Chromatin structure and histone codes

Question 1

What are histones?

Answer 1

• Histones are highly alkaline proteins found in eukaryotic cell nuclei.
• They are responsible for the first level of packaging and ordering of DNA into structural units called nucleosomes.

Question 2

What are nucleosomes?

Answer 2

• A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores.
• The octamer core is made up of a pair (so 2 each) of H2A, H2B, H3 and H4 histones.
• The positively-charged N-terminal tails are outside the octamer core.

Question 3

Describe the 4 levels of DNA folding.

Answer 3

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.

Question 4

What do chromosomes predominantly consist of?

Answer 4

1. DNA
2. Histone proteins
3. Non-coding RNA
4. Non-coding proteins

Question 5

What does compaction of nucleosomes involve?

Answer 5

• 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)

Question 6

What happens to histones during transcription or DNA replication?

Answer 6

• The nucleosomes must be removed from the DNA in front of the polymerase, and be replaced behind the polymerase.
• This is done by hosting remodelling factors (enzymes that remove and replace nucleosomes).

Question 7

What is the difference between heterochromatin and euchromatin?

Answer 7

1. Heterochromatin :
   - Darkly training areas of chromatin.
   - Few genes present.
   - It has a dense, higher order packaging of nucleosomes.
2. Euchromatin :
   - Lighty staining area of chromatin.
   - It is rich in genes.
   - It is made up of nucleosomes, but not dense higher order packaging.

Question 8

Name and describe the two types of heterochromatin.

Answer 8

1. 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.
2. 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 euchromatin in other cell types.

Question 9

What determined whether nucleosomes are packaged as euchromatin or heterochromatin?

Answer 9

There is one key level of control: chemical modification of lysine residues on histone tails, such as acetylation, methylation, etc.

Question 10

How do chromosomes appear when histones are extracted?

Answer 10

• They don’t completely fall apart.
• Instead, they appear as long DNA loops attached to a scaffold of tightly bound proteins.
• 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.

Question 11

Name the method learnt to investigate chromatin structure and describe it.

Answer 11

• 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

Question 12

How do proteins fit in DNA if it is so tightly packed?

Answer 12

• First, transcription factors open up the chromatin structure.
• Then, they recruit basal transcription factors. (TF2A,TF2B,…)

Question 13

How do the transcription factors open up the chromatin structure?

Answer 13

The transcription factors recruit chromatin modifying enzymes via a nuclear coactivator (NCoA) or corepressor (NCoR).

Question 14

What are the four different chromatin modifying enzymes? What are their functions?

Answer 14

1. HISTONE ACETYL TRANSFERASES (HATs):
   - acetylate lysine residues on histones, which leads to unpacking of chromatin
2. HISTONE METHYL TRANSFERASES (HMTs):
   - methylate lysine residues on histones, which leads to compaction of chromatin
3. HISTONE DEACETYLASES (HDACs):
   - de-acetylate histones
4. DEMETHYLASES (DMs):
   - de-methylate histones

Question 15

How does the thyroid receptor complex work?

Answer 15

1. The thyroid hormone receptor (TR) binds to the thyroid response element (TRE) on the DNA.
2. This triggers the recruitment of the histone modification enzymes HDAC and DM via the N-CoR (which causes demethylation).
3. A T3 (thyroid hormone) bonds to the TR.
4. After that, the histone modification enzymes HAT and HMT (histone methyl transferases, they methylate the histone tail) are recruited via the N-CoA (which causes acetylation, ie. the unpacking of DNA).

Histone tails are demethylated by histone demethylases (HDMs). [opposite of HMTs]

Question 16

What is the ‘histone code’?

Answer 16

The histone code is a hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins, primarily on their unstructured ends.