Lecture 30 - Epigenetics Flashcards
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 is the structure of a nucleosome?
146 bp of DNA wrapped around octamer core
Octamer: 2 of each of the following: • H2A • H2B • H3 • H4
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
Where does DNA methylation occur?
Methyl group at 5th position on the cytosine
Typically in the CpG islands
What is seen epigenetically in cancer?
Compare this with normal situations
Normal:
Global methylation
Cancer:
- Aberrant DNA methylation –
- Aberrant histone acetylation –
- Global demethylation → increased transcription
- Focal CpG hypermethylation → transcriptional repression (of TSGs in particular)
What are DNMT inhibitors used for?
Anti-cancer agents
DNA methylation inhibitors
No methylation of the tumour suppressor genes → removal of one of the ‘hits’
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 the regulation of histone acetylation
Regulated by the opposing actions of HAT and HDAC
HAT: histone acetylases (writer)
HDAC: histone de-acetylase (eraser)
What is the definition of epigenetics?
“Heritable changes in gene expression and cellular phenotype that are independent of changes in the underlying DNA sequence”
How many genes in the human genome?
20,000 - 25,000
How much of the genome is genes that encode protein?
What is the importance of the rest?
1-2%
The vast remainder of the sequences in the human genome are yet to be fully understood
Non-coding DNA:
• Previously considered “Junk DNA”
• Regulatory sequences - critical biochemical functions (such as miRNA)
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
Describe the effect of diet on epigenetics and disease
Apis mellifera study (honey bee)
3 types of bee:
• Worker bee (female)
• Drone (male)
• Queen bee (female)
Very different size and life span between the different bees
The only thing that determines whether a bee will become a worker or a queen is differential feeding during development
Royal jelly consumption throughout development → queen bee development
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
How is all the DNA in cells organised?
Chromatin: complex structure made up of nucleosomes
Nucleosomes are separated by 100 bp linker
Further compacted into 30 nm fibres
What is the Epi-Twin Study?
Big study going on in currently the UK
Study many many identical twins
Sequencing of the entire methylome: every methylation mark in genome
They will track the changes in the methylome over time
Describe the role of histones in DNA double stranded breaks
After a double stranded break, HSA.X is rapidly phosphoryated
Heterochromatin is much less susceptible to double stranded breaks, because it is so compacted
That is one way it protects itself
Is euchromatin or heterochromatin more susceptible to double stranded breaks?
Euchromatin is more susceptible, as it is less compacted
Describe methylation
Once there is methylation of the DNA strand at the CpG islands, a methyl-binding protein will come and bind to it
This adds bulk to the DNA
Transcription factors cannot access the DNA
No DNA transcription
In which regions are CpG found?
Promoters
Why would epigenetic changes be more favourable for tumour cells, as opposed to mutations in DNA?
Epigenetic changes are reversible, compared to DNA mutations, which aren’t
This gives the cancer cell a lot of flexibility
e.g. Epigenitic changes allow it to leave tissue and metastasise
Once it gets to a new location, it can rapidly undo these changes so it can colonise
This is not possible with changes to the DNA
Describe the various histone modifications
Histone acetylation
• More open chromatin
• Transcriptionally active
Histone methylation
• Transcriptionally inactive
What is the clinical application of HDACs?
HDACi’s have been developed and are being using clinically
Example:
1. Sodium butyrate (an HDACi)
Leads to cell death specifically in cancer cells
- Vorinostat
Selective death in cancer cells
What is the effect of the Agouti gene in mice?
Homozygous Agouti: Lethal
Heterozygous: Obese, cancer, diabetes
In classical epigenetic studies, how could the Agouti gene be ‘over-ridden’?
When the mother was fed a diet rich in methyl group donors (e.g. folate), the Agouti gene was methylated, and thus silenced
The phenotype was a normal healthy mouse
