Understanding Epigenetics & Early Equine Fetal Development

Understanding Epigenetics & Early Equine Fetal Development

Photo: Anne M. Eberhardt/The Horse

When I was first assigned this article, my immediate thought was, "Do I even understand epigenetics?" Not really! Pulling out my trusty dictionary and dusting off my old genetics textbooks yielded this delightful definition: the study of heritable changes in gene expression that occur without altering DNA sequences.

I obviously needed help. Three genetics experts immediately came to mind: George Seidel Jr., PhD, university distinguished professor at Colorado State University's College of Veterinary Medicine & Biomedical Sciences; Carey Satterfield, PhD, an assistant professor in physiology and reproduction at Texas A&M's College of Agriculture and Life Sciences; and Ernest Bailey, PhD, one of the University of Kentucky Gluck Equine Research Center's immunogenetics and genomics researchers. These individuals shared their "best" definitions and examples of epigenetics and its impact on early fetal development. But before delving into these details, we'll briefly review DNA and what genes do.

Decoding the Genetic Code

The term DNA is short for deoxyribonucleic acid. The "deoxyribo-" refers to a specific type of sugar, "nucleic" refers to the fact that most DNA is found in the nucleus of virtually every cell in an organism, and the "acid" refers to phosphoric acid. The deoxyribose sugar and phosphoric acid bond together and form the "backbones" of DNA--you could think of two chains of the bonded sugars as the two upright poles of a twisted ladder (at right). Bonded to each pole of the ladder like rungs are the genetic bases: adenine, cytosine, guanine, and thymine. These bases are usually represented by the letters A, C, G, and T. A base on one pole binds to a base on the other pole, forming the rungs. In essence, the presence and arrangement of these four compounds define our entire genetic code.

When a cell needs to perform a specific function, it reads its own genetic code and produces a protein. For example, when intestinal cells need to produce digestive enzymes to break down food and absorb nutrients, a specific region of the DNA "unzips" down the middle of its ladder rungs. The code of the bases on one side of the DNA ladder (only one side is readable) is then read and transcribed (copied) to make a single strand of RNA--¬ribonucleic acid. RNA is similar to DNA, but the sugar in the backbone is ribose instead of deoxyribose. This RNA then exits the nucleus, enters the cell's cytoplasm (the substance that fills a cell), and is used there as a code to put together the correct string of amino acids that form a protein, such as the digestive enzyme in this example. The base sequence on the RNA strand (which is a mirror image of the DNA from which it was copied) dictates which amino acids are strung together.

This entire process operates like a well-oiled machine and the body regulates it carefully to ensure no mistakes are made. If either the DNA or RNA is read incorrectly, the wrong amino acid is included in the protein, and a nonfunctional protein could be produced. In the case of intestinal cells, for example, if a mistake is made during transcription or translation, the protein will not function as a digestive enzyme, meaning it will not break down the food material in the intestines or absorb nutrients.

Genetic Mutations vs. Epigenetics

The concept of genetic mutations is probably a bit easier for most of us to grasp than epigenetics. With mutations, a change in the base order occurs. One of the most recent genetic mutations reported in horses is one in the gene that encodes an enzyme called glycogen synthase 1. The mutation makes the enzyme overactive, producing too much glycogen--a storage form of sugar in muscles. This then leads to a condition called polysaccharide storage myopathy (PSSM), a potentially life-threatening form of tying-up. This PSSM form is caused by a single change in the order of the thousands of bases making up the DNA coding for this protein.

In the case of epigenetics, changes occur in how often the genetic code is read--there is no change in the genetic code itself. Some genes are signaled to either hide or be turned off while other genes are signaled to produce more of the proteins they represent. One of the most widely described mechanisms responsible for "hiding" genes is called DNA methylation. In a nutshell, DNA methylation is when a methyl group (one carbon atom with three hydrogen atoms attached to it) is added to specific Cs on a strand of DNA. The pattern and arrangement of these "tagged" or "methylated" Cs dictate whether a particular gene is either silenced or expressed in greater than normal amounts.

Beyond "Simple" Epigenetics

The DNA methylation pattern in a particular cell is passed on from generation to generation of cells (i.e., it is a heritable trait in a cell line). "Heritable" can mean either heritable to a cell's daughter cells when that cell divides, or heritable to the next generation of animals after sexual reproduction. While many epigenetic marks are heritable within a cell line, the vast majority of epigenetic marks are removed or reset when eggs and sperm are produced and, thus, are not passed on to the next generation of animals.

The previous example of DNA methylation fits beautifully into the basic definition of epigenetics provided at the start of this article. Seidel, Satterfield, and Bailey each point out, however, that this definition of epigenetics is very narrow.

"I am actually one of those people who likes the narrow definition," Bailey explains. "Epigenetics explains inherited traits which may skip a generation or appear spontaneously, in defiance of Mendelian laws of genetics. This may explain maternal grandsire effects or other, yet-to-be-discovered influences of management in one generation on gene expression in the next. The key is to uncover a reproducible pattern."

In Bailey's opinion, our ability to follow gene expression has led some researchers to describe epigenetics as inclusive of random events involving genes. "During early development and growth of a foal the migration of cells and the random, stochastic timing of gene expression can have a big impact on the resulting phenotype (the way the horse 'looks')," he says. "In this case the phenomenon is a consequence of gene action, but is not necessarily hereditary."

For example, the gene responsible for the tobiano coat pattern is well-known, but the distribution of white spots is a product of cellular events during early development. "This also explains why twin colts can have a gene for white markings on the face, with one exhibiting a few white hairs and the other exhibiting a blaze," adds Bailey.

In contrast, Seidel and Satterfield note that additional research in this field has revealed that epigenetics is far more complex and involves factors that influence early fetal development. "I would define epigenetics as alterations in the pattern of gene expression, such as 'off/on' or 'little/a lot,' that are based on changes in the structural configuration of the DNA rather than its sequence," says Satterfield. "These changes can be permanent and have been shown to be heritable, but not always."

According to Satterfield, more is being learned about this topic every day, and, therefore, the definitions will need to be reevaluated constantly. "It is clear that epigenetic changes are both heritable or not, and this depends on the gene that is epigentically modified," Satterfield shares.

With this information in hand, each expert explains why this topic is important for horse owners:

Dr. Seidel "Identical twins provide a good example of how factors other than environment and mutations interact and influence genes," notes Seidel. "Some traits are strictly genetic. For example, identical twins will be the same sex because they either have two X chromosomes or one X and one Y chromosome. Some traits are part genetic but mostly environment, such as body weight. Other traits are epigenetic. In horses, these traits would include coat color pattern such as the shape of their spots and the length of their stockings."

According to Seidel, these coat color patterns depend on how different pigment-producing cells that invade hair follicles migrate during fetal development. Although there are genetic instructions about the general pattern of pigment cell migration, they are not exact about which individual hair follicles the cells will invade and, thus, produce pigmented hair.

"Epigenetics explains why genetically identical animals have different coat color patterns," Seidel summarizes.

So why should horse owners care about epigenetics? According to Seidel, mistakes are sometimes made in maintaining the correct methylation pattern as cells divide. If the methylation pattern is incorrect, the resulting cell no longer functions correctly. If a lot of cells have this defect in a tissue (muscle cells for example), problems such as weaker muscles can ensue.

Dr. Satterfield "All one has to do is look at the vast diversity within any species to see that epigenetics are important," he says. "Epigenetic changes occur in response to environmental stimuli and are believed to be a way in which the developing young can adapt to its environment to maximize its potential for survival."

New research is showing that the manner in which animals are handled during their early days (or possibly even weeks or months) of life can have a lifelong influence on their behavior and ability to respond to stress. "These changes are due to actual changes in how genes are turned on or off (at the DNA level) and are permanent, not simply a learned response that can be forgotten with time," Satterfield explains. "Although none of these studies have been performed in the horse, evaluating the horse industry and the critical role for human/animal interactions makes it easy to see how knowledge of epigenetics could shape industry practices in the future."

Dr. Bailey "With the ability to sequence complete genomes and to investigate gene expression, we are discovering that we are more than the sum of our genes," says Bailey. "Some genes are very good predictors of what an animal will look like, for example. When we sequence the gene called MC1R (melanocortin 1 receptor), we know whether or not the horse will have black hair or red hair--this is the basis of the genetic tests for black and chestnut coat color in horses. In this case genes are destiny."

In other cases DNA alone does not predict physical outcome. According to ¬Bailey, the best example of this is a phenomenon called "genomic imprinting."

"When DNA is processed into either eggs or sperm, certain genes are methylated," he says. "As a result, some genes are expressed in the offspring only when inherited from the father. Likewise, other genes are only expressed in the offspring when inherited from the mother."

For example, genes that enhance development of the placenta are active from the father and inactive from the mother, whereas genes that control early growth and development of the fetus in utero are expressed more from the mother's genes than from the father's.

Take-Home Message

Still not convinced that all equine enthusiasts should appreciate epigenetics and how genes are impacted during early fetal development? Consider one final comment from Bailey regarding a practical use of epigenetics in the breeding sector: "Millennia of horse breeding observations have led to effective husbandry practices; however, breeders are continually experimenting to find better ways to raise horses. Genomic studies involving imprinting have a great potential to uncover novel means to realize the full potential of each horse."

About the Author

Stacey Oke, DVM, MSc

Stacey Oke, MSc, DVM, is a practicing veterinarian and freelance medical writer and editor. She is interested in both large and small animals, as well as complementary and alternative medicine. Since 2005, she's worked as a research consultant for nutritional supplement companies, assisted physicians and veterinarians in publishing research articles and textbooks, and written for a number of educational magazines and websites.

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