Transcription regulation at about 60% of promoters is controlled by methylation of cytosines within CpG dinucleotides (where 5’ cytosine is followed by 3’ guanine or CpG sites).  5-methylcytosine (5-mC) is a methylated form of the DNA base cytosine (see Figure).  5-mC is an epigenetic marker found predominantly within CpG sites.  About 28 million CpG dinucleotides occur in the human genome.  In most tissues of mammals, on average, 70% to 80% of CpG cytosines are methylated (forming 5-methylCpG or 5-mCpG).  Methylated cytosines within 5’cytosine-guanine 3’ sequences often occur in groups, called CpG islands.  About 60% of promoter sequences have a CpG island while only about 6% of enhancer sequences have a CpG island.  CpG islands constitute regulatory sequences, since if CpG islands are methylated in the promoter of a gene this can reduce or silence gene transcription.
DNA methylation regulates gene transcription through interaction with methyl binding domain (MBD) proteins, such as MeCP2, MBD1 and MBD2.  These MBD proteins bind most strongly to highly methylated CpG islands.  These MBD proteins have both a methyl-CpG-binding domain as well as a transcription repression domain.  They bind to methylated DNA and guide or direct protein complexes with chromatin remodeling and/or histone modifying activity to methylated CpG islands. MBD proteins generally repress local chromatin such as by catalyzing the introduction of repressive histone marks, or creating an overall repressive chromatin environment through nucleosome remodeling and chromatin reorganization.
Transcription factors are proteins that bind to specific DNA sequences in order to regulate the expression of a gene.  The binding sequence for a transcription factor in DNA is usually about 10 or 11 nucleotides long.  As summarized in 2009, Vaquerizas et al. indicated there are approximately 1,400 different transcription factors encoded in the human genome by genes that constitute about 6% of all human protein encoding genes.  About 94% of transcription factor binding sites (TFBSs) that are associated with signal-responsive genes occur in enhancers while only about 6% of such TFBSs occur in promoters.
EGR1 protein is a particular transcription factor that is important for regulation of methylation of CpG islands.  An EGR1 transcription factor binding site is frequently located in enhancer or promoter sequences.  There are about 12,000 binding sites for EGR1 in the mammalian genome and about half of EGR1 binding sites are located in promoters and half in enhancers.  The binding of EGR1 to its target DNA binding site is insensitive to cytosine methylation in the DNA.
While only small amounts of EGR1 transcription factor protein are detectable in cells that are un-stimulated, translation of the EGR1 gene into protein at one hour after stimulation is drastically elevated.  Expression of EGR1 transcription factor proteins, in various types of cells, can be stimulated by growth factors, neurotransmitters, hormones, stress and injury.  In the brain, when neurons are activated, EGR1 proteins are up-regulated and they bind to (recruit) the pre-existing TET1 enzymes which are highly expressed in neurons.  TET enzymes can catalyse demethylation of 5-methylcytosine.  When EGR1 transcription factors bring TET1 enzymes to EGR1 binding sites in promoters, the TET enzymes can demethylate the methylated CpG islands at those promoters.  Upon demethylation, these promoters can then initiate transcription of their target genes.  Hundreds of genes in neurons are differentially expressed after neuron activation through EGR1 recruitment of TET1 to methylated regulatory sequences in their promoters.
The methylation of promoters is also altered in response to signals.  The three mammalian DNA methyltransferasess (DNMT1, DNMT3A, and DNMT3B) catalyze the addition of methyl groups to cytosines in DNA.  While DNMT1 is a “maintenance” methyltransferase, DNMT3A and DNMT3B can carry out new methylations.  There are also two splice protein isoforms produced from the DNMT3A gene: DNA methyltransferase proteins DNMT3A1 and DNMT3A2.
The splice isoform DNMT3A2  behaves like the product of a classical immediate-early gene and, for instance, it is robustly and transiently produced after neuronal activation.  Where the DNA methyltransferase isoform DNMT3A2 binds and adds methyl groups to cytosines appears to be determined by histone post translational modifications.
On the other hand, neural activation causes degradation of DNMT3A1 accompanied by reduced methylation of at least one evaluated targeted promoter.