Epigenetic Regulation

Overview

Definition

Epigenetic modification are modifications to the DNA or DNA packaging that affect gene expression without altering the genetic code (i.e., sequence of DNA) itself.

These modifications:

• Control which regions of DNA are available for transcription
• Are typically reversible
• Can be influenced by environmental factors
• Are heritable (i.e., epigenetic patterns are preserved during cell division)

Overview of epigenetic regulation

• Epigenetic factors:
  • Change phenotype without changing genotype
  • Can influence how genes are expressed at different ages
  • Contribute significantly to differential gene expression in different tissues
• Epigenetic modifications include modifications:
  • Directly to the DNA (e.g., DNA methylation)
  • To the DNA-binding proteins (e.g., histone modification)
  • To higher-order chromatin structures
• Epigenetic regulation plays a role in:
  • Cellular differentiation
  • X-chromosome inactivation in females
  • Disease processes:
    • Imprinted disorders: Prader-Willi syndrome (PWS), Angelman syndrome (AS)
    • Cancer
  • Adaptations to the environment, including:
    • Stress
    • Starvation or obesity
    • Exposures to toxins, pollution, and/or endocrine-disrupting chemicals

Review of DNA packaging in chromatin

The basic unit of DNA packaging is the nucleosome. DNA wraps 2¼ times around a core of 8 histone proteins, forming a nucleosome.

• Nucleosomes:
  • The histone core is made up of 2 of each of the following histones: H2A, H2B, H3, and H4.
  • H1 is a 9th histone, and it sits just outside the nucleosome.
  • There are approximately 146 base pairs of DNA associated with each nucleosome.
  • There are approximately 20–60 base pairs of free DNA between nucleosomes. 
  • Nucleosomes appear like beads on a string of DNA.
• Secondary structure of chromatin:
  • Solenoid model: a spiraling configuration of nucleosomes with 6 nucleosomes per turn
  • Zigzag model: a more irregular configuration of packed nucleosomes
• Further compaction of chromatin:
  • Secondary structures coil, and these coils supercoil.
  • Chromatin condenses into full chromosomes during cell division.
• Euchromatin versus heterochromatin:
  • Euchromatin: chromatin that is available for transcription (unwound, or loosely wound, DNA)
  • Heterochromatin: chromatin that is unavailable for transcription because it is too tightly wound

Epigenetic Modifications

The most important forms of epigenetic modification include direct methylation of the DNA, modifications to the histone proteins, and other chromatin modifications. 

DNA methylation 

• Methyl groups can be added to and removed from DNA.
• Methylation typically occurs:
  • On cytosine bases in DNA
  • In promoter and enhancer regions of a gene
• Methylation typically prevents transcription of a gene:
  • Regulatory proteins bind to the methylated cytosines → prevent access of the transcription machinery to the DNA → silence gene expression
  • Removing methyl groups → allows transcription → activates gene expression
• Enzymes involved in methylation:
  • DNA methyltransferases: enzymes that methylate DNA 
  • Methylcytosine dioxygenases: enzymes that remove methyl groups from DNA

Histone modifications

• How the DNA is wrapped around histone proteins affects which genes can be translated:
  • Tightly wrapped DNA is inaccessible to the transcriptional machinery.
  • Altering how genes are wrapped makes certain segments of DNA more or less accessible to transcriptional machinery.
• Modifying the histones:
  • Alters the affinity of the histone proteins for the DNA
  • Can recruit other proteins that affect chromatin structure
• The effect of the histone modifications (e.g., enhancing or suppressing transcription) depends on the specific combination of:
  • Which histone subunits were modified
  • Which amino acids within those subunits were modified
  • What the modifications were (e.g., methylation versus acetylation)
• Histone modifications are a type of posttranslational modification to the histone proteins.

Types of histone modifications

• Methylation:
  • In general, methylation is associated with inactive (i.e., nontranscribed) DNA.
  • Histone methyltransferases add methyl groups to lysines in the histone tail.
  • Histone demethylases remove the methyl groups.
• Acetylation:
  • In general, acetylation “unpacks” DNA, allowing transcription.
  • Histone acetyltransferases (HATs) can add acetyl groups to lysines in the histone protein.
  • Histone deacetylases (HDACs) remove the acetyl groups.
  • These enzymes typically contain zinc.
• Other types of histone modifications:
  • Ubiquitylation
  • Phosphorylation
  • Isomerization of proline
  • ADP-ribosylation of glutamic acids

Chromatin remodeling

Remodeling the chromatin and/or nucleosomes is another way the cell can regulate gene expression at the epigenetic level. Chromatin remodeling typically requires energy. Types of chromatin remodeling include:

• Moving or sliding the nucleosome down the DNA strand
• Remodeling the shape of the nucleosome
• Temporarily removing the nucleosome
• Replacing the histones

Imprinting

Overview

Imprinting comprises the specific epigenetic modifications that occur in sex-specific gametes (i.e., the modifications occur in only sperm or ova).

• Some genes are transcribed from the chromosomes of 1 parent but not the other. 
• This transcription is due to DNA hypermethylation (epigenetic silencing) of that same gene in the opposite parent.
• Clinical implication: Gene deletions in these areas cause different phenotypes in offspring depending on whether the mutation was inherited from the mother or the father.
• The imprinted gene is the hypermethylated, silenced gene.
• Classic examples of conditions related to imprinted genes: 
  • PWS
  • AS
• The genes associated with PWS and AS are both located at chromosome 15q11-13, but they are not the exact same genes.

Prader-Willi syndrome

• The Prader-Willi genetic region is:
  • Transcribed only from the paternal chromosome
  • Hypermethylated (i.e., silenced) on the maternal chromosome
• Paternal deletions in this region result in PWS.
• Clinical presentation: 
  • Hyperphagia with early-onset obesity
  • Hypogonadism
  • Mild developmental delay
  • Abnormal facial features
  • Short stature with generally small hands and feet

Angelman syndrome

• The Angelman genetic region is:
  • Transcribed only from the maternal chromosome
  • Hypermethylated (i.e., silenced) on the paternal chromosome
• Maternal deletions in this region result in AS.
• Clinical presentation: “the happy puppet”:
  • Microcephaly with seizures
  • Severe developmental delays
  • Minimal speech

Clinical Relevance

• Cancer: All cancers have abnormalities in their epigenetic regulation. Also, some common epigenetic “signatures” have been discovered in certain types of cancers. Examples of these signatures include global hypomethylation leading to the activation of oncogenes (e.g., RAS) and DNA methylation at promoter sequences silencing tumor suppressor genes. In addition, mutations can affect other histone modifications as well.
• Histone deacetylase inhibitors: Histone acetylation activates gene expression and HDACs remove the acetyl groups; therefore, HDAC inhibitors end up increasing gene expression. Some examples include romidepsin, panobinostat, and vorinostat, which are used in the treatment of T-cell lymphomas. In addition, valproic acid (an antiepileptic drug) also demonstrates HDAC inhibitor activity and is being explored for applications beyond seizure control related to this HDAC inhibitor activity.
• Alzheimer’s disease: neurodegenerative disease resulting in dementia. Alzheimer’s disease is thought to be the result of misfolded and/or abnormally modified proteins, including the β-amyloid peptide and tau proteins. Environmental and epigenetic factors are also implicated in its pathogenesis, though the exact mechanisms are still unknown. Patients present with progressive dementia.
• Hutchinson–Gilford progeria syndrome (HGPS): premature aging syndrome related to a rare genetic defect in laminin A, which is critical in stabilizing the nuclear membrane. Without normal, functional laminin A, the heterochromatin becomes very disorganized and unstable, and gene transcription is dysregulated. Patients with HGPS manifest with multiple progeroid symptoms by 2 years of age, including failure to thrive and dermatologic, musculoskeletal, neurologic audiologic, ophthalmologic, and life-limiting cardiovascular abnormalities.