The Epigenome Flashcards
What is the nucleosome?
Histone proteins and DNA form the first level of packing – the nucleosome
What is 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
What is chromatin? What are the two types of chromatin?
A generic term for the wound up DNA of which there are two types:
Euchromatin- gene-rich, transcriptionally active, dispersed appearance, unique DNA sequences
Heterochromatin- gene-poor, less transcriptionally active, condensed appearance, repetitive DNA sequence
What is the 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”
What is the purpose of the epigenome?
The epigenome is central to the regulation of gene expression
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
Epigenetics is being used to identify novel drug targets
What are the different types of epigenetic mechanisms?
Epigenetic Mechanisms:
- DNA Methylation - Histone modification - X-inactivation - Genomic Imprinting
What is DNA methylation and what occurs?
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
- DNMT1, DNMT3a and DNMT3b
It requires S-Adenosyl Methionine to provide the methyl group
In differentiated cells it occurs in CpG dinucleotides (the p stands for phosphate group)
The DNA methyltransferase catalyses the removal of a methyl group from S-Adenosylmethionine and places it onto the 5 position of the cytosine aromatic ring there giving ud 5-methylcytosine and S-Adenosyl homocysteine
What are the steps of demethylation?
For demethylation we have to have a group of TET enzymes that catalyse changes in that group that eventually result in the methyl being removed
The steps are:
Add a hydroxyl group
Change that group to a formyl group
Maybe change it to a carboxyl group
When it is in one of the last two groups the TDG catalyses a reaction that removes the hydroxyl cytosine group when it encounters them in the DNA
A process called base-excision repair (BER), catalysed by TDG returns the cytosine without the hydroxyl to the DNA
What does DNA methylation do?
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
What is histone modification and the different types?
This is the addition of chemical groups to the proteins that make up the nucleosome
There are a large number of known histone modifications 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
How are histone modification named?
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
What are the different types of histone modifiers?
Writers are enzymes that add histone modifications:
- Histone Acetyltransferase - HAT1
- Histone Methyltransferase - EHMT1
Erasers are enzymes that remove histone modifications:
- Histone Deacetylase - HDAC1
- Histone Demethylase - KDM1
Readers are proteins that bind to histone modification and alter gene activity and protein production:
- Bromodomain and extra-terminal (BET) proteins – BRD2
- Chromodomain proteins – CBX1
What are the roles of histone modification?
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?
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 – referred to as a Barr body under the microscope
Tsix is derived by transcription in the opposite direction and antagonises Xist RNA to keep one X active
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)
