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LitNet Akademies Jaargang 9(2), Augustus 2012 second epigenetic mechanism vital in gene regulation. Histones are small, highly basic nuclear proteins that function to stabilise and package chromatin. Specific modifications in an unstructured domain at the N-terminal of most histones allow epigenetic control of gene expression through changes in accessibility of the DNA sequence to transcription factors and other regulatory proteins. Histone modification is characterised by complex and diverse chemical changes, including acetylation, methylation, phosphorylation and ubiquitination. Unlike DNA methylation and histone modifications that silence genes by preventing transcription, non-coding RNA (ncRNA) prevents translation of mRNA to proteins (silencing). ncRNA, among which small nucleolar RNA (snoRNA), micro-RNA (miRNA), small interfering RNA (siRNA), piwi-interacting RNA (piRNA), and long non-coding RNA (lnRNA), form part of the RNA-induced silencing complex (RISC). RISC regulates gene expression through complementary (specific and less specific) base pairing between the ncRNA and target mRNA/DNA leading to the cleavage of the nucleotide target sequence by means of a DICER enzyme. A form of extreme epigenetics is seen in prions. Prions are a group of proteins with the unique capacity to fold into different conformations. They are stable conformational variants of normal proteins with distinct functions. Extreme environmental stress induces proteins to take on the prion conformation, a process that is reversible when the stress is relieved. Prion conformations are stably carried over to daughter cells during mitosis and meiosis, thereby allowing the inheritance of stress-induced acquired characteristics. In humans prions have mostly been associated with disease , but recent reports on baker’s yeast show that prion induction favours survival of the organism in altered environments. The altered patterns of protein folding in the organism, induced by the environment and inherited by offspring, can therefore be considered as an epigenetic mechanism allowing adaptation. Future work on prions in mammals may reveal their role in the maintenance of physiological conditions in ever changing environments. The epigenome is particularly sensitive to modification at conception, during gestation, around birth and during puberty. Epigenetic “scars” induced early in life may hold implications for health in adulthood. Transgenerational inheritance of alterations in the epigenome induced by environment remains controversial. Only marks transmitted to the F3 generation are truly transgenerational since in utero exposure effectively exposes the mother (F0), the foetus (F1) and primordial germ cells of the foetus (F2). Much remains to be learned about the epigenome; the hierarchical order, interdependency and interplay of epigenetic mechanism, as well as the processes dictating the loci in the genome where methylation is established and maintained. Environmental factors such as a diet rich in methyl donors has been shown to alter the coat colour of Agouti mice. Paternal alcohol use is linked to the development of foetal alcohol spectrum disorders caused by hypomethylation of two imprinted genes in sperm DNA. Besides diet and lifestyle, the psychological environment during early development and genetic factors can also modulate the epigenome. Regarding the relation between the epigenome, environment and diseases it is unclear whether environment directly or indirectly impacts the epigenome and whether small changes in the epigenome are the cause or effect of disease. Nonetheless, epigenetic marks associated with disease could serve as biomarkers of disease risk when present in a pre-existing epigenome, while disease-reactive epigenetic changes may serve to monitor disease severity, duration or treatment outcome. Manipulating the epigenome for therapeutic benefit is already illustrated in cancer treatment. Epigenetics holds important implications for study design; 44
LitNet Akademies Jaargang 9(2), Augustus 2012 genetics, epigenetics and environment need to be considered in disease association studies. The cell-type-specific nature of the epigenome excludes the analysis of mixed cell populations in the study of the epigenome. A wide range of molecular biology techniques are used to study epigenetic variation. The choice of technique depends on the goal of the study and, in the case of nucleic-acid-related epigenetic changes, whether variation will be investigated at a genome-wide, regional, or site-specific level. In this review epigenetics is addressed under the themes: background, types, heritability, modulators, health and diseases, as well as methods for the study of epigenetics. Epigenetics may hold significant implications for diseases known to be influenced by an impoverished environment and common to sub- Saharan Africa, such as tuberculosis, HIV/AIDS and malaria. Keywords: epigenetics; genetics; environment; evolution 1. Inleiding Die natuurlike omgewing verander voortdurend en lewende organismes het die uitdaging om hierby aan te pas. Sedert die antieke Griekse tyd word meganismes van aanpasbaarheid en oorerflikheid ontrafel. 1.1 Geskiedenis Die verlengde hoofde van Macrocephali oortuig Hippokrates (ong. 460 v.C.–370 v.C.) dat verworwe eienskappe oorerflik is (Adams 1891). Die teorie van epigenese, die stelselmatige ontwikkeling van organismes uit ’n ongedifferensieerde massa, word deur Aristoteles (384 v.C.–322 v.C.) voorgestel. William Harvey (1578-1657) se gevolgtrekking dat elke dier uit ’n enkele eiersel ontstaan, lê die grondslag vir moderne embriologie (1651). Die eerste formele evolusieteorie word deur Jean-Baptiste Lamarck (1744–1829) gepubliseer, waarin hy die wet van gebruik of onbruik en die wet van oorerwing van verworwe eienskappe voorstel (Lamarck 1809). Charles Darwin (1809–1882) se teorie van natuurlike seleksie in The Origin of Species (1859) stipuleer dat subtiele variasie in fenotipe, wat oorlewing en aanwas bevoordeel, oorgeërf word. Hy beskryf twee kragte in evolusie: natuurlike seleksie en die kragtiger “kondisies van bestaan” (omgewing). Hiermee impliseer hy dat natuurlike seleksie binne die grense van omgewing funksioneer. Darwin beskou egter The Origin of Species as ’n onvolledige beskrywing van die teorie van evolusie (Darwin 1888). Later bestudeer hy die bron van variasie waarop natuurlike seleksie inwerk en koppel sommige variasie in organismes aan omgewingsvariasie. In The Variation in Animals and Plants under Domestication (Darwin, 1868) ontwikkel hy die hipotese van pangenese, ’n teorie wat poog om te verklaar hoe omgewingsverworwe fisiologiese veranderinge oorgeërf word, selfs al kodeer genetiese inligting nie daarvoor nie (Darwin 1868). Pangenese word egter deur wetenskaplikes verwerp. Gregor Mendel (1822–1884) se wiskundige model verklaar hoe fenotipe deur genotipe bepaal word en dat genotipe oorgeërf word en herkombineer om nuwe variasies te skep (1866). 45
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