Chromatin structure and histone code Flashcards
What are histones?
Histones are proteins responsible for the first level of packaging.
What are nucleosomes?
DNA wrapped around 8 core histones (then one more histone holding them together) is called a nucleosome.
The octamer core is made up of a pair of H2A, H2B, H3 and H4 histones. The positively-charged N-terminal tails are outside the octamer core.
Describe the four levels of DNA.
1) Histones are proteins responsible for the first level of packaging, creating nucleosomes. This nucleosome structure increases DNA packaging 7-fold.
2) Nucleosomes pack themselves into 30nm fibers called solenoids, constituting the second level of packaging. This increases the packaging 6-fold.
3) The solenoid fibres pack themselves into 80-100 nm fibres, constituting the third level of packaging. This increases the packaging 3-fold.
4) The fourth level of packaging is represented by the mitotic chromosome. This represents 10,000-fold packaging.
What do chromosomes predominantly consist of?
- DNA
- histone proteins
- non-coding RNA
- non-histone proteins
What does compaction of nucleosomes involve?
- linker histones (eg. H1)
- interactions of histones tails with adjacent nucleosomes
- binding of packing proteins to histone tails (this plays a vital role in gene access)
Describe the situations when chromosome structure is not static.
During transcription or DNA replication, nucleosomes must be removed from the DNA in front of the polymerase, and replaced behind the polymerase. Histone remodelling factors are enzymes that remove and replace nucleosomes.
Briefly, list some differences between euchromatin and heterochromatin.
EUCHROMATIN:
- lightly staining areas of chromatin
- rich in genes
- made up of nucleosomes, but not dense, higher order packaging
HETEROCHROMATIN
- darkly staining areas of chromatin
- few genes
- dense, higher order of packaging of nucleosomes
Name and describe the two types of Heterochromatin.
CONSTITUTIVE HETEROCHROMATIN:
The constitutive heterochromatin remains condensed throughout the cell cycle and development. This chromatin contains highly repetitive sequences that are not transcribed and play a role in chromosome structure.
FACULTATIVE HETEROCHROMATIN:
The facultative heterochromatin contains genes that are not expressed in that cell type. This DNA is as tightly packaged as constitutive heterochromatin, but it may be packaged as heterochromatin in other cell types.
What determined whether nucleosomes are packaged as euchromatin or heterochromatin?
There is one key level of control: chemical modification of lysine residues on histone tails, such as acetylation, methylation, etc.
Describe the other levels of structure in chromatin, the loops and chromatin domains.
Chromosomes are treated to extract histones and most non-histone proteins. They don’t completely fall apart. Instead, they appear as long DNA loops attached to a scaffold of tightly bound proteins.
There is evidence that suggests that each loop may have a different degree of chromatin compaction. The scaffold isolates the chromatin in one loop from the next loop. So, one loop may have open chromatin and active genes, while the neighbouring loop may be tightly packed as heterochromatin.
Name the method learnt to investigate chromatin structure and describe it.
The method is DNAse digestion.
DNAse I cuts double-stranded DNA. Histone binding protects the DNA from DNAse digestion.
We do, however, have DNAse I sensitive sites (HSS):
- sequences of DNA without histones
- it may be naked DNA or binding transcription factors
- cut by very brief digestion with DNAse I
- found in promoters and enhancers
If the DNA is tightly packaged in higher order chromatin structures, how can all these proteins get to the DNA?
First, transcription factors open up the chromatin structure. Then, they recruit basal transcription factors. (TF2A,TF2B,…)
How do the transcription factors open up the chromatin structure?
The transcription factors recruit chromatin modifying enzymes via a nuclear coactivator (NCoA) or corepressor (NCoR).
What are the four different chromatin modifying enzymes involved?
HISTONE ACETYL TRANSFERASES (HATs):
-acetylate lysine residues on histones, which leads to unpacking of chromatin
HISTONE METHYL TRANSFERASES (HMTs):
- methylate lysine residues on histones, which leads to compaction of chromatin
HISTONE DEACETYLASES (HDACs):
- de-acetylate histones
DEMETHYLASES (DMs):
- de-methylate histones
Explain this mechanism at work, with the example of the thyroid hormone receptor
The thyroid hormone receptor (TR) binds to the thyroid response element (TRE) on the DNA. This triggers the recruitment of the histone modification enzymes HDAC and DM via the N-CoR (which causes demethylation). A T3 (thyroid hormone) bonds to the TR. After that, the histone modification enzymes HAT and HMT are recruited via the N-CoA (which causes acetylation, ie. the unpacking of DNA)
