Epigenetics
Genetics deals with the information coded by your DNA. Epigenetics deals with whether this information is actually being used, i.e., whether the genes coded by your DNA are being expressed or repressed. Epigenetic modifications can change the way DNA is packaged (tightly or loosely), which changes the way genes are expressed (less or more). Epigenetic modifications occur as your body develops, making your cells specialize into e.g. skin and liver cells by determining their gene expression patterns, but they can be also prompted by your lifestyle and environment.
Created: April 2022
Introduction
When one thinks of DNA, what comes to mind is a very, very long strand of nucleotides. The sequences of those nucleotides code for different genes. For a gene to be expressed, part of the DNA strand coding that gene has to be transcribed into mRNA molecule, which later gets translated into a protein that serves a certain function in your cell, e.g., catalyzes a metabolic reaction. Let's focus on the transcription from DNA to RNA part. For the transcription to happen, RNA polymerase, among other things, needs to bind to the DNA first. If it can't access a certain region of DNA for some reason, transcription will not happen, and a gene within that DNA region will not be expressed. So even though the information (the gene) is there, it is not being used.
RNA polymerase, which is a pretty big molecule, cannot "pass through" to the DNA regions that are packed tightly together, but it could bind to the DNA regions that are loosely packed. Therefore, the genes in the "tightly packed" DNA regions are expressed less, and the genes in the "relaxed" regions tend to be expressed more. The actual structure that packs the DNA is called chromatin. You can think of the DNA molecules as extremely long pieces of tape, which can be wound around cylinders to pack them into a more condensed structure so that they take up less space and are less prone to damage (if you had those extremely long DNA strands just float unpacked in the cell, they would get in the way and would be easy to break). Those cylinders are protein complexes called histones, made up of 8 histone proteins. The structure made of DNA and histones (tape and cylinders) is called chromatin. The packing of chromatin determines how genes are expressed, and is thus one of the points of focus for epigenetics (see Epigenetics of Hox Genes). Tightly packed chromatin associated with gene repression is called heterochromatin, while loosely packed chromatin associated with gene expression is called euchromatin.
Overall, epigenetics shows us one important thing- it's not just about the information being out there, it's whether it is being actually used.
Epigenetic Modifications
Epigenetic modifications can change the way chromatic is packaged (heterochromatin -> euchromatin and the other way round), and can thus modify gene expression. There are actually several other ways those modification can affect gene expression, but to keep things simple, let's focus on chromatin packaging. Note that epigenetic modifications DO NOT change the nucleotide sequence, they just change how accessible DNA is to RNA polymerase and other proteins needed for transcription from DNA to mRNA.
Both DNA and the histones it is wrapped around can be subject to epigenetic modifications. One of the most common epigenetic modifications include DNA methylation, which attaches a methyl group to DNA (Fig.1) and is known to reduce expression of the gene whose sequence (or its promoter's) has been methylated. DNA methylation commonly occurs at CpG sites, where cytosine coming before guanine (p stands for phosphate connecting the two nucleosides) is methylated. DNA methylation pattern can be passed from cell to cell during replication. This is useful, as a new cell in a given organ (e.g. liver) does not have to differentiate from stem (undifferentiated) cell to liver cell following the epigenetic landscape, but instead already has liver cell gene expression profile from the start and can quickly start to serve its function. Because DNA methylation can be conserved during replication, it is considered a long-term epigenetic modification.
Figure 1. DNA methylation and its particularly popular variant- CpG (cytosine-phosphate-guanine) methylation.
No less important in epigenetics are histone modifications, which include short-term changes. Histones can undergo methylation, acetylation, phosphorylation, and ubiquitination. Histone acetylation occurs when an acetyl group is attached to a lysine residue of a histone tail (the -NH2 group- the tip of the protein where most histone modifications take place). Histone acetylation results in relaxing the structure of chromatin, which usually leads to increased gene expression of the genes within this loosely packed region. Conversely, deacetylation of histones is associated with tightly-packed heterochromatin formation and gene repression. Histone deacetylation often accompanies DNA methylation.
Histones can be methylated on lysine or arginine residue, though lysine methylation is more common. Depending on the location of this methylation, it can result in either gene expression or repression. Attachment of three methyl group to the 9th or 27th lysine within the H3 protein (one of the proteins making up histones) often results in heterochromatin formation and thus gene repression. These modifications are called H3K9me3 and H3K27me3 for short, where K stands for lysine. On the other hand, three methyl groups attached to 4th or 36th lysine of H3 protein (H3K4me3 and H3K36me3) are associated with gene promotion.
Epigenetics and Lifestyle
It has been shown that epigenetic modifications, such as DNA methylation and histone modifications (acetylation etc.), can be induced by our lifestyles. The potential factors identified so far include diet, amount of exercise, obesity, smoking, alcohol consumption, stress, and environmental pollution. Some epigenetic modifications can be associated with a number of diseases, such as cancer, respiratory, cardiovascular, and neurodegenerative diseases, so avoiding the harmful epigenetic modifications through modifying our lifestyles could be one way to avoid those diseases. Note that both bad and good lifestyle choices can induce epigenetic modifications, the difference is in whether those epigenetic modifications have disadvantageous or advantageous effect on our health. Moreover, epigenetic modifications that result in a change of gene expression can be either disadvantageous or advantageous depending on the type of the gene whose expression was changed. This is why, in the examples below, you will see that the same type epigenetic modification can have either good or bad effect on one's health. It's all about where a given modification takes place- epigenetic repression of a gene responsible for DNA repair can lead to cancer, but repression of a gene that promotes uncontrolled cell division can protect us from cancer.
Several studies have focused on the impact on different foods and substances they contain on epigenetic modifications. For example, folate (folic acid) deficiency has been shown to cause reduced methylation (hypomethylation, leads to increased gene expression) of lymphocyte DNA in healthy postmenopausal women. This modification has been reversed by restoring optimum levels of folate. Since folate deficiency has been associated with colorectal cancer and cancer can often be linked to epigenetic changes, scientists are currently investigating whether supplying folate could have anticancirogenic properties in the context of epigenetic modifications. Polyphenols, found in soy beans, cruciferous vegetables, and green tea, were found to change the activity of enzymes responsible for DNA methylation as well as histone acetylation and deacetylation. Inhibition of enzymes causing DNA methylation (DNA methyltransferases) was observed both in vitro and in vivo using several dietary sources of polyphenols. EGCG, a polyphenol found in green tea that can inhibit DNA methylation enzyme and thus demethylate DNA, has been shown to reactivate genes which had been silenced in cell lines of esophageal, prostate, colon and breast cancer cells. Soy polyphenols were also shown to revert aberrant DNA methylation of cancer cells.
It seems that pollution can also have an effect on the epigenetic modifications. One study showed that exposure to toxic levels of arsenic in drinking water was linked to dose-responsive DNA hypermethylation (increased methylation) of the promoter regions of p53 and p16 genes as compared to controls. p53 and p16 are responsible for controlling the cellular division and act as safety breaks against cancer, and the methylation of their promoter regions is linked to reduced expression of those genes, therefore increasing the risk of cancer. Air pollution, specifically particulate matter (PM), also seems to have an effect of the epigenetic status. Foundry workers exposed to PM10 were found to have reduced methylation in the promoter region of iNOS (inducible Nitric Oxide Synthase) gene compared to controls, which can be linked to the increased production of the iNOS protein that is associated with inflammation and oxidative stress and which is expressed in a number of diseases and disorders. In addition, exposure to airborne benzene can also be linked to epigenetic modifications such as, for example, hypermethylation (leading to lower expression) of p15, which is a tumor suppressor gene, or hypomethylation (leading to increased expression) of MAGE-1, a member of MAGE (Melanoma Antigen Gene) family of genes which are aberrantly expressed in a number of cancers, including melanoma, brain, lung, breast, and prostate cancer.
Epigenetics in Regeneration
Regeneration is an ability shared by plants and animals. However, while only some animals have the ability to regenerate the entire body from its fragment, plants have been shown to achieve this in tissue culture (on a growth medium). Regeneration involves extensive dedifferentiation and redifferentiation of the plant cells, starting from the dedifferentiation of the leaf cells to form callus tissue, which then proceeds to redifferentiate and form a clone of the original plant from which the leaf fragment was taken (Fig.2). In plants, dedifferentiation can be promoted, and redifferentiation can be suppressed by DNA methylation.
DNA methylation is one of the most widely studied chemical modifications of DNA and a common epigenetic marker. It commonly occurs at the CpG (cytosine-phosphate-guanine) sites, when a methyl group attaches to a cytosine. DNA methylation status change is a common cause of epimutations- gene activity changes that can be inherited, but are associated with chromatin modification rather than a change of the DNA sequence itself. Unlike animals, plants can often pass on a stable methylation pattern to the next generation, which provides opportunities for extensive epimutation studies (Fig.3).
Figure 2. A whole plant can be regenerated from its fragment in tissue culture.
Figure 3. In plants, the DNA methylation pattern can be preserved between parent and progeny.
Epigenetic Recombinant Inbred Lines (epiRILs)
Plant epimutation can be investigated using epigenetic recombinant inbred lines (epiRILs) generated from the model plant Arabidopsis thaliana. The DNA sequence of epiRILs is mostly the same as that of the wild-type (WT) plant, but their DNA methylation patten varies- they have epigenetically mosaic chromosomes.
EpiRILs are the product of crossing homozygous wild-type Columbia (Col-0) Arabidopsis accession with the met1 Col-0 mutant (Fig.3). In the met1 mutants, the MET1 (cytosine methyltransferase) gene, which is used to maintain one common type of methylation (CpG), is knocked out. Thus, we are crossing an individual with wild-type methylation with an individual exhibiting reduced methylation. One chromosome of the F1 (1st generation) offspring of such crossing will have wild-type methylation pattern, and another chromosome will have no CpG methylation. When we propagate this F1 offspring through self-fertilization, we are going to get F2 individuals with various methylation patterns.
Next, to restore the MET1 function so that the following plant generations can maintain the newly acquired unique methylation patterns, only the F2 individuals homozygous (having 2 copies of a gene) for a functional wild-type MET1 allele are selected for next propagations. MET1 is used for methylation maintenance by copying the methylation pattern from template DNA strand to nascent strand during DNA replication, so while we restored the MET1 function in the subsequent generations, the methylation that was lost during the 1st crossing (WT Col-0 x met1 Col-0) remains mostly lost. We thus obtain numerous 2nd generation (F2) offspring with various methylation patterns. Those are then propagated through self-pollination for several generations in order to make the methylation patterns almost uniformly homozygous for each line. As the result of a unique methylation patterns, epiRILs obtained in this way might exhibit some interesting characteristics, such as fast growth. By looking at the differences between the methylation pattern of such useful epiRILs and wild-type Col-0 individuals, we can identify the DNA regions whose methylation contributes to useful characteristics in plants, which can later be used in agriculture.
Figure 4. Making epiRILs. You get many individuals with various methylation patterns and potentially useful characteristics to study and identify genes whose methylation is responsible for those useful characteristics.
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Graphics
Made by me; Figure 1 contains the diagram by Mariuswalter, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons