16- Epigenome Flashcards
define the epigenome
sum of all the (heritable) changes in the genome that don’t occur in the primary DNA sequence but do affect gene expression
epigenetic changes result in a change of phenotype not genotype
what is the DNA packaging problem?
the challenge of fitting the long, linear DNA molecules into the small space of the cell nucleus
cells must organise and compact the DNA to ensure efficient storage, replication and access to genetic information
define the genome
the complete set of genetic material in a cell
what is the hierarchal organisation of DNA?
nucleosomes - histone proteins wit 147bp of DNA wrapped around
30nm fibre
higher-order chromatin fibre
chromosomes
describe the two forms of chromatin
euchromatin - compartment A
- gene rich
- transcriptionally active
- has a more dispersed appearance as the nucleosomes are less close together making it more accessible for DNA activity
- responds to developmental/ environmental cues
- unique DNA sequences
heterochromatin - compartment B
- gene poor
- transcriptionally inactive
- denser appearance as the nucleosomes are closer together
- repetitive DNA sequences
list the four name epigenetic mechanisms
DNA methylation - methyl group added to a cytosine in a CpG dinucleotide
histone modifications - methylation, ubiquitination, acetylation, phosphorylation are the most common. affect chromatin structure and accessibility for transcription
X-inactivation - random, independent inactivation of one X chromosome in every somatic cell of a female
imprinting - silencing/ selective expression of a gene based on parental origin
how do epigenetic changes work with a chemical tag?
if a heterochromatin segment is inaccessible, a chemical tag can bind to DNA/ associated histones, force the nucleosomes to unwind to make the gene accessible to transcriptional machinery = can be turned on or off
mechanism for DNA methylation
cytosine typically at a CpG dinucleotide
get methyl from S-adenosyl methionine (SAM) catalysed by DNA methyltransferase (1,3a,3b)
the methyl is added onto cytosine
5-methylcytosine product and S-adenosyl homocysteine (SAH) by-product
mechanism for DNA demethylation
three steps under the activity of TET enzymes
5-methylcytosine - OH group added = 5-hydroxyethyl cytosine (recognised as an epigenetic signal)
OH group converted to formyl group = 5-formylcytosine
formyl group converted to carboxyl group = 5-carboxylcytosine
5-carboxylcytosine can undergo passive or active demethylation
passive demethylation - left to degrade overtime, loses its methyl group
active demethylation - base excision repair catalysed by thymine DNA glycosylase which recognises the modified cytosine, removes it and then adds it back in unmodified
how does DNA methylation affect gene expression?
DNA methylation occurs at CpG islands/ dinucleotides - often located at promoter regions
when unmethylated = TFs can bind, gene expression activity occurs normally
when methylated = TFs can’t bind, gene expression is repressed
describe the three types of enzymes involved in histone modifications - with examples
readers = bind to modified histone sites – affect gene expression and protein production
e.g. BET proteins, chromodomain proteins
writers = add histone modifications
e.g. histone methyltransferase, acetyltransferase
erasers = remove histone modifications
e.g. histone demethylase, deacetylase
where do histone modifications occur?
on the C- and N-terminal tails that stick out of nucleosome structures – have amino acids running down them
describe the effects of histone modifications
histone acetylation
= unwinds chromatin structure – from heterochromatin to euchromatin, making DNA more accessible to transcriptional machinery
= gene expression can occur
histone methylation
= can activate/ repress gene expression, depending on where it occurs
what is the importance of x-inactivation?
ensures genetic balance for gene dosage and equal gene dosage between males and females
males only have one X chromosome (heterozygosity) and their Y chromosome has virtually no genes
mechanism for X-inactivation
Xist gene on the X chromosome is transcribed into long non-coding RNA (lncRNA) which is non-protein-coding RNA
Xist lncRNA binds all over X chromosome
results in histone deacetylation of histones associated with that X chromosome
deacetylation = compacts chromatin structure, less accessible for gene expression
DNA methylation occurs – encourages repressive, more compact chromatin structure. makes it less accessible, decreases gene expression
inactivated X chromosome becomes a dense, compact transcriptionally active heterochromatic region = Barr body
