- Epigenetics literally means “above” or “on top of” genetics. It refers to external modifications to DNA that turn genes “on” or “off.” These modifications do not change the DNA sequence, but instead, they affect how cells “read” genes
- DNA are woven around protein called histones. dna and histones are covered by tags of alpha and methyl groups . this covering is called epigenome. dna is fixed but epigenome can be modified by various factors
- The epigenome changes in response to signals. Signals come from inside the cell, from neighboring cells, or from the outside world (environment).
- Early in development, most signals come from within cells or from neighboring cells. Mom’s nutrition is also important at this stage. The food she brings into her body forms the building blocks for shaping the growing fetus and its developing epigenome. Other types of signals, such as stress hormones, can also travel from mom to fetus.
- After birth and as life continues, a wider variety of environmental factors start to play a role in shaping the epigenome. Social interactions, physical activity, diet and other inputs generate signals that travel from cell to cell throughout the body. As in early development, signals from within the body continue to be important for many processes, including physical growth and learning. Hormonal signals trigger big changes at puberty.
- Even into old age, cells continue to listen for signals. Environmental signals trigger changes in the epigenome, allowing cells to respond dynamically to the outside world. Internal signals direct activities that are necessary for body maintenance, such as replenishing blood cells and skin, and repairing damaged tissues and organs. During these processes, just like during embryonic development, the cell’s experiences are transferred to the epigenome, where they shut down and activate specific sets of genes
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Epigenetics and Inheritance
We used to think that a new embryo’s epigenome was completely erased and rebuilt from scratch. But this isn’t completely true. Some epigenetic tags remain in place as genetic information passes from generation to generation, a process called epigenetic inheritance.
Epigenetic inheritance is an unconventional finding. It goes against the idea that inheritance happens only through the DNA code that passes from parent to offspring. It means that a parent’s experiences, in the form of epigenetic tags, can be passed down to future generations.
As unconventional as it may be, there is little doubt that epigenetic inheritance is real. In fact, it explains some strange patterns of inheritance geneticists have been puzzling over for decades.
- Overcoming the Reprogramming Barrier
Most complex organisms develop from specialized reproductive cells (eggs and sperm in animals). Two reproductive cells meet, then they grow and divide to form every type of cell in the adult organism. In order for this process to occur, the epigenome must be erased through a process called “reprogramming.”
Reprogramming is important because eggs and sperm develop from specialized cells with stable gene expression profiles. In other words, their genetic information is marked with epigenetic tags. Before the new organism can grow into a healthy embryo, the epigenetic tags must be erased.
At certain times during development (the timing varies among species), specialized cellular machinery scours the genome and erases its epigenetic tags in order to return the cells to a genetic “blank slate.” Yet, for a small minority of genes, epigenetic tags make it through this process and pass unchanged from parent to offspring.
The Challenges of Proving Epigenetic Inheritance
Proving epigenetic inheritance is not always straightforward. To provide a watertight case for epigenetic inheritance, researchers must:
- Rule out the possibility of genetic changes
In organisms with larger genomes, a single mutation can hide like a needle in a haystack. - Show that the epigenetic effect can pass through enough generations to rule out the possibility of direct exposure
In a pregnant mother, three generations are directly exposed to the same environmental conditions at the same time. An epigenetic effect that continues into the 4th generation could be inherited and not due to direct exposure.
Researchers face the added challenge that epigenetic changes are transient by nature. That is, the epigenome changes more rapidly than the relatively fixed DNA code. An epigenetic change that was triggered by environmental conditions may be reversed when environmental conditions change again.
The Epigenome learns from its experiences
Epigenetic tags act as a kind of cellular memory. A cell’s epigenetic profile — a collection of tags that tell genes whether to be on or off — is the sum of the signals it has received during its lifetime.
The Changing Epigenome Informs Gene Expression
As a fertilized egg develops into a baby, dozens of signals received over days, weeks, and months cause incremental changes in gene expression patterns. Epigenetic tags record the cell’s experiences on the DNA, helping to stabilize gene expression. Each signal shuts down some genes and activates others as it nudges a cell toward its final fate. Different experiences cause the epigenetic profiles of each cell type to grow increasingly different over time. In the end, hundreds of cell types form, each with a distinct identity and a specialized function.
Even in differentiated cells, signals fine-tune cell functions through changes in gene expression. A flexible epigenome allows us to adjust to changes in the world around us, and to learn from our experiences.
Early in development, genes are “poised” like runners in the starting blocks, ready to jump to action.
In a differentiated cell, only 10 to 20% of the genes are active. Different sets of active genes make a skin cell different from a brain cell.
Environmental signals such as diet and stress can trigger changes in gene expression. Epigenetic flexibility is also important for forming new memories.
Cells Listen for Signals
The epigenome changes in response to signals. Signals come from inside the cell, from neighboring cells, or from the outside world (environment).
Early in development, most signals come from within cells or from neighboring cells. Mom’s nutrition is also important at this stage. The food she brings into her body forms the building blocks for shaping the growing fetus and its developing epigenome. Other types of signals, such as stress hormones, can also travel from mom to fetus.
After birth and as life continues, a wider variety of environmental factors start to play a role in shaping the epigenome. Social interactions, physical activity, diet and other inputs generate signals that travel from cell to cell throughout the body. As in early development, signals from within the body continue to be important for many processes, including physical growth and learning. Hormonal signals trigger big changes at puberty.
Even into old age, cells continue to listen for signals. Environmental signals trigger changes in the epigenome, allowing cells to respond dynamically to the outside world. Internal signals direct activities that are necessary for body maintenance, such as replenishing blood cells and skin, and repairing damaged tissues and organs. During these processes, just like during embryonic development, the cell’s experiences are transferred to the epigenome, where they shut down and activate specific sets of genes.
There Are Many Types of Signals
To learn more, visit An Example of Cell Communication: The Fight or Flight Response
Proteins Carry Signals to the DNA
Once a signal reaches a cell, proteins carry information inside. Like runners in a relay race, proteins pass information to one another. The specifics of the proteins involved and how they work differ, depending on the signal and the cell type. But the basic idea is universal.
The information is ultimately passed to a gene regulatory protein that attaches to a specific sequence of letters on the DNA.
To learn more about how signals pass from protein to protein, visit The Inside Story of Cell Communication
Gene Regulatory Proteins Have Two Functions
1. SWITCH SPECIFIC GENES ON OR OFF
A gene regulatory protein attaches to a specific sequence of DNA on one or more genes. Once there, it acts like a switch, activating genes or shutting them down.
2. RECRUIT ENZYMES THAT ADD AND REMOVE EPIGENETIC TAGS
Gene regulatory proteins also recruit enzymes that add or remove epigenetic tags. Enzymes add epigenetic tags to the DNA, the histones, or both.
Epigenetic tags give the cell a way to “remember” long-term what its genes should be doing.
Experiences Are Passed to Daughter Cells
As cells grow and divide, cellular machinery faithfully copies epigenetic tags along with the DNA. This is especially important during embryonic development, as past experiences inform future choices. A cell must first “know” that it is an eye cell before it can decide whether to become part of the lens or the cornea. The epigenome allows cells to remember their past experiences long after the signals fade away.
Using the original DNA strands as a template, methyl copying enzymes attach methyl tags to newly replicated DNA copies. One original DNA strand and one copy will be passed to each daughter cell.
Insights From Identical Twins
Because identical twins develop from a single fertilized egg, they have the same genome. So any differences between twins are due to their environments, not genetics. Recent studies have shown that many environmentally induced differences are reflected in the epigenome
The insight we gain from studying twins helps us to better understand how nature and nurture work together. For well over a century, researchers have compared characteristics in twins in an effort to determine the extent to which certain traits are inherited, like eye color, and which traits are learned from the environment, such as language. Typically taking place in the field of Behavioral Genetics, classical twin studies have identified a number of behavioral traits and diseases that are likely to have a genetic component, and others that are more strongly influenced by the environment.
Depending on the study and the particular trait of interest, data is collected and compared from identical or fraternal twins who have been raised together or apart. Finding similarities and differences between these sets of twins is the start to determining the degree to which nature and environment play a role in the trait of interest.
Twin studies uncover genetic and environmental contributions
Twins share the same genes but their environments become more different as they age. This unique aspect of twins makes them an excellent model for understanding how genes and the environment contribute to certain traits, especially complex behaviors and diseases.
For example, when just one twin gets a disease, researchers can look for elements in the twins’ environments that are different. Or when both twins get a disease, researchers can look for genetic elements shared among similar twin pairs. These types of data are especially powerful when collected from large numbers of twins. Such studies can help pinpoint the molecular mechanism of a disease and determine the extent of environmental influence, potentially leading to the prevention and treatment of complex diseases.
To illustrate, for twins with schizophrenia, 50% identical twins share the disease, while only about 10-15% of fraternal twins do. This difference is evidence for a strong genetic component in susceptibility to schizophrenia. However, the fact that both identical twins in a pair don’t develop the disease 100% of the time indicates that other factors are involved
Nutrition and the Epigenome
Unlike behavior or stress, diet is one of the more easily studied, and therefore better understood, environmental factors in epigenetic change.
The nutrients we extract from food enter metabolic pathways where they are manipulated, modified, and molded into molecules the body can use. One such pathway is responsible for making methyl groups – important epigenetic tags that silence genes.
Familiar nutrients like folic acid, B vitamins, and SAM-e (S-Adenosyl methionine, a popular over-the-counter supplement) are key components of this methyl-making pathway. Diets high in these methyl-donating nutrients can rapidly alter gene expression, especially during early development when the epigenome is first being established.
Diet during early development can have long-lasting effects
Your mother’s diet during pregnancy and your diet as an infant can affect your epigenome in ways that stick with you into adulthood. Animal studies have shown that a diet with too little methyl-donating folate or choline before or just after birth causes certain regions of the genome to be under-methylated for life.
For adults too, a methyl-deficient diet leads to a decrease in DNA methylation, but the changes are reversible when methyl is added back to diet.
NutrientFood OriginEpigenetic RoleMethionineSesame seeds, brazil nuts, fish, peppers, spinachSAM synthesisFolic AcidLeafy vegetables, sunflower seeds, baker’s yeast, liverMethionine synthesisVitamin B12Meat, liver, shellfish, milkMethionine synthesisVitamin B6Meats, whole grain products, vegetables, nutsMethionine synthesisSAM-e (SAM)Popular dietary supplement pill; unstable in foodEnzymes transfer methyl groups from SAM directly to the DNACholineEgg yolks, liver, soy, cooked beef, chicken, veal and turkeyMethyl donor to SAMBetaineWheat, spinach, shellfish, and sugar beetsBreak down the toxic byproducts of SAM synthesisResveratrolRed wineRemoves acetyl groups from histones, improving health (shown in lab mice)GenisteinSoy, soy productsIncreased methylation, cancer prevention, unknown mechanismSulforaphaneBroccoliIncreased histone acetylation turning on anti-cancer genesButyrateA compound produced in the intestine when dietary fiber is fermentedIncreased histone acetylation turning on ‘protective’ genes, increased lifespan (shown in the lab in flies)Diallyl sulphide (DADS)GarlicIncreased histone acetylation turning on anti-cancer genes - Rule out the possibility of genetic changes