CG islands also remain unmethylated in most somatic tissues whether or not the associated gene is expressed. The unmethylated state is maintained by sequence-specific DNA-binding proteins, many of whose cis-regulatory sequences contain a CG. By binding to these sequences, which are spread across CG islands, they protect the DNA from methyl transferases. These proteins also recruit DNA demethylases, which convert 5-methyl C to hydroxy-methyl C, which 10,000 nucleotide pairs is later replaced by C either through DNA repair (see Figure 5–41A) or, passively, through multiple rounds of DNA replication. Unmethylated CG islands have several properties that make them particularly suitable for promoters. For example, some of the same proteins that bind to CG islands and protect them from methylation recruit histone modifying enzymes that make the islands particularly “promoter friendly.” As a result, RNA polymerase is often found bound to promoters within CG islands, even when the associated gene is not being actively transcribed. At unmethylated CG islands, the balance between polymerase and nucleosome assembly is thus tipped toward the former. Additional steps are needed to “push” the bound polymerase into transcribing the adjacent gene, and these are directed by transcription regulators that bind to cis-regulatory sequences of DNA (often well upstream from the CG islands). These regulators serve to release the polymerase with the appropriate elongation factors (see Figure 7–21C and D).
Genomic imprinting is Based on DnA Methylation
Mammalian cells are diploid, containing one set of genes inherited from the father and one set from the mother. The expression of a small minority of genes depends on whether they have been inherited from the mother or the father: when the paternally inherited gene copy is active, the maternally inherited gene copy is silent, or vice versa. This phenomenon is called genomic imprinting.
Roughly 300 genes are imprinted in humans. Because only one copy of an imprinted gene is expressed, imprinting can “unmask” mutations that would normally be covered by the other, functional copy. For example, Angelman syndrome, a disorder of the nervous system in humans that causes reduced mental ability and severe speech impairment, results from a gene deletion on one chromosomal homolog and the silencing, by imprinting, of the intact gene on the other homolog.
The insulin-like growth factor-2 (Igf 2) gene in the mouse provides a well-studied example of imprinting. Mice that do not express Igf 2 at all are born half the size of normal mice. However, only the paternal copy of Igf 2 is transcribed, and only this gene copy matters for the phenotype. As a result, mice with a mutated paternally derived Igf 2 gene are stunted, while mice with a mutated maternally derived Igf 2 gene are normal.
Figure 7–47 A mechanism to explain both the marked overall deficiency of CG sequences and their clustering into CG islands in vertebrate genomes. White lines mark the location of CG dinucleotides in the DnA sequences, while red circles indicate the presence of a methyl group on the CG dinucleotide. CG sequences that lie in regulatory sequences of genes that are transcribed in germ cells are unmethylated and therefore tend to be retained in evolution. Methylated CG sequences, on the other hand, tend to be lost through deamination of 5-methyl C to t, unless the CG sequence is critical for survival.