5 - Epigenetics Flashcards
Define epigenetics
and
Historical definition
Any process that allows a particular phenotypic state to be inherited without changes in the sequence of DNA
- Covalent modification of DNA (eg. methylation)
- Modification of histones
- Assembly of proteins or protein complexes on DNA (eg. transcription factors)
Historically: Process leading from fertilized zygote to organism
GIve the two barriers which Pol II has to overcome for transcription
What prevents Pol II from moving backwards during transcription?
- Histone tails at the entry site of the nucleosome
- Histone-DNA contacts at the nucleosome dyad
Secondary structure of the nascent (new) RNA restricts backwards movement of the polymerase during pauses, aiding transcription.
What is linker DNA?
The DNA exiting the nucleosome on either side
Bound by linker histones like H1 and contacts neighbor nucleosomes.
Give the core histones
H2A
H2B
H3
H4
Two of each in one histone.
What is energy (ATP) needed for to allow transcription under the dynamic model of transcription? (on a structural level)
To displace nucleosomes from specific DNA sequences
A remodeling complex displaces the histone octamer (nucleosomes slide along DNA, or reorganize the spacing between nucleosomes)
The most radical change is the total displacement of the octamer from DNA to generate a nucleosome free gap. Alternatively, H2A and/or H2B dimers can be displaced.
If nucleosomes are bound at a promoter, transcription factors (and RNA Pol) cannot bind. If transcription factors (and RNA Pol) are bound to the promoter, histone octamer cannot bind.
What determines which nucleosomes are to be displaced?
- Sequence specific factors bind to DNA
- Remodeling complex binds to site via factor
- Remodeling complex displaces octamer
Different cellular conditions can induce these factors and cause the remodelling complex to initiate displacement or reorganization of the nucleosomes over important (eg. promoter) regions of DNA.
True or false? Some activators of transcription can bind to DNA on a nucleosomal surface and do not require nucleosome displacement in order to occupy their sites on the DNA.
True!
Example: Hormone receptor and NF1 cannot bind simultaneously to the MMTV promoter in the form of linear DNA, but can bind when the DNA is presented on a nucleosomal surface.
Describe histone acetylation
Histone acetylation is associated with activation of gene expression
- Acetylation removes positive charge of histones, making negatively charged DNA bind more loosely.
- Histone acetyl transferases (HAT) acetylate.
- Histone deacetylases (HDACs) de-acetylate histones (associated with complexes of transcriptional repression)
Describe histone acetyl transferases
There are many HATs with different specificities (eg. specific to particular histones and particular positions).
- Often associated with transcription activators, forming large complexes.
What residues of histones can be methylated? What is the result of this?
Lysines and some arginines (with methyltransferases, this is reversible).
This can result in EITHER activation or repression, depending on the specific site of methylation.
Histone methylation is critical for ______? How?
Histone methylation is critical for heterochromatinization
Binding of HP1 to methylated histone H3 forms a trigger for silencing because further molecules of HP1 aggregate along the methylation chromatin domain.
Steps of heterochromatin formation:
- Chromatin nucleated at specific sequence and inactive structure propagates along chromatin fibre
- Genes are inactivated
- Length of inactive region varies from cell to cell (position effect variegation)
This variegation can cause patchy phenotypes. The probability that a gene will be inactivated in a given cell depends on its distance from the heterochromatin region (as the heterochromatin can extend)
Give detailed steps for the formation of heterochromatin (specifically telomeres)
Formation of heterochromatin:
- Rap1 binds to DNA
- Sir3/Sir4 binds to acetylated H3/H4 N-terminal tails
- Sir2 deacetylates histones
- Sir3/Sir4 complex polymerizes (heterochromatin formed)
- Sir3/Sir4 attach telomeres to nuclear matrix
