Epigenome Flashcards
How is DNA packed?
- using histone proteins
- Histones and DNA form the first level of packing - the nucleosome.
What is the solution to fit in very long DNA into tiny nucleus?
- nucleosomes are wound up to form 30nm fibres
- fibers are then wound up further with scaffold proteins to generate higher order structures
- chromosomes are most densely packed form of genomic DNA
What are the two forms of nucleosome DNA arrangement (called chromatin)?
- euchromatin
-compartment A
-gene rich
transcriptionally active
- dispersed appearance (lighter area) - compartment B heterochromatin
- gene poor , less transcriptionally active.
- condensed appearance (darker area)
- full of repetitive DNA
What regulates gene expression?
- mechanisms that regulate how unwound, nucleosomes are and how far apart they are
- how accessible DNA is bc if DNA is inaccessible then it can’t be expressed.
Define 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 DNA methylation?
- addition of methyl group in the 5’ position of a cytosine
- this is catalysed by DNA methyltransferase enzymes : DNMT1, DNMT3a and DNMT3b
- requires S- adenosyl methionine to provide the methy group
- in differentiated cells it occurs in CpG dinucleotides.
How does DNA methylation and gene expression change transcription?
- DNA methylation turns transcription off by preventing binding of transcription factors
- DNA methylation patterns change during development and are an important mechanism for controlling gene expression.
What is histone modification?
- addition of chemical groups to the proteins that make up nucleosome
- there are a large number of known histone modifications (>100) and many are of unknown function
- large range of enzymes catalyse modification .
What are some common histone modifications?
- methylation
-acetylation
phosphorylation - ubiquitination
=> many different amino acids can be modified and may have 1-4 groups added
=> this gives large number of modifications
How are histone modifications named?
- named based on histone affected, amino acid, and the actual modification.
- Eg: H3K4Me3
histone 3,lysine (K) at position 4 is tri methylated.
What are examples of writers?
=> writers are enzymes that add histones
- histone acetyltransferase (HAT1)
- histone methyltransferase (EHMT1)
What are examples of erasers?
=> enzymes that remove histone modification
- histone deacetylase (HDAC1)
- histone demethylase (KDM1)
What are examples of readers?
=> readers are proteins that bind to histone modification and effect gene expression hence protein production.
- bromodomain and extra-terminal (BET)
- Chromodomain proteins (CBX1)
what is the role 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 modification occur concurrently (acetylation, methylation etc happen at the same time)
What is x- inactivation?
- every human female somatic cell (non reproductive cells) has 2 X chromosomes and every human male has an X and an Y
- Y chromosome has virtually no genes
- by inactivating one X chromosome in females it ensures all human somatic cells have the same number of active copies of every gene.
Outline the process of X- inactivation.
- the Xist gene is transcribed as a long noncoding RNA (lncRNA) from the x- activation centre (Cic) 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
What is 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.
What is impriniting?
- selective expression of genes related to parental origin of the gene copy
- every autosomal genes tend to be found in clusters
- there are very few imprinted genes (~250)
outline the mechanism of imprinting genes.
- imprinting is mediated by imprinting control regions (ICRs)
- one copy is silenced by DNA methylation leading to inactivation
- LncRNA are essential to the process
- imprinting patterns are reset during gametes
How can we apply epigenetic to cancer?
=> global DNA methylation is altered in tumour cells
-hypermethylation of tumour suppressor genes - hypomethylation of tumour activating genes
What are some epigenetic enzymes that are mutated in tumour cells?
- DNMT3A and TET1/2
- histone acetyltransferase
- histone methyltransferases
- histone kinases
- histone readers (acetyl/methyl/phosphoryl)
- histone demthylases.
What are examples of pharmacoepigenetic drugs?
=> DNA methyl transferase inhibitors
- 5- Azacytidine (Vidaza)
- myelodysplastic syndrome
=> Histone deacetylase inhibitors
-romidepsin (istoddax)
=> seven drugs FDA- approved so far.
