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LitNet Akademies Jaargang 9(2), Augustus 2012 Epigenetika: die skakel tussen genetika en omgewing Opsomming Liza Bornman, Gerrit Koorsen en Vanessa O'Neill Liza Bornman, Gerrit Koorsen en Vanessa O’Neill: Departement Biochemie, Universiteit van Johannesburg Epigenetika verwys na oorerflike en verbygaande variasie in geenuitdrukking en proteïenvouing wat nie bepaal word deur variasie in DNA-basisvolgorde of proteïenaminosuurvolgorde nie. Epigenetiese variasie word moontlik gemaak deur DNA-metilering, histoonmodifikasie, regulering deur verskeie vorme van niekoderende RNA en prionbemiddelde variasie in proteïenvouing. DNA-metilering, histoonmodifikasies en niekoderende RNA is nukleïensuurverwante epigenetiese meganismes wat geenuitdrukking beïnvloed. Prions, daarenteen, verteenwoordig ’n proteïenverwante epigenetiese meganisme wat proteïenvouing en gevolglik proteïenfunksie beïnvloed. Die genoom, epigenoom en omgewing saam bepaal die fenotipe. Moduleerders van die epigenoom het die grootste impak tydens oorgangsfases in ontwikkeling, byvoorbeeld rondom bevrugting en vroeë fases van die embrio, , anders as hul impak op die epigenoom van gedifferensieerde selle. Epigenetiese “littekens” wat vroeg in die lewe deur omgewingsfaktore geïnduseer word, hou implikasies in vir gesondheid in volwassenheid. Kennis oor die verhouding tussen die epigenoom, omgewing en siekte is steeds vaag. Dit is onduidelik of die omgewing ’n direkte of indirekte impak op die epigenoom het en of klein veranderinge in die epigenoom die oorsaak of gevolg van siekte is. Epigenetiese variasie geassosieer met siektes kan gebruik word as biomerkers vir siektevatbaarheid indien dit teenwoordig is in die voorafbestaande epigenoom. Epigenetiese variasie deur siekte geïnduseer kan gebruik word om die erns en duur van siekte of die uitkoms van behandeling te monitor. ’n Verskeidenheid molekulêr-biologiese en biochemiese tegnieke word gebruik om epigenetiese variasie te bestudeer. Die keuse van tegniek is afhanklik van die tipe epigenetiese meganisme wat bestudeer word, die doel van die studie, en, in die geval van nukleïensuurverwante meganismes, of die modifikasie op genoom-wye, streek- of lokus-spesifieke vlak bestudeer word. In hierdie oorsigsartikel word epigenetika bespreek onder die temas: agtergrond, tipes, oorerflikheid, moduleerders, gesondheid en siekte, en metodes ter bestudering. Epigenetika regverdig die herskryf van die moderne evolusieteorie. Dit ondersteun die oorerwing van verworwe eienskappe en werp nuwe lig op meganismes wat inligting kommunikeer vanaf die omgewing na die genoom, transkriptoom en proteoom. Trefwoorde: epigenetika; genetika; omgewing; evolusie 42
Abstract Epigenetics: The link between genetics and environment LitNet Akademies Jaargang 9(2), Augustus 2012 All living organisms face the constant challenge of adapting to an ever changing environment. The mechanisms that bring about adaptation have been under investigation for centuries. Aristotle (384 BC–322 BC), the Greek philosopher and author of the theory of epigenesis, postulated that each embryo of an organism develops systematically from an undifferentiated mass. Epigenesis was the first theory to point to development based on specific cues. It contrasted with preformation: the idea that all organisms develop from miniature versions of themselves in the gametes. Jean-Baptiste Lamarck (1744–1829), a French naturalist and author of the term biology, published the first formal theory of evolution in which he proposes two laws of evolution – the law of use or disuse and the law of inheritance of acquired characteristics. In his theory of natural selection Charles Darwin (1809–1882) postulated that subtle variation in the phenotype of an organism, favouring survival, will be carried over to the offspring. In The Origin of Species (1859) Darwin describes two forces in evolution – natural selection and conditions of existence (environment). Of these two forces, Darwin argues the latter to be more powerful, implying that natural selection can take place only within the boundaries of a specific environment. The term epigenetics was coined by Conrad Waddington in 1942, and he defined it as the interaction between genes and the environment to produce phenotype. Today epigenetics is widely used to refer to the heritable and transient changes in gene expression not caused by nucleotide sequence variation, but collectively instigated by epigenetic marks classified as DNA methylation, histone modification and non-coding RNA. In addition to these nucleicacid-related modifications, prion-mediated variation in protein folding was more recently identified as a protein-conformation-based epigenetic mechanism in baker’s yeast. Epigenetic marks respond to changes in the environment, allowing adaptation. Unlike the genome, plasticity of the epigenome is observed over a short time, responding to, and dictating change within, one generation. The phenotype is therefore determined by the interaction between the genome, epigenome and environment. The most widely studied and best understood epigenetic modification is DNA methylation. The methylation of a DNA sequence involves the covalent binding of a methyl group on the 5th carbon position of a cytosine ring in a reaction catalysed by DNA methyl transferase 1 (DNMT-1). Cytosine methylation occurs largely in the context of CpG dinucleotides and clusters of these dinucleotides are known as CpG islands (CGIs). The epigenome undergoes major reprogramming marked by global demethylation during early embryogenesis when paternal and maternal genomes merge to form the zygote and during gametogenesis in the primordial germ cells (PGCs) of the embryo. Lineage-specific DNA methylation patterns are established by de novo DNA methyl transferases, DNMT3A and DNMT3B, around implantation and are maintained by DNMT-1. Intrinsic and extrinsic (environmental) factors influence the establishment and maintenance of epigenetic marks. DNA and histone methylation hinge on the level of S-adenosylmethionine (SAM), the universal methyl donor generated by the methionine (one-carbon) cycle in interaction with the folate cycle. During specific stages of development the epigenome is selectively demethylated, bestowing a unique epigenetic signature on each cell type. DNMT-1 maintains methylation patterns and abnormal hypomethylation is a cause of altered gene expression in diseased tissue. In addition to DNA methylation, specific modifications on histones form a 43
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