The epigenome Flashcards
Genome
- The complete set of genetic material in a cell
- The DNA sequence that is present in a single full set of chromosomes
• Histone proteins and DNA form the first level of packing – the nucleosome
Packing solution
Histones
Nucleosomes
Fibres and higher structures
Chromosomes are the most densely packed form of genomic DNA
Epigenome
- 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”
- The epigenome is central to the regulation of gene expression
Epigenetic mechanism
- DNA Methylation
- Histone modification
- X-inactivation
- Genomic Imprinting
DNA methylation
- 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
- It requires S-Adenosyl Methionine to provide the methyl group
- In differentiated cells it occurs in CpG dinucleotides
DNA methylation enzymes
DNMT1, DNMT3a and DNMT3b
TET
Ten-Eleven translocation enzyme
TDG
Thymine DNA glycosylase
BER
Base excision repair
2-OG
2-oxoglutarate
DNA methylation and 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
Histone modifications
- 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 histone modifications
- Methylation
- Acetylation
- Phosphorylation
- Ubiquitination
H3K4Me3
Histone 3, the Lysine (K) at position 4 is tri-methylated
HAT1
Histone Acetyltransferase
EEHMT1
Histone Methyltransferase
HDAC1
Histone deacetylase
KDM1
Histone demethylase
Role of histone modifications
- 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
X-inactivation pt 1
- 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
X inactivation pt 2
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
Genomic 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)
- 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
ADME
Absorption
Distribution
Metabolism
Excretion
Enzymes related to mutated tumour cells
DNMT3A and TET1/2 Histone Acetyltransferases Histone Methyltransferases Histone Kinases Histone Readers (acetyl/methyl/phosphoryl) Histone Demethylases
Cancer and epigentics
Global DNA methylation is altered in tumour cells
Hypermethylation of tumour suppressor genes
Hypomethylation of tumour activating genes
Epigenetic enzymes are often mutated in tumour cells
Pharmacoepigenetic drugs
• DNA Methyl Transferase Inhibitors 5-Azacytidine (Vidaza) Myelodysplastic syndrome Histone Deacetylase Inhibitors Romidepsin (Istodax) Cutaneous T-cell lymphoma Seven drugs FDA-approved so far