Nucleosomes; chromatin and chromosome structure Flashcards
Why is the chromosome structure needed?
- To package the DNA so it all fits inside the cell
- To protect the DNA from breakage/ chemical attack
- To allow controlled access to only those parts that need to be active in a particular cell.
Describe the structure of the nucleosome
- Nucleosome consists of an octomer of histone proteins - H2a, H2b, H3 and H4
- 2 of each of these form the octomer
- The DNA wraps around the octomer to form the nucleosome
The histone proteins are very positively charged, contain high % of arginine and lysine residues, while DNA is negatively charged. What does this mean for the interaction between the two?
- It emans that the interaction between the histone proteins and the DNA is very strong
Briefly describe the structure of the histone proteins within a nucleosome
- H3 and H4 histones are clustered in one region while H2A and H2B are clustered within another egion of the nucleosome
- The globular regions of the hsitone proteins tend to be in the core of the nucleosome while the histone tails project away from the core
What do a multiple nucleosomes linked together along a stretch of DNA look like?
- Look like beads on a string
Describe an experiment used to visualise nucleosome organisation
- Partially digest DNA in micrococcal nuclease and then run the DNA using gel electrophoresis
- This gives DNA fragments with several nucleosomes
- The resulting ladder can be used to measure nucleosome spacing
- The ladder of fragments is produced because the only parts of the DNA that the micrococcal nuclease is able to cut is the linker DNA
- The ladder reveals that nucleosome spacing is regular but varies between species/cell types
What is the role of Histone H1 in the packaging of chromatin?
- Histone H1 binds to both the nucleosome and the linker DNA between nucleosomes which helps organise the DNA into a 30nm fibre
- This is because Histone H1 from adjacent nucleosomes are able to interact with each other and pack the nucleosomes together
Apart from interaction between adjacent Histone H1’s, how else are nucleosomes be brought together to form the 30nm fibre?
- You can get interaction between the histone tails of one nucleosome with the histone core of an adjacent nucleosome
How is chromatin further packaged once the 30nm fibre is formed?
- A set of proteins, e.g. topoisomerase II, form a chromosomal scaffold
- Loops of the 30nm fibre then interact with this chromosomal scaffold at particular points
What is the advantage of using chromosome scaffold to organise chromatin?
- Fact that loops of 30nm fibre interact with chromosome scaffold means that each loop can be modified independnetly from another loop
Give some examples of non histone chromatin structural proteins
- High Mobility Group
- Topoisomerase II
- Polycomb/Trithorax group
- Telomere binding proteins e.g. SIR proteins in yeast
What are the different types of chromatin?
What are the 2 types of heterochromatin?
- Constitutive - Found around the centromere and telomere plus satellite sequences, same in all cells
- Faculative - Contains silent genes, regulated genes and differs between cell types
Describe some of the macro changes that occur to chromatin during DNA metabolism (DNA syntehsis and degradation)
- Individual loops of the 30nm fibre can be decondensed to allow easier access to regions of the DNA required for gene expression, repair and replication
Explain how chromatin structure is dissassembled during transcription
- RNA polymerase advances up the DNA on the nucleosome
- DNA is then displaced from the nucleosome and forms a closed loop with the RNA polyermase as it does so
- Torsion ahead of the RNA polymerase then causes the nucleosome to be transfered from infront of the RNA polyermase to behind it - The DNA is then re-wound around the nucleosome
Explain how chromatin structure is dissassembled during DNA replication
- Nucleosomes ahead of the replication fork are removed
- They are then seperated into two groups: H3/H4 core tetramer and the H2A and H2B
- Nucleosomes are then re-added to DNA behind or after the replication fork using a mixture of locally used old histones and new histones
- Because DNA has been replicated you require double the amount of nucleosomes
Explain how chromatin structure is dissassembled during DNA repair
- Due to a double strand break two things can occur to the nucleosome/s that are located where the break is:
- Eviction of the nucleosome/s from the area of the break
- Sliding of the nucleosomes away from the break
- Both of these allow access to the broken DNA by the DNA repair machinery
Histone remodelling factors are responsible for modifying histone proteins during processes such as DNA replication/transcription. What are some of the processes that they’re able to catalyse?
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Desposition (sliding) - Catalyses sliding of nucleosomes to make space and then deposition of new nucleosome
- Can also slide/move nucleosomes to prevent DNA bindng protein from accessing its binding site
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Site exposure - Can catalyse reposition nucleosomes to exposure binding site of a DNA binding protein on DNA
- Can also cataylse ejection of a nucleosome to exposure a binding site
- Can also unwrap a part of the DNA from the nucleosome to expose a binding site
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Altered composition - All histone types have dimers which impart different effects on the DNA wrapped around them so there may be a situation when one histone dimer in a nucleosome needs to be exchanged for another and this can be done via these factors
- Dimers can also be ejected from the nucleosome
What regions are conserved between the different families of the transcription histone remodelling factors?
- HELICc region
- DExx region
- Both these regions are ATPases
Where do most of the histone modifications occur on the histones themselves? What does this mean for inheritance of these modifications?
- Most histone modifications occur on the histone tails
- This means that these histone modifications can be read without unwrapping the nucleosome making it easier for these modifications to be passed down
What is the histone code hypothesis?
- The hypothesis states that post-translationally modified histones, either alone or in various combinations serve as extremely selective binding sites for specific regulatory proteins that drive distinct nuclear processes e.g. transcription, replication, repair.
For each type of post-translational histone modification, giev the name of the group of enzymes that catalyse each process
- Histone acetylation - Carried out by histone acetyltransferases
- Histone deacetylation - Carried out by histone deacetylases
- Histone methylation - Carried out by histone methyltransferases
- Histone demethylation - Carried out by histone demethylases
- Histone phosphorylation - Carried out by Protein kinases
- Histone dephosphorylation - Carried out by protein phosphatases
What are some of the variants of the core histones?
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Histone H3 variants
- H3.3
- CENPA - only found in centromeres
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Histone H2A variants
- H2AX - involved in DNA repair and recombination
- H2AZ
- macroH2A
- H2ABBD
- Histones H4 and H2B don’t have any known variants
