A .EPIGENETICS
The cells in a multicellular organism have normally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)–genetics. The lack of identified genetic determinants that fully explain the heritability of complex traits, and the inability to pinpoint causative genetic effects in some complex diseases, suggest possible epigenetic explanations for this missing information. The desire to understand the “deprogramming” of differentiated cells into pluripotent/totipotent states, has led to “epigenetic” becoming shorthand for many regulatory systems involving DNA methylation, histone modification, nucleosome location, or non-coding RNA. Epigenetics was coined by Waddington (1942) to refer to the study of the “causal mechanisms” by which “the genes of the genotype bring about phenotypic effects.”
An epigenetic system is heritable, self-perpetuating, and reversible. Whether histone modifications (and many non-coding RNAs) are epigenetic is debated; it is likely that relatively few of these modifications or RNAs will be selfperpetuating and inherited.
Robin Holliday defined epigenetics as “the study of the mechanisms of temporal and spatial control of gene activity during the development of complex organisms” The development and maintenance of an organism is orchestrated by a set of chemical reactions that switch parts of the genome off and on at strategic times and locations. Epigenetics is the study of these reactions and the factors that influence them.
Epigenetics has different meanings for different scientists. Molecular biologists define epigenetics as “the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence” (Riggs et al. 1996). Functional morphologists Herring (1993), for whom epigenetics refers to “the entire series of interactions among cells and cell products which leads to morphogenesis and differentiation” and further it was stated that “epigenetic influences range from hormones and growth factors to ambient temperature and orientation in a gravitational field.”
Epigenetic Mechanisms
Several epigenetic mechanisms regulate genes i.e. DNA methylation and changes to histone proteins, around which DNA is packed, or involve functional non coding RNAs. In general, low levels of DNA methylation (hypomethylation) are associated with higher gene activity and high levels of methylation with gene silencing. Repeat associated CpG islands and non regulatory CpG sites generallyexist in a methylated state.
Epigenetics and 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.
The Challenges of Proving Epigenetic Inheritance
Proving epigenetic inheritance is not always straightforward. To provide a watertight case for epigenetic inheritance following postulates:
- 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.
The Human Epigenome Project
Research into epigenetics has provided new and exciting advances in plant technology, potential cancer treatments and new tools for researchers trying to identify the function of genes. In recognition of the importance of DNA methylation in epigenetics, it is now the subject of the multi-million dollar Human Epigenome Project.
B. DNA METHYLATION
In DNA, methylation occurs in the CpG islands, a CG rich region, upstream of the promoter region. The letter “p” here signifies that the C and G are connected by a phosphodiester bond. In humans, DNA methylation is carried out by a group of enzymes called DNA methyltransferases. These enzymes not only determine the DNA methylation patterns during the early development, but are also responsible for copying these patterns to the strands generated from DNA replication. DNA methylation is a biochemical process that is important for normal development in higher organisms. It involves the addition of a methyl group to the 5′ position of the cytosine pyrimidine ring or the number 6 nitrogen of the adenine purine ring and the modification is inherited through cell division.
DNA methylation stably alters the gene expression pattern in cells such that cells can “remember where they have been” or decrease gene expression; for example, cells programmed to be pancreatic islets during embryonic development remain pancreatic islets throughout the life of the organism without continuing signals telling them that they need to remain islets. DNA methylation is typically removed during zygote formation and re-established through successive cell divisions during development. However, the latest research shows that hydroxylation of methyl group occurs rather than complete removal of methyl groups in zygote. Some methylation modifications that regulate gene expression are inheritable and are referred to as epigenetic regulation. DNA methylation is essential for normal development and is associated with a number of key processes including genomic imprinting, X-chromosome inactivation, suppression of
repetitive elements, and carcinogenesis. Alterations of DNA methylation have been recognised as an important component of cancer development. Hypomethylation, in general, arises earlier and is linked to chromosomal instability, loss of imprinting, whereas hypermethylation is associated with promoters that can arise secondary to gene (oncogene suppressor) silencing, but might be a target for epigenetic therapy.
Epigenetics
Methylation contributing to epigenetic inheritance can occur through either DNA methylation or protein methylation.
DNA methylation in vertebrates typically occurs at CpG sites (cytosine-phosphateguanine sites, that is, where a cytosine is directly followed by a guanine in the DNA sequence) and the methylation results in the conversion of the cytosine to 5-methylcytosine. The formation of Me-CpG is catalyzed by the enzyme DNA methyltransferase. Human DNA has about 80%-90% of CpG sites methylated, but there are certain areas, known as CpG islands, that are GC-rich (made up of about 65% CG residues), wherein none are methylated. These are associated with the promoters of 56% of mammalian genes, including all ubiquitously expressed genes. One to two percent of the human genome is CpG clusters, where there is an inverse relationship between CpG methylation and transcriptional activity.
Protein Methylation typically takes place on arginine or lysine amino acid residues in the protein sequence. Arginine can be methylated once (monomethylated arginine) or twice, with either both methyl groups on one terminal nitrogen (asymmetric dimethylated arginine) or one on both nitrogens (symmetric dimethylated arginine) by peptidyl arginine methyltransferases (PRMTs). Lysine can be methylated once, twice or three times by lysine methyltransferases. Protein methylation has been most-studied in the histones. The transfer of methyl groups from S-adenosyl methionine to histones is catalyzed by enzymes known as histone methyltransferases. Histones that are methylated on certain residues can act epigenetically to repress or activate gene expression. Protein methylation is one type of post-translational modification.
THE ROLE OF DNA METHYLATION IN MAMMALIAN EPIGENETICS
Genes constitute only a small proportion of the total mammalian genome, and the precise control of their expression in the presence of an overwhelming background of noncoding DNA presents a substantial problem for their regulation. Noncoding DNA, containing introns, repetitive elements, and potentially active transposable elements, requires effective mechanisms for its long-term silencing. Genes are transcribed from methylation-free promoters even though adjacent transcribed and nontranscribed regions are extensively methylated. Gene promoters are used and regulated while keeping noncoding DNA, including transposable elements, suppressed.
Role of DNA methylation in Regulating Gene Activity
DNA methylation prevents the expression of genes by altering the amount of messenger RNA. Enzymes attach chemical tags called methyl groups to the bases from which DNA is made.
DNA Methylation in Plants
DNA methylation in plants is more diverse than in animals. In addition to methylating CpGs, plants also methylate the cytosine at CpNpG and CpNpNp sequences, where N can be any base. Plants also have a greater variety of enzymesinvolved in methylating DNA than animals. Methylation of plant DNA occurs in transposon sequences, regions of repeated DNA sequences and in the coding region of genes.
DNA Methylation Patterns are Heritable
Once a gene has been methylated, all the daughter cells from that cell retain the methylation, making it a heritable change. Some genetic conditions are caused by inappropriate over or under methylation of the same region of DNA, such as Prader-Willi and Angelman’s syndromes.
The link between DNA Methylation and Cancer
Cancer is now recognised as both a genetic and epigenetic disease. While some types of cancers can be inherited, other cancers result from changes to DNA that accumulates throughout life. There are three types of cancer-causing genes: oncogenes, tumour suppressor genes and DNA repair genes.
Age Related Cancers
DNA methylation is a dynamic process, with the enzymes involved constantly working to methylate and demethylate CpG sites throughout the genome. Inappropriate methylation patterns leads to inactivation of genes that should be expressed, which poses a particular problem when those genes are tumour suppressor genes vital for controlling normal cell growth.