Cindy Boer

34 | Chapter 1.2 enced by genetic variation, but the majority of the variation in methylation is caused by other factors, including environmental and stochastic variation. Indeed, variation in DNA methylation increases with age[5] and is thought to have a role in the relation between environmental risk factors and disease risk. As all epigenetic marks, DNA methylation is dynamic; methyl groups can be added and removed from the DNA by specialized proteins, DNA‐methyl‐transferases (DNMTs) and ten‐eleven translocation (TET) proteins, respec- tively (see Box 1 for an explanation of epigenomic terms). Chromatin structure The spatial organization of the DNA itself in the cell nucleus, the chromatin structure, is also important for the functional read‐out of the genome. Histones are critical compo- nents of the chromatin ( Figure 1 ). In fact, DNA‐bound histones play major roles in the regulation of gene transcription. Posttranslational modifications (PTM) of specific amino acids in the N‐terminal tail of histones, such as methylation, phosphorylation, acetylation, and ubiquitylation, remodel the shape of the chromatin. This, in turn, alters the DNA's ac- cessibility for proteins involved in the transcription machinery, thereby regulating gene expression[6]. Histone PTMs are dynamic and a number of enzymes are able to add or remove histone marks. For example, acetyl groups can be added by histone acetylases (HATs) and removed by histone deacetylases (HDACs). Next to histone PTMs, also the spatial organization of the chromatin itself in the nucleus can modulate gene expression. Chromosome‐conformation capture techniques have shown that the genome is divided into so‐called topological associated domains (TADs), which are large (megabase scale) compartments of the genome. These regions interact more frequently with themselves than the rest of the genome and enhancers usu- ally contact genes located within these TADs but not outside[7]. Distant enhancers and their target gene promoters are brought into contact with each other using the formation of so‐called “DNA‐loops,” mediated by, for example, CTCF and cohesins ( Figure 1 ). Non‐coding RNAs Besides chromatin‐related marks and structure, non‐coding RNAs (ncRNAs) are also frequently included among the mechanisms of epigenetic control[8]. They are clas- sified as small RNAs (<200 nucleotides) and long RNAs (>200 nucleotides). The best‐ known subset of small RNAs are microRNAs (miRNAs, 18 to 25 nucleotides), which in- hibit protein synthesis by binding to the 3 ′ ‐untranslated region of target mRNAs. Long non‐coding RNAs (lncRNAs) modulate the activity of both nearby genes and distant genes by a variety of mechanisms. For instance, they often serve as scaffolds for transcription factors and other molecules involved in initiation of transcription, including repressive