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<p style="text-align: center;"><span style="font-size:24px">The DNA is not your destiny.- Epigenomics </span></p>
<p style="text-align: right;">Sangin Kim </p>
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<h3>DNA methylation[<a href="https://en.wikipedia.org/w/index.php?title=Epigenomics&action=edit&section=3" title="Edit section: DNA methylation">edit</a>]</h3>
<p>The first epigenetic modification to be characterized in depth was DNA methylation. As its name implies, DNA methylation is the process by which a <a href="https://en.wikipedia.org/wiki/Methyl_group" title="Methyl group">methyl group</a> is added to DNA. The enzymes responsible for catalyzing this reaction are the <a href="https://en.wikipedia.org/wiki/DNA_methyltransferase" title="DNA methyltransferase">DNA methyltransferases (DNMTs)</a>. While DNA methylation is stable and heritable, it can be reversed by an antagonistic group of enzymes known as DNA de-methylases. In eukaryotes, methylation is most commonly found on the carbon 5 position of <a href="https://en.wikipedia.org/wiki/Cytosine" title="Cytosine">cytosine residues</a> (5mC) adjacent to <a href="https://en.wikipedia.org/wiki/Guanine" title="Guanine">guanine</a>, termed <a href="https://en.wikipedia.org/wiki/CpG_site" title="CpG site">CpG dinucleotides</a> (Russell 2010 p 531-32; Laird 2010). DNA methylation patterns vary greatly between species and even within the same organism. The usage of methylation among animals is quite different; with <a href="https://en.wikipedia.org/wiki/Vertebrate" title="Vertebrate">vertebrates</a> exhibiting the highest levels of 5mC and <a href="https://en.wikipedia.org/wiki/Invertebrate" title="Invertebrate">invertebrates</a> more moderate levels of 5mC. Some organisms like <em><a href="https://en.wikipedia.org/wiki/Caenorhabditis_elegans" title="Caenorhabditis elegans">Caenorhabditis elegans</a></em> have not been demonstrated to have 5mC nor a conventional DNA methyltransferase; this would suggest that other mechanisms other than DNA methylation are also involved (Bird 2002).</p>
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<h3>Histone Modification[<a href="https://en.wikipedia.org/w/index.php?title=Epigenomics&action=edit&section=4" title="Edit section: Histone Modification">edit</a>]</h3>
<p>In <a href="https://en.wikipedia.org/wiki/Eukaryote" title="Eukaryote">eukaryotes</a>, genomic DNA is coiled into protein-DNA complexes called <a href="https://en.wikipedia.org/wiki/Chromatin" title="Chromatin">chromatin</a>. <a href="https://en.wikipedia.org/wiki/Histone" title="Histone">Histones</a>, which are the most prevalent type of protein found in chromatin, function to condense the DNA; the net positive charge on histones facilitates their bonding with DNA, which is negatively charged. The basic and repeating units of chromatin, <a href="https://en.wikipedia.org/wiki/Nucleosome" title="Nucleosome">nucleosomes</a>, consist of an <a href="https://en.wikipedia.org/wiki/Histone_octamer" title="Histone octamer">octamer of histone proteins</a> (H2A, H2B, H3 and H4) and a 146 bp length of DNA wrapped around it. Nucleosomes and the DNA connecting form a 10 nm diameter chromatin fiber, which can be further condensed (Barski et al. 2007; Kouzarides 2007).</p>
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<h3>Histone modification assays[<a href="https://en.wikipedia.org/w/index.php?title=Epigenomics&action=edit&section=7" title="Edit section: Histone modification assays">edit</a>]</h3>
<p>The cellular processes of <a href="https://en.wikipedia.org/wiki/Transcription_(genetics)" title="Transcription (genetics)">transcription</a>, <a href="https://en.wikipedia.org/wiki/DNA_replication" title="DNA replication">DNA replication</a> and <a href="https://en.wikipedia.org/wiki/DNA_repair" title="DNA repair">DNA repair</a> involve the interaction between genomic DNA and nuclear proteins. It had been known that certain regions within chromatin were extremely susceptible to <a href="https://en.wikipedia.org/wiki/Deoxyribonuclease" title="Deoxyribonuclease">DNAse I</a> digestion, which cleaves DNA in a low sequence specificity manner. Such <a href="https://en.wikipedia.org/wiki/Hypersensitive_sites" title="Hypersensitive sites">hypersensitive sites</a> were thought to be transcriptionally active regions, as evidenced by their association with <a href="https://en.wikipedia.org/wiki/RNA_polymerase" title="RNA polymerase">RNA polymerase</a> and <a href="https://en.wikipedia.org/wiki/Topoisomerase" title="Topoisomerase">topoisomerases I and II</a> (Gross 1988).</p>
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<h3>DNA Methylation assays[<a href="https://en.wikipedia.org/w/index.php?title=Epigenomics&action=edit&section=9" title="Edit section: DNA Methylation assays">edit</a>]</h3>
<p>Techniques for characterizing primary DNA sequences could not be directly applied to methylation assays. For example, when DNA was amplified in <a href="https://en.wikipedia.org/wiki/Polymerase_chain_reaction" title="Polymerase chain reaction">PCR</a> or bacterial cloning techniques, the methylation pattern was not copied and thus the information lost. The <a href="https://en.wikipedia.org/wiki/Hybridization_probe" title="Hybridization probe">DNA hybridization technique</a> used in DNA assays, in which radioactive probes were used to map and identify DNA sequences, could not be used to distinguish between methylated and non-methylated DNA.</p>