Epigenetics Flashcards
Define Epigenetics. Now.
Epigenetics is the study of the changes in the regulation of gene activity and expression that are not dependent on DNA sequence. This can refer to stable changes that may or may not be heritable between cells.
What are the effectors of epigenetic effects?
DNA methylation, histone modification and non-coding (nc)RNA regulation.
What is DNA methylation?
The addition of repressive methyl groups to DNA bases. In higher animals this takes the form of cytosine methylation at CpG islands, which are most densely clustered near transcription start sites in order to better regulate a gene.
What organisms use DNA methylation?
Cytosine methylation is present in humans, drosophila and in plants but not in worms or yeast.
What is deamination?
Cytosine can be deaminated to form uracil, a process which is often photoinduced.
What are the consequences of deamination?
It creates a transition mutation (U paired with G) that is corrected by uracil glycosylase.
What happens when methyl-cytosine is deaminated, and what are the consequences?
5-methyl-cytosine deamination creates a thymine base, a different mismatch/transition mutation which is more likely to go unnoticed and so introduce mutation into one of the daughter strands during replication.
What are the three hypotheses of how DNA methylation represses genes?
- Unmethylated DNA naturally has a more open structure allowing for easier binding of transcription factors and other non-histone proteins, including the PIC.
- Methyl groups actually impede the binding of TFs to DNA.
- Methylated CpG islands recruit methyl-CpG-binding Proteins that inhibit transcription. This is the most subtantiated theory.
How do methyl-CpG binding proteins interact with the methyl groups?
With their aptly named Methyl-CpG Binding Domains (MBDs)
What families of proteins possess MBDs?
• Methyl CpG Binding Proteins (I know, change the name)
o Most sequence specific family
o Examples include MeCP1, MeCP2, MBD1, 2 and 4.
• SRA-SET and RING finger associated domain proteins
o Examples include UHFR1 and UHFR2
• Zinc Finger proteins such as Kaiso
What are the two types of DNA methylation addition?
De novo and maintenance
What is maintanence methylation?
This is performed directly after replication to ensure that methyl groups are present on the daughter strand also, otherwise all methylation patterns would be lost within a few generations.
What facilitates maintanence methylation?
Methyltransferase enzymes are recruited to hemimethylated CpG islands and add on the new methyl group to the corresponding Cytosine.
DNMT1 is the methyltransferase responsible for Maintenance Methylation.
What is De Novo Methylation?
The addition of new methylation to totally unmethylated CpG sites by de novo methylases such as DNMT3a and DNMT3b.
When does De Novo Methylation occur?
mostly during development, shortly after fertilisation when the original methylation patterns are stripped away
What is the mechanism of De Novo Methylation?
How this is directed in order to maintain methylation is the right places and remove it at sequences needed for development is unknown, but often appears to be directed by sequence specific DNA binding proteins that recruit the methyltransferases.
What do DNMTs use as a substrate?
DNMTs use S-adenosyl methionine (SAM) as a source of methyl groups, transferring the Me group from SAM to the cytosine in the CpG island.
What does DNMT2 do and why?
It methylates tRNA cytosines (hence also being known as NSun2 tRNA methyltransferase). The exact purpose of this is unclear but knockout studies show that it is absolutely necessary for proper protein synthesis.
What happens to mouse embryos that have both DNMT3a and b knocked out and why?
DNMT3a and b are required for initial reprogramming of the genome so the mutants for both methylases (E and F) are not born and do not even develop into anything mouse-shaped.
What happens to mouse embryos that have either DNMT3a or b knocked out and why?
Mutants with only 3a knocked out (A) are born but are stunted, whereas 3b knockout is (B) more serious and the embryo does not develop.
What happens to mouse embryos that have DNMT1 knocked out and why?
As it is a methylase that is used during replication but not for de novo methylation, the DNMT1 knockouts survive for longer than double DNMT3 knockouts.
DNMT -/- is still a recessive lethal mutation that prevents embryos from developing for longer than ten and a half days and causes highly abnormal morphology of what does result.
What is the agouti gene?
Mice have a gene called agouti which produces a yellow hair colour. It switches on cyclically to produce banded hair that looks brownish.
What is the a agouti mutation?
The a mutation knocks out the agouti yellow colour. This is a recessive mutation so still produces the agouti phenotype with one regular agouti gene (A)
What is the Avy gene (Agouti Viable Yellow)?
The agouti gene does not turn off, leading to entirely yellow mice.