The Epigenome Flashcards
1
Q
Define what is meant by the Genome?
A
- The complete set of genetic material in a cell
- The DNA sequence that is present in a single full set of chromosomes
2
Q
What is meant by the Nucleosome?
A
The Nucleosome is the Histone proteins and DNA that form the first level of packing
3
Q
What is the packing solution?
A
- Nucleosome are wound up to form 30 nm fibres
- Fibres wound up further with scaffold proteins to generate higher order structures
- Chromosomes are the most densely packed form of genomic DNA
4
Q
What’s are the two types of Chromatin?
A
Euchromatin and Hetero Chromatin
5
Q
What is Euchromatin?
A
- Gene rich
- Transcriptionally active
- Dispersed appearance
- Unique DNA sequences
6
Q
What is Hetero chromatin?
A
- Gene poor
- Less Transcriptionally active
- Condensed Appearance
- Repetitive DNA sequences
7
Q
What is meant by the Epigenome?
A
- The sum of all the heritable changes in the genome that do not occur in the primary DNA sequence and that affect gene expression
8
Q
What does an Epigenetic change result in?
A
A Change in the phenotype but not in the genotype
9
Q
Give an overview of the Epigenome
A
- The Epigenome is central to the regulation of gene expression
- Gene expression is regulated by DNA methylation and Histone modifications
- X activation and imprinting are important Epigenetic mechanisms for controlling expression from groups of genes
10
Q
What are Epigenetics used for?
A
Used to identify novel drug targets
11
Q
What are some epigenetic mechanisms?
A
- DNA Methylation
- Histone modification
- X-inactivation
- Genomic Imprinting
12
Q
Describe what DNA methylation is
A
- In humans, it is the addition of a methyl group in the 5’ position of a cytosine
- The reaction is catalysed by the DNA methyltransferase enzymes
- Requires an S-Adenosyl Methionine to provide the methyl group
- Occurs in the CpG dinucleotides in differentiated cells
13
Q
How is DNA Methylation linked to gene expression?
A
- DNA methylation turns transcription off by preventing the binding of transcription factors
- DNA methylation pattern changes during development and are an important mechanism for controlling gene expression
14
Q
What is Histone Modification?
A
- The addition of chemical groups to the proteins that make up the Nucleosome
- There are large numbers of known Histone modifications (>100) but many of them are unknown functions
- There are a wide range of enzymes that can catalyse modification’s
15
Q
What are some common modifications?
A
- Methylation
- Acetylation
- Phosphorylation
- Ubiquitination
16
Q
What happens when amino acids are modified?
A
- Amino acids can be modified and can have anywhere between 1-4 groups added
- This gives a large number of modifications
- Others are known but poorly understood
17
Q
What are Histone modifications names based on?
A
Based on 3 different factors:
- The Histone
- The amino acid
- The Actual modification
18
Q
What are the 3 types of Histone modifiers?
A
- Writers
- Erasers
- Readers
19
Q
Give some examples of “writer” Histone modifiers
A
- Histone Acetyltransferase - HAT1
- Histone Methyltransferase - EHMT1
20
Q
Give some examples of “Erasers” Histone modifiers
A
- Histone Deacetylase: HDAC1
- Histone Demethylase: KDM1
21
Q
Give some examples of “Reader” Histone modifiers
A
- Bromodomain and extra-terminal (BET) proteins: BRD2
- Chromodomain proteins: CBX1
22
Q
What are the roles of Histone modifications?
A
- Histone acetylation at Lysone residues relaxes the chromatin structure, by reducing positive charge on the Histones and makes it accessible for transcription factors
- Histone methylation is more complex and can repress or activate transcription depending on where it occurs
- Histone modifications can occur concurrently and so their effects will interact
23
Q
What is X-Inactivation?
A
- The inactivation of one of the 2 X chromosomes in every somatic cell in females
- This is needed as the Y chromosome has virtually no genes, so there is only one group of each chromosome gene in males (Hemizygosity)
24
Q
What does X Inactivation ensure?
A
Ensures that every somatic cell in all humans has the same number of active copies of every gene
25
Describe how X inactivation works (PART 1)
- The Xist gene is transcribed as a long noncoding RNA (lncRNA) from the X-inactivation centre (Xic) and binds all over the X-chromosome
- Histone acetylation removed and histone and DNA methylation occurs
26
Describe how X inactivation works (PART 2)
- Inactive X-chromosome is heterochromatic – Barr body
- Tsix is derived by transcription in the opposite direction and antagonises Xist RNA to keep one X active
27
Give an example of X inactivation
- All tortoiseshell cats are female
- Tortoiseshell cats have one X with an orange fur allele and one X with a black fur allele
- Random X inactivation results in patches of orange and black fur
28
What is Genomic Imprinting?
- It is the selective expression of genes related to the paternal origin of the gene copy
- Every autosomal gene has one Paternal and one Maternal copy
29
How are imprinted genes usually found?
Imprinted genes tend to be found in clusters
30
How common are imprinted genes?
Not very common. Very few imprinted genes (~250)
31
What is imprinting mediated by?
By the Imprinting control regions (ICRs)
32
How does imprinted genes work?
- One copy is silenced by DNA methylation catalysed by DNMT3a and Histone methylation leading to inactivation
- LmcRNAs are essential to the process
- Imprinting patterns are reset during gamete formation
33
What are the two general mechanisms for epigenetic modification?
- DNA methylation
- Histone modification
34
What are the two specific mechanisms for epigenetic modification?
- X inactivation
- Genetic Imprinting
35
CANCER EPIGENETICS
Where is the global DNA methylation altered in tumour cells?
- Hypermethylation of tumour suppressor genes
- Hypomethylation of tumour activating genes
36
Where are epigenetic enzymes often mutated?
In tumour cells
37
Give some examples of these Epigenetic enzymes
- Histone Methyltransferases
- Histone Acetyltransferases
- Histone Kinases
- Histone readers
- Histone Demethylases
38
Give some examples of Pharmaco - Epigenetic drugs
DNA Methyl Transferase Inhibitors
- 5 - Azacytidine (Vidaza)
- used to Treat Myelodysplastic syndrome
39
Give some examples of Pharmaco - Epigenetic drugs
Histone Deacetylase Inhibitors
- Romidepsin (Istodax)
- Used to treat Cutaneous T-cell lymphoma
