General Ideas and Radical Concepts in Epigenetics and DNA Methylation

General Ideas and Radical Concepts in Epigenetics and DNA Methylation

General ideas and radical concepts in epigenetics and DNA methylation
Research Project, K. Randazzo /
Jonathan Gutierrez
In order to understand the ideas behind epigentics, it is important to understand general concepts behind basic genetics, and the inherited information received from a male and female organism during reproduction.
The standard explanation of genetics explains that DNA provides the instruction to make RNA, and that RNA creates proteins that control all cellular activity through protein synthesis and regulation.
In the past, the general belief in biology, was that you received a very specific genetic code
(DNA) from each parent, your mother passing an X-chromosome along with her genetic information. The father passing a Y-chromosome or an X-chromosome, which determines the gender of the offspring as well as passing his own unique and specific genetic traits.
After sexual reproduction and conception, the newly formed organism is created through the union of two haploid cells and combination of gametes from each contributing parent. From the point of its conception, the zygote begins to grow, develops, and divides. Eventually developing into a new generation of a particular species. Possessing similar traits of its elder generation, and many generations past.

Directly after the creation of a zygocyte, the cell begins to divide and develop

independently of its parents. Containing a genetic “blue print” and all the relative information to develop into a normal healthy human being in the refection “mom and dad” and

Once the child began to develop, it is predetermined to look a specific way, have very unique traits, hair color eye color, etc.

On the bad side, be predisposed to developing a wide range of genetic diseases and disorders, also contained in the DNA code.

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Recent advancements and research in bio-technologies, are starting to suggest that the information that you received from your parents is only half the story. The relatively new scientific field of epigentics is suggesting that we have the power to manipulate the very genetic code passed to us by our parents that, once believe, was the ultimate determining factor in our development

In a sense, our inherited destiny of hereditary disease, bad teeth, being obese or having too many freckles.

Many researcher and geneticists around the world have begun research studies in the realm of epigentics for a wide range of reasons. Many using monozygotic twins (identical twins) who’s DNA is genetically identical to the other, to study the changes that occur in their genetic code and gene expression as they age.

Epigenetics is a relatively new field of genetics, that studies chemical alterations on chromosomes, which result in changes in gene expression by condensing the chromosome or affecting the binding of transcription factors. Methylation of CpG islands is one such alteration. Twin studies have opened the doors to understanding how these changes occur: They’re inherited.

Epigenetics affects many areas of biology. In animals, one of the most important changes happens during embryonic development. Genes use epigenetics to guide proper development of stem cells into different cells of the body.[11]

In some cases, different DNA methylation effects from the mother and father compete to determine which parent contributes the trait. For example, when a donkey and horse mate, the resulting mule is different depending on which species was mother or father. This also explains why individuals with the same genome, such as identical twins, exhibit different characteristics, depending on whose epigenetic effects - mom's or dad's- won out in each baby[3]

If DNA really is the predetermined map of our development and eventually create an adult from an embryo from its specific “blue print” as received from each parent. Epigentics answers and creates more questions. As well as challenges the everyday view that we are just the combined image of our parents and DNA does not have the final word.

Gene expression and general epigenetic theory

Epigentics or Epigenome translates into “above the Genome” and can be best described as anything affecting or manipulating the genome and gene expression that is not already encode in DNA itself.

In the past gene expression patterns and translation of genetics information was thought to be contained with in the DNA, a set of instructions telling embryonic cells or stem cell to distinguish itself by developing into a hepatocyte, skin cell or one of thousands of different cells contained in the body. Since 10-20% of genes are “active” in anyone cell, This prevents genes of one cell type from being expressed in another, for example, the gene for eye color is expressed in the eye, and not in the liver or skin cells[3] but recent research is beginning to develop a much more interesting picture

Gene expression. The process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as rRNA genes or tRNA genes, the product is a functional RNA. The process of gene expression is used by all known life - eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea) and viruses - to generate the macromolecular machinery for life. Several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein.[2] Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation, morphogenesis and the versatility and adaptability of any organism. Gene regulation may also serve as a substrate for evolutionary change, since control of the timing, location, and amount of gene expression can have a profound effect on the functions (actions) of the gene]

in a cell or in a multicellular organism.[2][3

Control of gene expression can be handled in different ways. Sometimes, small molecules bind to DNA, changing its ability to give instructions. These molecules originate as proteins, protein complexes or small bits of RNA. For example, in times of drought, the body produces molecules to modify DNA and turn on or off genes that help it endure difficult circumstances.[16]

Giving the organism a very specific trait, blue or brown eyes, brown hair or a muscular build.

The Epigentic phenomenon is best represented in the process of cellular differation in normal development of a human child.

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Long before the child’s birth, during the first few weeks of child development. Stem cell are going through a process of differentiation being distinguished into unique cells, some will become liver cells, other cardiac cells, among countless others.

Genetically, all these cells are the same. Each containing genes that the other has. Skin cells have the necessary gene and genetic information to become lung cell, or cardiac cell, or blood cell. With all the genes being genetically identical and contains all of the human genome, how does a cell know how to change into its desired cell? How does it know what to become?

Since you can not tell the genetic difference from one cell to the next, yet have many highly specialized and complex cells with the body, the process in which each cell become unique and have very different gene expression, has been termed -Epigentics.

Through Epigenetic mechanisms, genes that the cell or tissue does not need are specifically turned off or “Silenced” and while gene expression that is necessary to the functionality and specialization of the cell are protected from silencing, by the same epigenetic mechanisms. The Entire human genome is passed on to daughter cells, along with epigenetic information that keeps the same properties of the parent cell. re: a liver cell divides into another liver cell and not a lymphatic cell. Turns out that there are two different modifications that can affect DNA. One is a Biochemical modification that attaches directly to the DNA, silencing a specific area of genetic information, The other control the physical shape of the DNA strand itself by effecting the protein in which DNA is wrapped, again, effectually expressing or silencing the specific trait or gene. In sense a second genome.... The Epigenome,

Gene Expression through methylation and histone markers in mice

DNA methyltransferase is an enzyme in cells that recognizes CpG islands, strings of cytosines and guanines, and attaches a methyl group to cytosine. This DNA methylation is absent during embryonic development due to the high level of replication and gene expression. The alteration is thought to condense the chromatin around histone, closing off access to the DNA for transcription factors as gene expression wanes and is shut off. In fact, altered methylation patterns are thought to play a role in the development of some cancers, which result from aberrant cellular programming.[22,23][1]

Methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with specifically a methyl group, rather than a larger carbon chain, replacing a hydrogen atom. These terms are commonly used in chemistry, and biological sciences.

In biological systems, methylation is catalyzed by enzymes; such methylation can be involved in modification of heavy metals, regulation of gene expression, regulation of protein function, and RNA metabolism. Methylation of heavy metals can also occur outside of biological systems. Chemical methylation of tissue samples is also one method for reducing certain histological staining artifacts.[22]

These Methyl groups are very common and can be found in foods, house hold chemicals and environmental pollutants. These methyl groups if acquired and introduced to the DNA structure can interfere and affect the way that DNA translates into RNA, and in turn proteins and cellular function. The process is referred to as DNA methylation and in simple terms, turns gene on and off.

Methyl groups attach to a specific point in the DNA Strand and inhibit its ability to translate or express, in a way mask it from sharing its genetic information.[22]

“If the genome were like the hardware of a computer, the epigenome would be the software that tells the computer, how to work and when.” Randall Jirtle PhD., a professor of radiation oncology at Duke University.[24]

Through his work in the field of epigentics and the epigenome, Randall Jirtle of Duke has been able to manipulate the epigenome in genes of the mice that cause obesity and hair color, through feeding the mice food with specific nutrients and toxins. He has been able to change accumulation of adipose

tissue and hair color in mice that are genetically identical. Through controlling the variable in which the mice are introduced to, mainly diet and nutrition, he has been able to manipulate the agouti gene or agouti signaling peptide.

In mice, the agouti gene encodes a paracrine signaling molecule that causes hair follicle melanocytes to synthesize pheomelanin, a yellow pigment, instead of the black or brown pigment, eumelanin. Pleiotropic effects of constitutive expression of the mouse gene include adult-onset obesity, increased tumor susceptibility, and premature infertility. This gene is highly similar to the mouse gene that encodes a secreted protein that may (1) affect the quality of hair pigmentation, (2) act as an inverse agonist of alpha-melanocyte-stimulating hormone, (3) play a role in neuroendocrine aspects of melanocortin action, and (4) have a functional role in regulating lipid metabolism in adipocytes.[25]

By feeding a group of mice (group A) a diet high in methyl groups, he was able to silence the agouti gene, creating mice with average body weight and mass (approx 34 grams) and who had dark brown hair pigmentation. The mice were also less prone to genetic encourage disease such as cancer and diabetes. The genetic traits were passed on to further generations, even of the newer generations that were feed a normal diet. They retained the gene expression and methylation characteristics from parent mice.

In contrast by feeding a group (group B) of mice a diet rich in toxins that disrupted and destroyed the methyl groups given to group (A) mice, he recorded that they were of a much lighter pigment and skin color, although of a normal and average weight in young mice, as they developed into adult-hood, almost 100%of mice suffered from adult-onset obesity. Weighing an average of 70 gram, almost twice the weight of group (A). They had much higher occurrence of diabetes and other diseases related to a dramatically increased BMI, Secondary conditions such as reduced cardiovascular efficiency and increase in cardiac disease. As well as arthritis, decreased life expectancy and other diseases associated with high levels of adipose tissue.

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In a interview with NOVA, and PBS broadcasting company, Dr. Jirtle, stated,

“this research shows that this potentially has severe repercussions on our health, and essentially, the old phrase “you are what you eat” is true, but you are also what your parents eat and your grandparents and so on ate”. He goes on to encourage, healthy life style changes for future generations, not only through learned and influenced habits in our children, but what is genetically passed on.

Phenotype expression through Histone Modification

The second way on which Gene expression occurs is through DNA physical relationship with the histone. In biology, histones are strong alkaline proteins found in eukaryotic cell nuclei, which package and order the DNA into structural units called nucleosomes.[1] [2] They are the chief protein components of chromatin, act as spools around which DNA winds, and play a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long.

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For example, each human cell has about 1.8 meters of DNA, but wound on the histones it has about 90 millimeters of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes.[3]Histones act as spools around which DNA winds. This enables the compaction necessary to fit the large genomes of eukaryotes inside cell nuclei: the compacted molecule is 40,000 times shorter than an unpacked molecule. Histones undergo posttranslational modifications which alter their interactin with DNA and nuclear proteins.

The H3 and H4 histones have long tails protruding from the nucleosome which can be covalently modified at several places. Modifications of the tail include, methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination and ADP-ribosylation. The core of the histones H2A and H3 can also be modified. Combinations of modifications are thought to constitute a code, the so-called "histone code."[9][10] Histone modifications act in diverse biological processes such as gene regulation, DNA repair and chromosome condensation (mitosis).

Through the introduction of methyl group and other proteins, Scientists have been able to change the structure of the DNA by changing or “loosening” the histone. Differing from the Methyl groups and DNA methylation, which attach directly to the DNA strand and inhibit the DNAs’ ability to produce RNA and functional proteins? Histone formation is controlled by several proteins that when introduced to the histone, change the general structure of the histone, relaxing or Contracting it. Allowing DNA to unwind and be “loose “against the histone.

When DNA is in this state, the gene are easily expressed and are turned “on” where as the lack of these proteins cause the histone to contract and tighten up, Hiding a gene from being expressed. In retrospect, Turning the gene “off” by manipulating the protein that cause this effect and change the tension and mechanical properties of the histone structure we can control gene expression. Ultimately choosing which genes we turn “on” and allow to be expressed. Genes such as obesity, longevity, or hair color. Turning gene off that cause the over production in cholesterol and other substances which cause harm in excess or scarcity.

Epigenetic manipulation through environmental variables

A certain laboratory strain of the fruit fly Drosophila melanogaster has white eyes. If the surrounding temperature of the embryos, which are normally nurtured at 25 degrees Celsius, is briefly raised to 37 degrees Celsius, the flies later hatch with red eyes. If these flies are again crossed, the following generations are partly red-eyed – without further temperature treatment – even though only white-eyed flies are expected according to the rules of genetics.

Environment affects inheritance

Researchers in a group led by Renato Paro, professor for Biosystems at the Department of Biosystems Science and Engineering (D-BSSE), crossed the flies for six generations. In this experiment, they were able to prove that the temperature treatment changes the eye color of this specific strain of fly, and that the treated individual flies pass on the change to their offspring over several generations. However, the DNA sequence for the gene responsible for eye color was proven to remain the same for white-eyed parents and red-eyed offspring.

The concept of epigenetics offers an explanation for this result. Epigenetics examines the inheritance of characteristics that are not set out in the DNA sequence

This change in phenotype and gene expression is a direct result on the environmental stresses placed in the fruit flies Histone configuration, believing that the introduction of temperature variations inhibited the proteins involved with histone expression and tension.