A Look At Genes Genomes And Genetics Biology Essay
One of the characteristics of living organisms is that they are made up of one or more cells. A cell consists of three main parts:
the cytoplasm, where chemical processes which maintain the cell alive and functioning are carried out;
the cell membrane which forms a barrier that controls what moves in and out of cells; and
the nucleus which contains the genetic material in the form of deoxyribonucleic acid (DNA). This genetic material contains the instructions which the cell uses to construct a group of biological molecules knows as proteins. Proteins have a very important role in the maintenance of both the cell structure and in regulating its function.
A single DNA molecule is built up from millions of smaller molecular units called nucleotides. A nucleotide consists of a sugar molecule to which are attached a phosphate group and a nitrogen-containing base as shown in figure 1. In a DNA molecule one finds four different types of nucleotides. These differ in the type of base they have attached to the sugar. The base could be any one of adenine (A), guanine (G), cytosine (C) or thymine (T).
The sequence in which different nucleotides occur in a DNA molecule is important because this sequence can be translated into a set of instructions that will determine the nature of proteins. If this sequence is altered, the structure and function of proteins will also be altered.
Changes in the sequence or amount of bases in DNA are called mutations. Mutations occur randomly and spontaneously and are usually rare, but rates can be significantly increased by factors called mutagens. Mutagens include high energy radiation such as UV rays, X-rays and Î³-rays as well as some chemicals such as formaldehyde, tobacco smoke, food preservatives, caffeine and pesticides.
Until recently mutations were believed to be the main source of genetic variation. When mutations occur in somatic (non-reproductive) cells, these will only affect that particular organism and will be lost when the organism dies. If mutations occur in gametes (sex cells), these will be passed on to offspring produced by the organism.
In human somatic nucleated cells one finds forty six DNA molecules.  To fit into the nucleus, these DNA molecules are wound around several groups of histone proteins - just like a piece of thread is wound onto a reel - to form structures known as chromosomes (refer to figure 2). Human somatic cells therefore contain forty six chromosomes. Half of these are acquired from one's mother and half from one's father when a sperm and an ovum fuse during fertilisation giving rise to a single-celled organism described as a zygote.
Fig. 2 Organisation of DNA in a chromosome
source: Karen Buttigieg - Robert Tanti, Biological Concepts for Intermediate Level,
Malta 2008, 63.
Scientists have identified regions on each chromosome which contain the information for the cell to synthesize different proteins. Each one of these units of information is described as a gene and the complete set of genes in a cell is described as the genome. Genes are passed on from parents to offspring and hence can be described as units of heredity. The field of biology which studies genes and the pattern of inheritance of the information contained within them is genetics.
Initially geneticists thought that each gene contains the instructions for the construction of a single protein and when the human genome project was launched they expected to find c. 130,000 genes. However, the project revealed that there are between 20,000 and 25,000 genes.  The most likely explanation for this observation is that the instructions contained in a single gene can actually be used to produce several different proteins.
To construct any individual protein molecule we acquire a set of instructions from our mother and a set from our father. These instructions are similar but not necessarily identical. Thus organisms may acquire alternative forms of the same gene from their parents. These alternative forms of the same gene are described as alleles and constitute what is referred to as the genotype of the organism. The presence of two copies of a gene in the same cell, gives the advantage that if one of the copies is damaged, the remaining copy can still produce the protein it codes for (it serves as a sort of 'insurance policy').
For the major part of the life of a cell, when the cell would be carrying out its function, chromosomes resemble thin threads spread throughout the nucleus. In this form, chromosomes are collectively called chromatin. This chromatin can exist in a loose or compact form depending on how tightly the DNA molecule is wound around the histone proteins. Just as a thread has to be unwound from its reel to be of any use, DNA has to be loosened from its histone proteins for the genes to be expressed (turned 'on') i.e. for the instructions they contain to be used for the synthesis of proteins. Therefore, in its compact form chromatin cannot be used for protein synthesis and the gene is said to be 'silenced' (turned 'off'). The addition to the histone proteins of small molecules known as methyl and acetyl groups (the processes being described as acetylation and methylation respectively) plays a very important role in silencing genes. 
During cell division, the genetic information contained in the nucleus of a mother cell must be moved into two daughter cells. For this to occur the DNA molecule making up each chromosome must be replicated and each copy passed on to each of the daughter cells.
When DNA replication is complete chromatin coils up into the much more compact chromosomes, which can be seen clearly as separate structures with a light microscope as shown in figure 2. This compact organisation of the DNA is important so that during cell division, when DNA is passed to the two daughter cells, strands of genetic material do not get entangled.
1.2 From genome to epigenome: what is epigenetics?
The Greek prefix epi- means 'on top of' or 'in addition to'. So, epigenetics refers to the study of the molecular marks which exist in addition to genes, the traditional units of inheritance.  Stephen Beck of Sanger Centre in Cambridge coined the term epigenome to refer to the collection of these epigenetic marks across the whole genome, which control when and which genes are expressed. 
Although epigenetics as a field has been around for just a few decades, and most of the progress in understanding the epigenome has occurred in the past ten years or so, the term epigenetics was first used by Conrad Waddington in the 1940s in an attempt to link genetics and developmental biology which were up to that time considered as two separate fields. 
As proposed by Waddington, epigenetics was meant to be the study of those mechanisms through which the environment interacts with the genes of an organism and gives rise to the physical features of the organism, described as its phenotype. 
Waddington's definition implies that epigenetics provides an important link between nature (heritable genes) and nurture (environment). Epigenetics has revealed that".  As Strohman argues, genes are necessary but not sufficient to determine cell function.  Nature and nurture work hand in hand to mold the phenotype of an organism in order to increase its chance of survival.
In 1987, Robin Holliday published a paper in which he re-considered Waddington's use of the term epigenetics, and applied it to those situations where changes in DNA methylation resulted in changes in the expression of genes.  According to Haig this
In the last fifteen years, use of the term 'epigenetics' has spread. Its definition has also continued to evolve over the years to reflect knew scientific knowledge. The most popular definition of epigenetics in use today is: the study of heritable changes in gene expression (in the progeny of cells or of individuals) induced by environmental factors, which occur without any alterations in the nucleotide sequence of DNA.  In other words, epigenetics holds that what we do and what we experience in our lives can modify the behavior of genes, which in turn modifies the phenotype of an organism without changes in the genotype. These changes can be passed on to future generations even if the initial conditions that caused the change disappear.
Holliday used the term 'epigenotype' to refer to the actual pattern of gene activity in a specialized cell type. 
Various metaphors have been proposed to explain the relationship between genetics and epigenetics. According to Dolinoy et al. if one thinks of the genome as a computer hard disk, the programmes (software) which enable access to the information stored in the hard disk, would be the epigenome.  Eva Jablonka and Marion Lamb compare the genome to a complex musical score which needs an orchestra of cells (the musicians) and epigenotypes (the instruments) to express it.  Just as an orchestra conductor controls a philharmonic concert, epigenetic mechanisms govern the expression of DNA within each cell of an organism. Understanding these mechanisms could drastically change evolutionary and developmental biology. 
1.3 How does it work?
A human zygote is derived from the fusion of two gametes during fertilisation. The zygote then divides to give rise to a mass of totipotent cells which will differentiate into the three germ layers of the embryo: the ectoderm, mesoderm and endoderm, together with the extra-embryonic tissues. The three germ layers continue to differentiate to give rise to the c. 200 different cell types which make up the body. These cells have different forms and functions and yet they all have exactly the same genetic instructions. Moreover, differentiated cells maintain (i.e. 'remember') their form and function as they give rise to a whole lineage of daughter cells through repeated cell divisions. In other words, when for instance skin cells divide, they will give rise to other skin cells and not any other type of cell. How is this possible?
This is made possible by those mechanisms that ensure that a particular set of genes will be active in a particular cell type while another set will be active in a different cell type.
Holliday distinguishes between household and luxury genes which code for the production of household and luxury proteins (including enzymes).  The former are active in all somatic cells and are responsible for normal cellular processes. The latter have more specialised functions and are developmentally regulated or expressed only in response to certain environmental factors. In other words, different types of cells 'switch on' different sets of luxury genes which give the cells their unique forms and functions. This particular set would be kept permanently 'switched off' in a different cell type. The epigenotype would include Thus brain cells and skin cells have the same genotype but a different epigenotype because they activate and repress different sets of luxury genes.
So, while the genome is the same for all the cells in an organism, the epigenome shows tissue-specific variation, thus distinguishing cells from each other.
Epigenetics provides an insight into how genome function is regulated: how genes are switched 'on' and 'off' as well as where and when all this happens to maintain an organism alive. According to Reik, by altering the timing and quantity of certain gene products in specific cells, epigenetics can result in dramatic changes in the phenotype of an organism. 
Several decades after Waddington coined the term epigenetics, specific mechanisms which superimpose information, in the form of chemical marks or 'tags', on the base sequence of DNA and hence control gene expression, have been identified. The nature and importance of some of these mechanisms is well understood, but some other mechanisms remain speculative. What these mechanisms have in common though is that they seem to
One type of mechanism involves the attachment of chemical 'tags' directly to DNA while in another mechanism chemical 'tags' are attached to histone proteins around which the DNA is coiled. Epigenomics is the study of the distribution and modification of these chemical 'tags' on a genome-wide scale.  A third type of mechanism involves interactions of the DNA with regulatory RNA molecules.
Finally, it is important to note that these epigenetic mechanisms operate in every cell and are essential for the correct natural development and normal functioning of the organism. However, the disruption of these mechanisms could detrimentally affect one's health.  Epigenetics seeks to understand not only how these mechanisms regulate gene activity during cellular growth and differentiation but also in the development of disease and ageing.
1.4 Epigenetic mechanisms
In this section I will give a brief review of the three main types of epigenetic mechanisms and consequence of their disruptions.
1.4.1 Chemical modification of cytosine bases
One mechanism of switching genes 'on' and 'off' is through chemical modification of DNA by methylation. This was the first epigenetic 'tag' to be discovered and is according to Razin and Weinhold the most studied and probably the best understood epigenetic mechanism, even because with the existing technology it is the easiest to study. 
DNA methylation involves the attachment of methyl groups (each containing one carbon and three hydrogen atoms) to CpG dinucleotides.  In regions known as promoter regions, which mark the beginning of genes, one usually finds CpG dinucleotides repeated several times and forming sequences known as CpG islands.  An increase in the number of methyl groups on these CpG islands (hypermethylation) results in the silencing (turning 'off') of the gene. 
Distinct CpGs are methylated in different types of cells, thus generating methylation patterns that are cell type-specific. Thus, as Razin explains, this DNA methylation pattern confers to each cell type an epigenomic identity. 
Interest in the function of DNA methylation has increased considerably in the past years due to its role in the development of common adult-onset diseases, such as cancers, high blood pressure, type II diabetes and obesity, as well as other chronic conditions, such as asthma, and coronary heart disease.  Even though these pathologies do not manifest themselves until later in life, there is evidence that they may be epigenetically determined in early stages of embryonic development. 
Aberrant DNA methylation patterns have also been associated with ICF syndrome, Rett syndrome and Fragile X syndrome.  Genomic hypomethylation (loss of methyl groups from a DNA molecule) is also characteristic of autoimmune diseases such as systemic lupus erythematosus or rheumatoid arthritis. 
Even though, as highlighted in the previous sections, DNA methylation (or lack of it) could have deleterious effects, it also plays an important role in cell differentiation and embryonic development.  Correct DNA methylation is for instance critical for X-chromosome inactivation,  imprinting,  and silencing of transposons.  X-chromosome inactivation and imprinting are the most extensively studied epigenetic phenomena in mammals.
126.96.36.199 X-chromosome inactivation
In mammals there is a particular pair of chromosomes which among other things determine the sex of an organism. These are described as the sex chromosomes and are labeled X and Y. A female has two X chromosomes while a male has an X and a Y chromosome. A Y chromosome is shorter than an X chromosome and lacks some of the genes found on the latter.
X-chromosome inactivation is a process by which one of the two X chromosomes present in the cells of female mammals is randomly inactivated so that the female, would not have twice as many X chromosome gene products as the male which has a single copy of the X chromosome. 
188.8.131.52 Parental imprinting
The presence of two copies of a gene in the same cell, gives the advantage, that if one of the copies is damaged, the remaining gene can still produce the protein it codes for. However, for most genes one functioning gene is sufficient and the other is not expressed. If two alleles differ, the one that is expressed will give rise to a particular phenotype while the other has no effect on the appearance of the organism. The expressed gene is described as the dominant gene while the other is a recessive gene.
The activity of some alleles (i.e. whether an allele is turned 'on' or 'off') depends however on the parent of origin rather than on dominance or recessiveness. These genes are described as being imprinted. Studies have demonstrated that epigenetic 'tags', in particular DNA hypermethylation, are responsible for genomic imprinting.  These 'tags' enable the cell not only to distinguish the allele that was inherited from the mother from that inherited from the father but also to decide which copy to use to make proteins.
While there is evidence that imprinting is necessary for the normal development of an embryo,  imprinted genes have no 'insurance policy' and are therefore subject to the harmful effects of mutations and environmentally induced epigenetic changes.  In other words, it would become a problem if the gene copy which is usually expressed had to be damaged.
Imprinting may influence whether specific genes which predispose individuals to illness are activated or silenced. Jirtle and Weidman suggest that imprinted genes could be responsible for increased susceptibility to asthma, cancer, diabetes and obesity. 
Prader-Willi syndrome and Angelman syndrome are two completely different conditions which arise due to deletion of the same part of chromosome 15.  Ubeda reports that the parent from whom the mutation is inherited determines which one of the two diseases a child will develop. When the deletion is inherited from the father, the child has Prader-Willi syndrome, but when the deletion is inherited from the mother, it results in Angelman syndrome.  Beckwith-Wiedemann syndrome  is also often caused by abnormalities in imprinting of genes located on chromosome 11, which are involved in growth regulation. 
These observations were the first human evidence that there was something else apart from genes that could determine the traits exhibited by an individual.
Parent-of-origin effects have also been reported to show up in other neurobehavioral conditions, such as autism,  Alzheimer's disease,  bipolar disorder and schizophrenia.  Jirtle and Weidman hypothesised that such disorders stem from imprinting errors during early brain development. 
184.108.40.206 Silencing of transposons
Transposons or transposable elements are short sequences of DNA that can move from one position to another in the genome of a cell. When they insert themselves next to or within a gene on a chromosome, they can alter the gene's normal functioning.  Methylation can switch transposons 'off' thus preventing them from having harmful effects. 
1.4.2 Histone modifications
Various ways in which histone proteins can be chemically modified have been described.  Jenuwein and Allis describe the specific pattern of histone modifications as a 'histone code'. This code determines which parts of the genome will be expressed at a particular point in time in a give cell type. 
Phosphorylation  and deacetylation  of histone proteins have been shown to inhibit gene activation by altering the way in which DNA is wrapped around the histones, while acetylation promotes gene expression.  Szyf and Meaney have reported that some specific methylation events are associated with gene silencing and some with gene activation.  Moreover, what is interesting is that these modifications are maintained during DNA replication and cell division.
1.4.3 Regulatory RNA molecules
Apart from DNA, genetic material also occurs in cells in the form of a molecule known as ribonucleic acid (RNA). Various forms of RNA occur in cells.
Only a small percentage of our DNA contains the instructions for the synthesis of proteins while the rest was mainly considered as 'junk'. Now researchers are discovering that some of this DNA which was hitherto considered useless is in fact responsible for the production of so called 'non-coding RNA' molecules which play an important role in epigenetic processes. 
Powledge reported that "at least half a dozen types of non-coding RNAs have been discovered" among which long non-coding RNAs and microRNAs have been the most studied. 
One particular type of long non-coding RNA is involved in the process of X-chromosome inactivation in mammals (discussed in section 220.127.116.11),  while microRNAs have been shown to bind to specific sites on certain genes and switch them 'off'.  This is described as 'RNA interference' and has been correlated with several pathological processes including the development of various cancers  and behavioural diseases. 
Dykxhoorn and Lieberman point out that the increasing evidence that certain microRNAs can silence the action of particular genes and the fact that these RNA molecules are quite cheap to synthesise artificially, are expected to stimulate research in this area with the aim of developing new cancer therapies. 
To sum up briefly, one can define epigenetics as the study of the "interplay of DNA methylation, histone modifications and expression of non-coding RNAs, in the regulation of gene expression patterns".  However, other epigenetic mechanisms apart from the three discussed here are likely to be discovered in the near future as epigenetic research proceeds at a very rapid pace.
1.5 The reemergence of Lamarckism
Jean-Baptiste Lamarck proposed that environmental pressures bring about permanent changes in an organism's genetic traits and body form during an individual's life. These changes are then passed on to offspring. In a classical example, Lamarck suggested that giraffes had a short-necked ancestor which pressed by the shortage of food kept stretching its neck to be able to reach tree leaves higher up beyond the reach of other animals. All this stretching caused the neck to be lengthened permanently. The longer neck was inherited by offspring, which stretched their necks further thus giving rise to the modern giraffe.
Tow claims that until recently the mechanisms enabling this type of rapid response were neither understood nor accepted by many biologists.  The concept of inheritance of acquired characteristics was in fact rejected after the acceptance of Darwin's theory of evolution. But now, epigenetic research is showing that Lamarckism is real and enough evidence has been compiled to convince and attract large numbers of researchers towards this budding field.
Over the past two decades scientists have discovered several characteristics that are acquired during different stages in the life of an individual and that are then also inherited by offspring. These traits are transmitted from generation to generation in the form of epigenetic modifications to the DNA or histones.
By switching genes 'on' or 'off' epigenetic mechanisms provide a rapid way for the genome to respond and for organisms to adapt to a changing environment without having to change the base sequence of DNA which would otherwise limit flexibility of future generations that may encounter very different conditions.  Stöger thinks of the epigenome as a sort of interface between nurture and nature - between the highly dynamic environment around us and the highly static genome.  Quoting Randy Jirtle, Leslie Pray affirms that epigenetics provides a "rapid mechanism by which [an organism] can respond to the environment without having to change its hardware". 
Tow insists that the Darwinian and Lamarckian approaches to evolution are complementary as are genetics and epigenetics.  Our increased understanding of epigenetic change and the recent evidence indicating the role of epigenetics in development doesn't make this new field more important than genetics. For example there is consensus that genetic and environmental factors play an important role in disease development, but now we also need to consider epigenetic factors. 
1.6 Unique aspects of the epigenome
While the DNA sequences in the genome are static, the epigenome is dynamic and changes with cell type, during the life of a cell, in response to biological signaling systems, and with environmental changes including lifestyles (eating, drinking, smoking, substance abuse, exercise, work-related stress). 
Rothstein et al.  compared genetic and epigenetic changes and highlighted the following unique aspects of epigenetic changes:
The percentage of offspring which inherit epigenetic changes is higher than the percentage of offspring inheriting mutations. 
Epigenetic changes allow more rapid evolutionary change than genetic mutations thus permitting a particular species to adapt quickly to changes in the environment. 
Epigenetic changes depend on the dose of epigenetic-altering factors and also on the timing of exposure. During embryonic development (prenatal) and early newborn life (neonatal), organisms are more sensitive to epigenetic influences and these are therefore more likely to have harmful effects.  This is because "the DNA synthetic rate is high [during embryonic development], and the elaborate DNA methylation patterning and chromatin structure required for normal tissue development is established during early development".  Another critical period during which the epigenome is susceptible to changes induced by environmental factors is during gamete production (gametogenesis). 
Like genetic changes, epigenetic alterations are stable and heritable. When epigenetic mechanisms were discovered, it was believed that epigenetic changes are reset during gamete formation,  however it has been shown that some epigenetic marks fail to be erased during gametogenesis. 
In this way not only can cells retain their epigenetic marks throughout the life of an organism (the pattern is stable) but the epigenetic profile on some genes can also persist across generations (the pattern is heritable) despite lack of exposure to factors which induce epigenetic changes in subsequent generations.  Thus, as Rauscher suggests, this calls for a re-definition of the unit of heredity: "the unit of heritability is not simply the hardwired DNA sequence of a gene, but the gene plus its modifications". 
While the low success rate of gene therapies confirms that genetic mutations are very difficult to reverse, another unique aspect of epigenetic changes is that they can sometimes be easily reversed through drug treatment that adds or removes the chemical 'tags' involved.  This makes epigenetic research very attractive and might have important implications for the development of therapies for many adult-onset diseases including cancers, as well as for ageing.
Like genetic changes, epigenetic alterations are passed on to the daughter cells when a cell divides but epigenetic changes tend to be tissue-specific. While genetic changes are inherited by entire cell lineages i.e. if a mutation occurs in a somatic cell, then all its daughter cells will carry the altered genotype, and if a mutation occurs in a gamete all the cells of the organism will be affected; on the other hand epigenetic changes occur in specific groups of cells which respond to the same environmental signals (including for instance, hormones, nutrients and stress).  Szyf maintains that this could influence the effects of drugs in different tissues. 
Epigenetic changes are also species-specific, so, for epigenetic research, animal studies may be less reliable if used to predict risk for humans than they are for genetically inherited traits. 
1.7 Why am I writing this thesis?
Epigenetics has become one of the most exciting fields of post-genomic biology. Scientists are becoming more aware of the importance of this field and several major research projects in the last decade have focused on this field with the result that new discoveries and developments are being made at an accelerating rate.
As I will illustrate in the forthcoming chapters, epigenetics not only reveals how environmental, dietary, behavioural and medical experiences which are the result of our lifestyles can modify gene expression and how these modifications can be inherited transgenerationally, but it also offers scientists the potential to reprogramme genomes without genetic modification.
Epigenetic research could thus find important application in the development of cures for many serious diseases as well as in cloning and stem cell technologies, both of which have been the subject of considerable controversy. With the emergence of any new scientific knowledge or technology, society has to be aware of the potential for its misuse. For this reason, scientists, legislators and policy makers need to consider the extent to which traditional bioethical principles apply to epigenetics.
Although a large amount of literature on the ethics of genetic research has been published in the past twenty years, the literature available on the ethics of epigenetic research is very limited. My thesis will thus try to increase awareness on the ethical implications that this emerging science creates.
A piece of DNA which contains the information for the synthesis of a protein.
Alternative forms of the same gene inherited from each of the parents.
The study of genes and the pattern of inheritance of the information contained within them.
The complete set of genes in a cell.
The specific allele makeup of an organism usually with reference to a specific character under consideration.
The physical characteristics of an organism which result from expression of particular alleles.
The study of heritable changes in gene expression induced by environmental factors, which occur without any alterations in the nucleotide sequence of DNA.
The collection of epigenetic marks across the whole genome, which control when and which genes are expressed.
The study of the distribution and modification of epigenetic marks on a genome-wide scale.
The actual pattern of gene activity in a specialised cell type.
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