6
Epigenetic Mechanisms
Regulating Gene Expression
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Fig. 1. Alternate states of DNA methylation in mammalian DNA. Methylation occurs only on cytosines
present in CpG dinucleotides in mammalian DNA. A CpG dinucleotide sequence in one DNA strand
mandates the presence of a complementary CpG dinucleotide in the other strand of double-stranded
DNA. (A) If both cytosines in such a site are unmethylated, the site is said to be completely
unmethylated. This structure is often found in actively expressed or potentiated genes, especially in the
5' regulatory region. (B) An unmethylated site can undergo de novo methylation to form a fully methylated site in which both cytosines are methylated. This structure is often found associated with
repressed genes. Conversely a demethylase activity can convert a fully methylated site to a fully
unmethylated site in the absence of DNA replication. (C) Upon semi-conservative replication of a fully
methylated site, a hemimethylated site is formed. This structure is typically transient as a maintenance
DNA methyl transferase rapidly recognizes a hemimethylated site and returns it to a fully methylated
state. The function of the maintenance methylase provides a mechanism to heritably maintain DNA
methylation patterns. C, cytosine; G, guanine; N, any base; p, phosphate bond; CH3, methyl group.
Fig. 2. Alternate states of chromatin structure. (A) In eukaryotic cells double-stranded DNA is typically complexed with clusters of histones called nucleosomes to form a beads on a string structure.
This structure, which forms a fiber of approx 10 nm in diameter, is typically found in genes that are
undergoing active transcription as shown in the Expressed State in this figure. The RNA polymerase
II complex is able to traverse and transcribe portion of this structure to produce mRNA transcripts.
(B) Long-term repression of gene transcription is accomplished by condensation of chromatin to
form a 30 nm fiber as shown in the Repressed State in this figure. This condensed structure is
refractory to binding by transcription factors and/or RNA polymerase II inhibiting initiation of transcription. Open circles, nucleosomes within the transcribed portion of the gene; filled circles,
nucleosomes between genes; hatched oval, the RNA II polymerase complex.
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Fig. 3. Organization of DNA loop domains. Adjacent chromatin loop domains can exist in alternate
states of condensed (closed) or decondensed (open) structure. Genes within closed domains are typically repressed. Genes within open domains are potentiated for transcriptional activation. Activation
of transcription requires transcription factor binding and initiation of RNA synthesis by RNA polymerase II. (Modified with permission from Krawetz, et al. [1999]).
Fig. 4. Distinction of genes or alleles based on differential replication timing. The potential for
differential timing of replication during S phase to maintain an epigenetic distinction between different genes or between different alleles of the same gene is depicted in this figure. The model is based
on the concept that protein-DNA interactions become disrupted during DNA replication. These
interactions must be re-established following replication. If certain proteins are present in limiting
quantities, those genes or alleles that replicate earliest during S phase will gain preferential access to
bind these proteins. In this way one gene or allele will bind a disproportionate quantity of a specific
protein(s) and become distinguished from another gene or allele, even if both genes or alleles share
similar protein-binding sequences. (Reproduced with permission from Simon, et al. [1999]).
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Fig. 5. Interactions among epigenetic mechanisms to regulate gene expression. Multiple epigenetic
mechanisms contribute to regulation of transcriptional activity in mammals. An example
of how this may occur is presented in this figure. (A) A fully repressed gene is often found to be
hypermethylated, complexed with methylated-DNA binding proteins, comprised of deacetylated
histones, and in a condensed chromatin structure characterized by a 30-nm structure that inhibits
binding of transcription factors or RNA polymerase. (B) Derepression leading to transcriptional
activation begins with demethylation of the gene, which in turn leads to dissociation of methylated-DNA binding proteins and acetylation of histones. (C) Potentiation of chromatin structure is
marked by decondensation of the chromatin fiber from the 30 nm structure to the 10 nm beads on
a string structure. (D) Displacement of nucleosomes creates an assayable DNase I hypersensitive
site which marks the presence of naked DNA that is available for binding by transcription factors.
(E) Binding of ubiquitous transcription factors to the core promoter region and tissue-specific transcription factors to enhancer regions attract the RNA polymerase II complex to the gene promoter.
(F) Binding of the RNA polymerase II complex initiates transcription. (G) Ongoing transcription is
characterized by sequential binding of multiple RNA polymerase II complexes to facilitate synthesis of multiple RNA transcripts. Open circles, nucleosomes within the transcribed portion of the
gene; filled circles, nucleosomes between genes; squares containing Ms, DNA methylation; hexagons, methylated-DNA binding proteins; small filled hexagons, circles and rectangles, bound transcription factors; large, hatched oval, RNA polymerase II complex.
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