For Histone methylation see right hand panel.

Epigenetics has two main elements; DNA methylation and histone modifications. Transcriptional activation of tissue-specific genes generally involves both DNA demethylation and changes in chromatin structure, evident as changes in the pattern of accessibility to restriction enzymes or DNase I.These elements control how the DNA is structured, and the structure of DNA determines its function. DNA methylation is a modified form of DNA typically associated with a resting state which turns down DNA activity. Histone modifications manifest themselves by either ramping up DNA or toning it down.

Methylation of DNA

Methylation of CpG: Addition of a methyl moiety to the 5th position of DNA cytosin base (5-methycytosin) is an evolutionarily conserved feature of most vertebrate and plant genomes. Such DNA methylation yields a fifth coding element for the genome, and plays diverse roles in modulation and expression of the associated genomic information. In mammals, DNA methylation occurs predominantly at CpG dinucleotides, and underlies a variety of transcriptional regulatory phenomena, including imprinting, X-chromosome inactivation, transgenerational epigenetic inheritance and stable silencing of gene activity. Vertebrate cells contain a family of proteins that bind methlated DNA. These proteins interact with chromatin remodeling complexes and histone deacetylases that condense chromatin so it becomes transcriptionally inactive. DNA binding factors which bind methylated CpG residues, such as MeCP2, associate with the mSin3/histone deacetylase (HDAC) corepressor complex, providng a mechanistic link between DNA methylation and the formation of repressed, higher-order chromatin structures. 

The proteins mediating CpG methylation ahve been identified, and their roles in mammalian development have been investigated. The DNA methyltransferase Dnmt1 maintains CpG methylation during DNA replication by methylating the newly synthesized daughter DNA strand, using the methylation pattern of the parental strand as a template. Dnmt1 binds the proliferating cell nuclear antigen PCNA and can be found in a complex bound to hemimethylated DNA at replication foci in late S pahse. However, Dnmt1 does not efficiently modify unmethylated CpG in vivo; de novo DNA methylation is accomplished by two other DNA methyltransferases, Dnmt3a and Dnmt3B, which symmetrically methylate CpG pairs on both DNA strands.

In vertebrates, DNA methylation is found primarily on transcriptionally silent regions of the genome, such as the inactive X chromosome (discussed below). X Inactivation is the transcriptional inactivation of one of the 2 X chromosomes in female somatic cells that occurs early in the development of a female embryo when it consists of a few thousand cells. One of these 2 chromosomes becomes highly condensed. X chromosome is initiated and spreads form a single site in the middle of the X chromosome called the X-inactivation center (XIC) which is a large DNA sequence that codes for an RNA molecule, XIST RNA which is expressed solely from the inactive X chromosome. The XIST RNA does not get translated into protein but rather stays in the nucleus where it participates in the formation and spread of heterchromatin. In activation of one of the females X chromosomes is absolutely necessary to insure an equal dosage of X chromosome gene products between males and females. Mutations that interfere with such dosage are lethal.

Genomic imprintinginvolves the methylation of genes which usually silences nearby gene expression. The imprinting is epigenetic which means that it is heritable. Imprinted genes are usually found organized as clusters. The clusters often include genes for noncoding RNAs, the expression of which often correlates with repression of nearby protein coding genes. One studied example of coding and noncoding gene partners is Igf2/Air. In one model, an Air transcript recruits a repressor complex to chromatin in a way similar to X inactivation above. Specific sequences around the imprinted genes in the cluster are recognized by the Air-containing ribonucleoprotein complexes. AirRNA coats this region in a similar manner to X inactivation.

Demethylation of DNA

In contast to what is known about how genes are methylated, little is known about how genes are demethylated, either during development or during somatic differentation. An “active” model of tissue-specific gene demethylation has been propsoed in which demethylases catalyze localized demethylation of those genetic loci that have been targetd for activation by differentiative signals. An alternative “passive” model of CpG demethylation proposes that lineage-specific DNA binding factors synthesized in differentiating cells interfer with maintenance methylation by inhbiting access of Dnmt1 to unmodifed CpG on newly replicated DNA strands.