Most evidence suggests that epigenetic effects are brought about by physical changes to chromatin structure. We will consider three types of molecular mechanisms that alter chromatin structure and underlie many epigenetic phenotypes: (1) changes in patterns of DNA methylation; (2) chemical modifications of histone proteins; and (3) RNA molecules that affect chromatin structure and gene expression.

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DNA METHYLATION The best-understood mechanism of epigenetic change is methylation of DNA. As we have seen, DNA methylation refers to the addition of methyl groups to the nucleotide bases. In eukaryotes, the predominant type of DNA methylation is the methylation of cytosine to produce 5-methylcytosine, which is often associated with repression of transcription. DNA methylation often occurs on cytosine nucleotides that are immediately adjacent to guanine nucleotides, together referred to as CpG dinucleotides (p represents the phosphate group that connects the C and G nucleotides). DNA regions that have many CpG dinucleotides are referred to as CpG islands. In mammalian cells, CpG islands are often located in or near the promoters of genes. These CpG islands are usually not methylated when genes are being actively transcribed. However, methylation of CpG islands near a gene leads to repression of transcription.

The fact that epigenetic changes are passed to other cells and (sometimes) to future generations means that the changes in chromatin structure associated with epigenetic phenotypes must be faithfully maintained when chromosomes replicate. How are epigenetic changes retained and replicated through the process of cell division?

Methylation of CpG dinucleotides means that two methylated cytosine bases sit diagonally across from each other on opposite strands. Before replication, cytosine bases on both strands are methylated (Figure 12.23). Immediately after semiconservative replication, the cytosine base on the template strand has a methyl group, but the cytosine base on the newly replicated strand does not. Special methyltransferase enzymes recognize the hemimethylated state of CpG dinucleotides and add methyl groups to the unmethylated cytosine bases, resulting in two new DNA molecules that are fully methylated. In this way, the methylation pattern of DNA is maintained across cell division.

HISTONE MODIFICATIONS Epigenetic changes can also occur through modification of histone proteins. As we saw in Section 12.3, these modifications can alter chromatin structure and affect the transcription of genes. These types of modifications have been called epigenetic marks. For example, the addition of three methyl groups to lysine 4 in the H3 histone (H3K4me3) is often found near transcriptionally active genes. Methylation of lysine 36 in the H3 histone (H3K36me3) is also associated with increased transcription. On the other hand, the addition of three methyl groups to lysine 9 in H3 (H3K9me3) and to lysine 20 in histone 4 (H4K20me3) is associated with repression of transcription. Many additional histone modifications have been shown to be associated with the level of transcription.

Several models have been proposed to explain how histone modifications are faithfully transmitted to daughter cells. During the process of DNA replication, nucleosomes are disrupted and the original histone proteins are distributed randomly between the two new DNA molecules. Newly synthesized histones are then added to complete the formation of new nucleosomes (see Chapter 8). Most models assume that after replication, the epigenetic marks remain on the original histones; these marks then recruit enzymes that make similar changes to the new histones, maintaining the histone modifications across cell division.

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EPIGENETIC EFFECTS OF RNA MOLECULES Evidence increasingly demonstrates that RNA molecules play an important role in bringing about epigenetic effects. The first discovered and still best-understood example of RNA mediation of epigenetic change is X inactivation, in which a long noncoding RNA called Xist suppresses transcription on one of the X chromosomes in female mammals. The Xist lncRNA coats one X chromosome and then attracts a protein called polycomb repressive complex 2, which deposits methyl groups on lysine 27 of histone H3, creating a H3K27me3 epigenetic mark that alters chromatin structure and represses transcription.