Epigenetics Flashcards
What is epigenetics?
This is a unique transcriptional programme that allows two cells with exactly the same genome to look completely different and carry out completely different functions i.e. organs or larvae –> fly transition.
This epigenome is stable through cell division and generations. At a basic level this is due to heterochromatin - dark non transcribed DNA and euchromatin - light transcribed DNA. Genes closer to heterochromatin are transcribed less than those that are far away. Can use this to analyse genes that are involved in modifications.
How is the difference between euchromatin and heterochromatin acheived?
Mediated by packig of nucleosomes which are 147bp wrapped twice around a histone. Epigenetic modifications take place on long unstructured histone tails rich in arginine and lysine.
What are the 5 types of epigenetic modifications?
Histone modification RNA Histone variants Chromatin remodelling DNA methylation
Describe how histone modifications and RNA turn on and off genes
Histones can be modified through methylation, acetylation, phosophorylation and ubiquination.
Acetylation can mask a lysine’s positive charge whilst methylation can’t.
Lysine -acetylation opens chromatin and increases expression
Lysine methylation is context dependant: H3K4 = increase expression, H3K27 - decrease
Tri-methylation of lysine 9 (H3K9me3) decreases expression
RNA is required to train/acquire some histone modifications but it is unclear how or why. Adding in RNAse = disappearance of some modifications.
How is DNA methylation involved in the epigenome code?
This occurs on Adenine in prokaryotes and C in eukaryotes.
Can only happen in CpG dinucelotides (not islands). This is a late event and is a long term switch off of DNA when present on promtor and body.
This is used to keep junk DNA quiet such as transposable elements, retroviruses and centromeres.
Evidence for this is: cytosine analogue that can’t be methylated causes reactivation of retroviruses. KO mice for methylation enzymes results in cancer - hypomethylation is a hallmark of cancer i.e. de-differentiation.
What writes the methylation code and how does it result in genes being switched off?
DMT1 is associated with the replication fork and maintains methylation on both strands
DNMT3a and 3b involved in de novo methylation
De methylation of DNA is a passive process due to replications. Rarely it can actively occur e.g. in early development and some cancers. This is done with TET enzymes (10-11 translocation protein) which converts 5-methyl-cytosine to 5-hydroxymethylcystosine. This is either a stable intermediate for the de methylation process or prevents binding of proteins that would normally.
Proteins bind to the methylated regions and recruit histone modifications. For examples MeCP2 binds to methylated CpGs and recruit HDAC which de acetylates.
So overall what are the signs seen on open expressed DNA vs closed non expressed DNA?
Repressive markers = H3K9/27me3, MBD (methylated binding domain proteins), methylation of CpG and HP1/Polycomb
Active markers = H3K4me3 and H3K4ac
What are chromatin remodelling factors for?
On its own DNA hypomethylation and histone modifications aren’t enough for TF to bind and interact with DNA. So CRF moves or displace nucleosomes and allow looping so that TF can bind an interact with enhancers and promotors. This interacts with polymerase II –> transcription.
How can we analyse histone modifications?
ChIP Seq - Chromatin immuno-precipitation and sequencing
What reads and writes the epigenome code?
Writers - kinases, acetyltransferases, methyltransferases and ubiquitin ligases
Eraser - phosphatases, HDAC and LSD1 etc.
Readers - effector proteins that read and intercept the code by binding onto the modifications.
How are histone molecules shared between the two strands during DNA replications?
At the replications fork histones are shared equally and then new naive histones are recruited and these recruit readers and writers to copy the code from the origonal histones.
Give some examples of diseases related to chromatin
Weaver syndrome - H3K27 methyltransferase mutations . Causes overgrwoth, advanced bone age, body dysmorphisms, learning difficulties and macrocephally.
Brachydactyly - HDAC4 mutation - intellectual disability, behavioural problems, dysmorphisms, obesity and brachydactyly.
ATR-x sydrome - chromatin modelling factor mutation - alpha thal, developmental delay, characteristic facial appearence, microcephaly and genital abnormalities.
