Lecture 18 - Epigenetics and Disease Flashcards
What is the difference between epigenetics and epigenomics?
- Epigenetics = Heritable changes in gene expression and cellular phenotype that are independent of changes in the underlying DNA sequence
- Epigenomics = The study of the complete set of epigenetic modifications on the genetic material of a cell (genome)
What are the different contribution of epigenetics to ageing and disease?
- Nature
o Many diseases have a clear genetic basis – Down’s, Angelman’s, Fragile X, thalassemia’s
o Inborn errors of metabolism
Maple syrup urine disease
Phenylketonuria
Familial hypercholesterolemia
o Complex genetic traits associated with obesity and type II diabetes
o Genetic predispositions such as in neurodegenerative conditions and cancer
BCRA1 and BCRA2 mutations in cancer - Nurture
o 1/3 of disease is typically attribute to epigenetics and lifestyle factors
o Epigenetic drift: e.g., Identical twins are born with the same epigenome, epigenetic profiles begin to diverge as they age, differences increase as twins live longer and spend more time apart
o Epigenetic marks are removed randomly as people age
o Environmental influences change the pattern of epigenetic marks - Chance
o Stochastic events play a major role in disease
o Particle interaction with biological molecules
o Free radical damage causes genomic instability – underlying cause of disease – oxidative stress causes DNA damage as well which leads to mutations
What is chromatin?
- Organisation of DNA base pairs is facilitated by compaction and condensation into a complex structure known as chromatin
What is nucleosome?
- The fundamental unit of chromatin
- DNA (146 bp) is wrapped around an octameric histone core consisting of two molecules each of H2A, H2B, H3 and H4
- Further compacted into smaller units
What are epigenetic modifications?
- DNA and chromatin methylation
- Protein (histone) acetylation
- Chromatin ubiquitination (targets proteins for degradation)
- Glycosylation (nutrient sensor)
- Phosphorylation (DNA double-strand breaks)
What is an example of an epigenetic modification?
o Example of an epigenetic mechanism in response to DNA damage: Phosphorylation of the histone variant H2A.X upon the induction of DNA-double strand breaks
What is DNA methylation?
- An addition of a methyl group onto DNA – usually on a cytosine site
- CpG islands: genomic DNA may be methylated at the 5th position of cytosine, typically in the sequence of CpG
- DNA methyltransferase catalyses the addition of CH3 (methyl) from the donor onto the DNA
- CpG island is a promoter region of a gene
- When the CpG island becomes very heavily methylated it switches OFF
How does DNA methylation cause gene silencing?
- Methyl-binding proteins recognise methyl groups
- Causes a repression complex after many bindings
How is DNA methylation aberrant in cancer?
- Global demethylation – increased transcription
- Focal CpG island hypermethylation – transcriptional repression
- Methylation-associated silencing of tumour suppressor genes one of the predisposing hits in Knudson’s classical two hit model of carcinogenesis = EpiMutation
How can DNMT inhibitors act as anti-cancer agents?
- PTEN/PI3K/Akt pathway physiologically plays a key role in the control of many processes essential for the cellular life
- The tumour suppressor PTEN negatively controls the PI3K/Akt pathway and its epigenetic loss, frequent in cancer cells, leads to the aberrant pathways activation
- DNMT inhibitors restore PTEN expression by epigenetic mechanisms
Describe the Agouti mouse study
Genetically identical mice
Agouti gene: gives the mouse the typical colour
Two groups of mice with different nutrition:
Normal diet + high in methyl donors:
* Methyl donors: Folic acid, vitamin Bs
Normal diet
Both groups of mice fed toxic bisphenylate (found in plastics)
Outcomes:
1. Methyl donor group
* Methylation of Agouti gene
* Despite bisphenylate
→ Thin, healthy mouse, brown coat colour
Normal group
* No methylation
* Bisphenylate brings about toxicity
→ Obese, diabetic mouse, like coat colour
What is histone methylation?
- Histone methyltransferases
- Histone demethylases
Trimethylation of lysine 4 on histone 3 (H3Kme3) is associated with transcriptionally active genes
Trimethylation of lysine 9 on histone 3 (H3K9me3) is associated with inactive genes
What is histone acetylation ?
- Histone acetyltransferases (HATs)
- Histone deacetylases (HDACs)
Regulated by the opposing actions of (HATs) which add and HDACs which take one off
What are the types of HDACs?
Class III HDACs – sirtuins (metabolism)
* NAD+ dependent HDACs – Class III
* Sirtuins 1-7
Involved in ageing and longevity as it mimics caloric restriction
E.g., resveratrol (red wine); pterostilbene (blueberries)
Class I, II and IV = metal dependent HDAC enzymes (Zinc = cofactor)
* Class I – HDACs
* Class II – IIa HDACs and IIb HDACs
* Class IV – HDAC 11
What are the types of cancer therapies based on altering the histone acetylation status of cells?
- Prototypical HDAC inhibitor Trichostain A – hydroxamic acid
o SAHA (Vorinostat) which is used clinically for CTCL
o Heavily acetylated histones cause the chromatin to decondense/open up which leads to cell death, apoptosis, killing of the cancer cells this is a result of accumulation of acetylation - Sodium butyrate – small chain fatty acid
o Important pre-biotic and good for microbiome
o Antiepileptic
o Histone deacetylase inhibitors
o Dietary sources
o Products of anaerobic bacterial fermentation in the gut
o Regulate anti-inflammatory immune responses and enhances the epithelial barrier function - Faecal microbiota transplantation (FMT)
o FMT = the administration of minimally manipulated microbial community from stool of a healthy donor into the patient’s intestinal tract
Differentiate between Heterochromatin and Euchromatin
Heterochromatin:
* Dense chromatin
* Inactive regions
Euchromatin:
* Open chromatin
* Active transcription
What can DNA double stranded breaks lead to?
These are lethal lesions
If they are not properly repaired, it leads to genomic integrity and carcinogenesis
What are the following associated with:
* H3K4me3
* H3K9me3
H3K4me3: Transcriptionally active genes
H3K9me3: transcriptionally inactive genes
Take home messages:
Very minor differences can have very different consequences
What are the enzymes associated with the following:
* Histone tail methylation
* Histone tail acetylation
Histone methyltransferases
Histone demethylases
Histone acetyltransferases (HAT)
Histone deacetylases (HDAC)
Describe what was observed in identical twin studies
Identical twins are born with the same epigenome
Differences increase in monozygotic twins as they age
Epigenetic profiles begin to diverge as they age: epigenetic marks are:
Removed at random
Changed through environmental influences
Is euchromatin or heterochromatin more susceptible to double stranded breaks?
Euchromatin is generally more susceptible to double-stranded breaks than heterochromatin. Euchromatin is a less compact and more transcriptionally active form of chromatin
What is the clinical application of HDACs?
The clinical application of HDACs centers around the use of HDAC inhibitors, which are drugs that can modulate HDAC activity and affect gene expression. HDAC inhibitors have been approved by regulatory agencies for the treatment of certain types of cancer, including cutaneous T-cell lymphoma and multiple myeloma.
In classical epigenetic studies, how could the Agouti gene be ‘over-ridden’?
The over-expression of the Agouti gene can be “over-ridden” by dietary changes that affect the epigenetic state of the gene.
Why would epigenetic changes be more favourable for tumour cells, as opposed to mutations in DNA?
Epigenetic changes are reversible: This means that epigenetic changes can be more easily adapted to changing environmental conditions
Epigenetic changes can affect multiple genes: This makes epigenetic changes more efficient in promoting the growth and survival of tumor cells.
Epigenetic changes can occur rapidly: Epigenetic changes can occur more rapidly than mutations in DNA
Epigenetic changes are less detectable: more challenging to treat
