The term epigenetics is used to describe heritable genetic modifications that are not attributable to changes in the primary DNA sequence. Epigenetic modifications play a crucial role in gene expression, and thereby underpin the development, regulation, and maintenance of the normal cell. Lifestyle, nutrition, and environmental factors can all lead to epigenetic changes.

Two of the most commonly studied epigenetic modifications involve:

  1. Protein - DNA interactions (i.e., binding of proteins to DNA)
  2. Methylation of cytosine (C) nucleotides in the context of a CpG dinucleotide

Because the expression of miRNAs can impact epigenetic mechanisms, they can also contribute to epigenetic changes.

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Methylation Analysis
As CpG DNA methylation is not preserved during DNA amplification, studying methylation requires that the DNA be treated to either preserve or select for methylation status prior to DNA sequencing. Techniques used to prepare DNA for methylation analysis include: the selection of methylated DNA by affinity enrichment, enzymatic compartmentalization using methylation sensitive enzymes, or chemical treatment of the DNA using bisulfite.		 Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
Proteins bound to DNA can impact the expression of genes, as well as the accessibility and packaging of DNA. To study these interactions, protein–DNA complexes can be isolated by chromatin immunoprecipitation (ChIP) and then characterized by sequencing the associated DNA. This approach is called ChIP - Seq.

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