Epigenetics Flashcards
what is epigenetic?
- epi means above or beyond/below
- refers to a range of chemical modification that control gene accessibility but do not alter the underlying genetic code
what are the two main targets of epigenetic modifications?
- DNA modification - methylation
2. Histone modification - chemical modification of proteins that surround the DNA
what are the characteristics of DNA methylation
- addition of methyl group to C-5 position of cytosine residues
- most cytosine methylation occurs in 5’-CG-3’ sequence
- occurs almost exclusively at cytosines that are immediately followed by guanine CpG dinuleotide
what are CpG islands? where are they found?
- CpG sites are non-randomly distributed throughout the genome concentrated in hot spots or GpG rich regions knows as CpG islands
- they re found in 50% of promoter region of genes
the human genome is methylated uniformly
A. true
B. false
B. false, human genome is not methylated uniformly, it contains regions of unmethylated segments interspersed by methylated regions
where is 5’ methyl cytosine found?
it is found in approx 4% of genomic DNA primarily at cytosine-guanine dinucleotides (CpGs)
what does DNA methylation with a. promoter region and b. CpG islands result in ?
a. methylation with promoter region correlates with transcriptional silencing
b. methylation of CpG islands is believed to dysregulate gene transcription - through the inhibition of TF binding either directly or indirectly via histone activation
Define the following
a. DNMTs
b. SAM
c. SAH
a. DNA methylation writers are a group of enzymes refried to as DNA methyl transferases (DNMTs)
b. S-adenosyl methionine (SAM) is converted to S-adenosyl homocysteine) through methyl group transfer from SAM to SAH and is catalysed by DNMTs
how many DNMTs are present in mammals?
there are 4 DNMTs
- DNMT1 - maintenance methylase
- DNMT2
- DNMT3a and DNMT3b - ‘de novo’ methylases
- DNMT3L
what is the function of DNMT1 and requirement to produce the effect?
DNMT1
- maintains the pattern of DNA methylation after DNA replication
- requires hemi-methylated DNA substrate to produce the DNA pattern methylation on the newly synthesised strand
what is the function of DNMT3a and DNMT3b?
- adds methyl groups to CG dinuleotides which are previously unmethylated on both strands
- re-establish the methylation pattern
why are DNMTs required?
- DNMTs are required for transcriptional silencing of a number of sequence classes
- DNMT3B or DNMT1 deficient mice - embryonic lethal
- DNMT3A null mice die by 4 weeks
what is the role of DNA methylation?
plays a role in
- long term silencing of genes
- silencing of repetitive elements (e.g. transposons)
- X-chromosome inactivation
- in the establishment and maintenance of genes
- supresses the viral gene expression
- supresses any deleterious elements that have been incorporated into genome of host over time
- in carcinogenesis
how is cytosine converted into 5-methylcytosine?
- At CpG dinucleotides
- displaces TFs
- attracts methyl bidding proteins which are associated with gene silencing and chromatin compaction
what is chromatin made of?
chromatin is made up of DNA, RNA and proteins (mainly histone and some non-histone acidic proteins)
what is the function of chromatin?
- packages DNA
2. regulates DNA accessibility through chromatin structure modification
what is the length of DNA inside and outside the nucleus?
outside the nucleus - 2m
inside the nucleus - 5-10 micrometer
- the chromatin packs the long DNA into a compact one found inside the nucleus
what are the two state chromatin is found in?
- euchromatin
2. heterochromatin
what are the features of euchromatin and heterochromatin?
euchromatin DNA - generally active - less compact (less intense staining) heterochromatin DNA - generally not active - compact (intense staining indicating tighter packaging)
what is nucleosome?
- it is fundamental repeating unit of chromatin
- DNA wraps around histones to form condensed nucleosomes
- made of ‘nucleosome core particle’ and ‘linker DNA’ (54bp DNA)
what is histone?
- it is the largest protein in chromatin
- highly conserved
- assembled into octameric complexes
what does the nucleosome core particle consists of?
histone octamer (146bp) + histone 1
what is composition of nucleosome?
nucleosome = core of 8 histone molecules + H1 histone + DNA
- histone octamer
- A 147bp DNA segment wrapped around histone octamer
- adjacent nucleosome connected via linker DNA (~60bp)
- histone H1 at the base of nucleosome near DNA binding to linker DNA
- space between the beads in 14nm
what is the histone core composed of?
1. two copies of each four histones x2 H2A x2 H2B x2 H3 x2 H4 2. structures domain called histone fold and unstructured 'N-terminal tail'
what is the function of nucleosome?
- acts as signalling hub by providing scaffold for the binding of chromatin enzymes
- displays a combinatorial array of post translation modifications (PTMs)
- PTMS further regulated the recruitment of chromatin enzymes and tunes both -
a. nucleosome stability
b. higher order compaction of chromatin
what is the role of epigenetic writers, readers and erasers in DNA modification?
- epigenetic writers introduce the chromatin modifications
- epigenetic erasers remove these modifications
- epigenetic readers - recognise the modifications and allow epigenetic regulator to bind to them at specific regions to facilitate gene transcription
what is the role of chromatin modifications in regulating DNA?
chromatin modifications play an important role in DNA regulation by regulating transcription, repair and replication
what are the features if ‘switched on’ and ‘switched off’ genes? in terms of
- activity of chromatin
- methylation state of cytosine
- acetylation state of histones
switched on -> transcription possible 1. active (open) chromatin 2. unmethylated cytosine 3. acetylated histone switched off -> transcription impeded 1. silent (condensed) chromatin 2. methylated cytosine 3. deactivated histone
what are the features of histone tail?
- forms 30nm fibre by forming H bonds with adjacent nucleosome tails
- histone tails provide site for covalent t modifications like phosphorylation, methylation, acetylation etc
- such modifications determine the interaction of histones with other proteins which in turn regulate the chromatin structure and transcription etc
what are the types of histone modifications?
- phosphorylation
- methylation
- acetylation
- ubiquitination
- biotinylation
acetylation is catalysed by which enzymes?
HAT - histone acetyltransferase (addition acetyl)
HDAC - histone deactylase (removal of acetyl)
how does acetylation reduce affinity of tail or what impact does it have on chromatin structure?
- it removes the +ve charge of the histone tail thus reducing the affinity for -ve charged phosphate groups of DNA
- this relaxes the high order chromatin structures
- it also increases the access of transcription factors to DNA through structural changes in nucleosome or nucleosomal arrays
what is a bromodomain?
- they are found in TFs
- BD recognise acetylated lysine through HATs residues on histone tails
what is methylation and it is carried out by which enzymes?
- methylation is the addition of methyl functional group to lysine or arginine of the histone tail
- it is carried out by “histone methyltransferase (HMT)”
- arg can be methylated once or twice but lys can be methylated once/twice or thrice
a. what is a non-coding RNA?
b. what is its prevalence in humans?
c. what is its role?
- non-coding RNA (ncRNA) is a RNA molecule that is not translated into protein
- in humans 97-98% of transcriptional output is ncRNA
- its function is to regulate gene expression at transcriptional and post-transcriptional level
what are the two types of ncRNA? what is it role?
- short ncRNA <200 nts (nucleotides)
- long ncRNA >200 its
- they both play a role in heterochromatin formation, DNA methylation targeting, histone modification and gene silencing