The epigenome Flashcards
Define genome
- The complete set of genetic material in a cell
* The DNA sequence that is present in a single full set of chromosomes
Describe the packing solution
- Nucleosomes are wound up to form 30nm fibres
- Fibres are then wound up further with scaffold proteins to generate higher-order structures
- Chromosomes are the most densely packed form of genomic DNA
Define euchromatin and hetrochomatin
Gene poor and gene-rich
refer to the diagram
What is the epigenome and what does it result in?
- The sum of all the (heritable) changes in the genome that do not occur in the primary DNA sequence and that affect gene expression
- An epigenetic change results in “A change in phenotype but not in genotype”
What is the function of the epigenome?
• The epigenome is central to the regulation of gene expression
How can gene expression be regulated?
- DNA methylation and histone modification are mechanisms by which gene expression is regulated
- X-inactivation and imprinting are important epigenetic mechanisms for controlling expression from groups of genes
What are the 4 epigenetic mechanisms?
- DNA Methylation
- Histone modification
- X-inactivation
- Genomic Imprinting
What is DNA methylation?
What is it catalysed by?
What does it require?
• DNA methylation in humans is the addition of a methyl group in the 5’ position of a Cytosine
• This is catalysed by DNA methyltransferase enzymes
o DNMT1, DNMT3a and DNMT3b
• It requires S-Adenosyl Methionine to provide the methyl group
How does DNA methylation regulate gene expression?
- In general, DNA Methylation turns transcription off by preventing the binding of transcription factors
- DNA methylation patterns change during development and are an important mechanism for controlling gene expression
Give some common examples of histone modifications
What is histone modification?
Histone modification
• This is the addition of chemical groups to the proteins that make up the nucleosome
• There are a large number of known histone modifications (>100) and many are of unknown function
• Large range of enzymes catalyse modification
Common Modifications
• Methylation
• Acetylation
• Phosphorylation
• Ubiquitination
• Many different amino acids can be modified and they may have 1-4 groups added
• This gives the large number of modifications
• Others are known but poorly understood
- Modifications are named based on the histone, the amino acid and the actual modification
- For example, H3K4Me3 means that on Histone 3, the Lysine (K) at position 4 is tri-methylated
Name the histone writers, readers and erasers
Writers • Histone Acetyltransferase - HAT1 • Histone Methyltransferase - EHMT1 Erasers • Histone Deacetylase - HDAC1 • Histone Demethylase - KDM1 Readers • Bromodomain and extra-terminal (BET) proteins – BRD2 • Chromodomain proteins – CBX1
What does histone acetylation and methylation do?
- Histone acetylation at Lysine 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
What is X inactivation and why do males not need it?
- This is the inactivation of one of the two X chromosomes in every somatic cell in females
- This is needed as the Y chromosome has virtually no genes, so there is only one copy of each X chromosome gene in males (hemizygosity)
- X-inactivation ensures that every somatic cell in all humans has the same number of active copies of every gene
Describe the mechanism of X inactivation
- 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
- 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
- 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
What is imprinting?
- Imprinting is the selective expression of genes related to the parental origin of the gene copy
- Every autosomal gene has one paternal and one maternal copy
- Imprinted genes tend to be found in clusters
- There are very few imprinted genes (~250)
What are imprinted genes mediated by?
- Imprinting is mediated by imprinting control regions (ICRs)
- One copy is silenced by DNA methylation catalysed by DNMT3a and histone methylation leading to inactivation
- LncRNAs are essential to the process
- Imprinting patterns are reset during gamete formation
What is Pharmacoepigenetics?
On image
Is DNA methylation altered in tumour cells?
What is hypo and hyper methylation?
Global DNA methylation is altered in tumour cells
• Hypermethylation of tumour suppressor genes
• Hypomethylation of tumour activating genes
Are epigenetic enzymes mutated in tumour cells?
Epigenetic enzymes are often mutated in tumour cells
• DNMT3A and TET1/2
• Histone Acetyltransferases
• Histone Methyltransferases
• Histone Kinases
• Histone Readers (acetyl/methyl/phosphoryl)
• Histone Demethylases
Give some Pharmacoepigenetic Drugs
DNA Methyl Transferase Inhibitors • 5-Azacytidine (Vidaza) • Myelodysplastic syndrome Histone Deacetylase Inhibitors • Romidepsin (Istodax) • Cutaneous T-cell lymphoma
