein called HP1, which reduces the expression of genes in cells, specifically recognizes and binds to histones with this modification.
Researchers have also found that histones acetylated at certain locations cause genes to be expressed at higher levels. Histones normally package and organize the DNA in a cell, and acetylation of histones at specific locations can cause the DNA to be less tightly packed by the histones. This in turn makes it easier for genes to be expressed.
Researchers have identified specific enzymes that are responsible for attaching chemical modifications to DNA or to histones. For example, researchers have found that proteins called histone acetyltransferases are responsible for adding acetyl groups to histones.
Imprinting: Individuals have two copies of most genes, one inherited from the father and one from the mother. Researchers have found that some genes inherited from a mother have different epigenetic modifications than the same genes from a father, a phenomenon called imprinting. Commonly, the DNA of imprinted genes has higher levels of methylation, which causes them to be expressed at lower levels. The DNA is chemically modified to contain methyl groups, and these methyl groups alter the level of gene expression.
Using model organisms, such as mice or flies, researchers have found that the imprinting of genes is important for normal development. For example, researchers have found that if a gene called Igf2 is not properly imprinted in mice, higher levels of Igf2 will be expressed. The increased amount of Igf2 causes problems with development, and the mice develop a condition similar to Beckwith-Wiedemann syndrome, a condition in which developing organs in the fetus become enlarged.
Cloning: Epigenetic research has important consequences for the field of cloning. Cloning is a technique in which researchers remove the DNA from the egg of an organism and replace it with new DNA. The egg with the new DNA can then be used to produce an organism that contains the new DNA in all the cells of its body or to produce embryonic stem cells. Embryonic stem cells are a type of cell that has the potential to develop into any type of tissue or organ, such as blood, skin, or liver.
Attempts at reproductive cloning often fail, and the success rate of generating a healthy, living organism through cloning is very low. The low success rate of cloning is thought to be caused by improper epigenetic modification of some genes in cloned organisms. The abnormal expression of these genes may lead to developmental defects and death.
Disease: When genes are not epigenetically modified properly, they may be produced at abnormally high or low levels, which can cause diseases. Cancer is one disease in which researchers have discovered epigenetic abnormalities. For example, researchers have found that patients with lung cancer have several genes on chromosome 6 that have high levels of methylation, which causes the genes to be produced at lower levels. This abnormal expression is thought to be involved in cancer progression. Furthermore, researchers have found that some chemicals known to cause cancer may cause abnormal levels of epigenetic modifications in cells.
Implications
Fighting diseases: Epigenetics can be used to better understand how some diseases work. This is because defects in epigenetic modifications may cause specific genes to become expressed at higher or lower levels, and this abnormal expression may play a role in causing a disease. By identifying these genes that are not properly regulated, scientists can better understand how a disease is caused, and they may be able to use this information to develop therapies to fight it.
Understanding the effects of chemicals: Some chemicals may cause sickness or disease by changing the sequence of DNA, but other chemicals may cause disease by affecting the level of epigenetic modifications. By identifying the epigenetic changes that result from exposure to chemicals, researchers may be able to better understand how certain chemicals deregulate genes and cause disease.
Limitations
Researchers may learn how genes are regulated and whether they are expressed at high or low levels by performing epigenetics experiments. However, these experiments may not be able to tell researchers whether increased or decreased levels of gene expression have specific consequences, such as causing a disease. Additional follow-up experiments may be needed to determine whether an epigenetic modification that affects gene expression levels has a beneficial effect on health or leads to disease.
Future research
Researchers are interested in extending their knowledge of where different epigenetic modifications are located in the human genome. Currently, researchers have an understanding of which epigenetic modifications occur at specific locations or near specific genes, but they do not yet have a global understanding of epigenetic modifications throughout the whole human genome. The genomic DNA sequence of an organism is the DNA sequence of every chromosome an organism has. Current large-scale efforts are under way in which researchers are studying the entire human genome to better understand which regions have epigenetic modifications and what those modifications do. This future research aims to give researchers a better global understanding of how gene expression is regulated in human cells.
Author information
This information has been edited and peer-reviewed by contributors to the Natural Standard Research Collaboration (www.naturalstandard.com).
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