Transcriptional Gene Regulation (Regular TFs, Inducible TFs, Chromatin, Histone Mods, DNA methylation)

Question 1

What is transcriptional regulation?

Answer 1

It is involved in the control of RNA polymerase’s ability to bind to DNA and initiate transcription

Question 2

What are general (basal) transcription factors?

Answer 2

General transcription factors proteins that bind to specific DNA sequences and regulate gene expression by either activating/repressing transcription
- basal TFs needed for transcription of ANY gene
- RNA polymerase can only attach to the promoter with the help of basal TFs

Question 3

Give examples of general TFs and state their role in transcription

Answer 3

TFIID, TFIIH, TFIIF, TFIIB, TFIIE
- TFIID recognises TATA box
- TFIIH unwinds DNA at start of transcription

Question 4

What are inducible TFs?

Answer 4

Inducible TFs are activated in response to external stimuli. Signalling cascades are key to their activation.

Question 5

How do signalling cascades begin?

Answer 5

• They begin when an extracellular ligand binds to a cell surface receptor which causes a change in the receptor
• This triggers the activation of intracellular signalling molecules (protein kinases/G proteins).
• Signalling molecules then activate downstream signalling pathways which lead to activation of inducible TFs.

Question 6

Give an example of such a signalling cascade

Answer 6

Nuclear factor kappa B (NF-kB) pathway.

Question 7

How is the NF-kB signalling pathway activated?

Answer 7

It is activated when
- the kinase complex that phosphorylates an inhibitor of kB protein becomes activated
- this leads to ubiquitination of IkB and proteasomal degradation
- this releases active NF-kB which translocates to the nucleus

Question 8

List 3 common features of inducible TFs

Answer 8

1. Activation domain - regulates activation of transcription when bound to DNA
2. They bind to specific short DNA sequences in promoter regions
3. They are often cytoplasmic and translocate to the nucleus after activation

Question 9

How do inducible TFs regulate expression? (altering expression levels)

Answer 9

Inducible TFs regulate transcription by:
- Binding to specific DNA sequences and recruiting co-activators/co-repressors to the promoter/enhancer regions
- This action modulates the activity of RNA polymerase
- This results in the initiation/repression of transcription of target genes, leading to changes in the levels or mRNA and ultimately protein

Question 10

How do inducible TFs regulate transcription? (heterodimers/homodimers)

Answer 10

Inducible TFs can interact with other TFs to form hetero/homo dimers that bind to specific DNA sequences.
This binding can either activate/repress transcription

Question 11

What is chromatin? What is it’s basic unit? What is this basic unit made up of?

Answer 11

Chromatin is a complex of DNA and histones and its basic unit is the nucleosome which is made up of 147 base pairs of DNA wrapped around an octamer of core histones.

Question 12

Why is chromatin structure important in regulating transcription?

Answer 12

The structure of chromatin is important as it dictates whether or not transcription machinery (TFs, RNA polymerase) will have access to the DNA. Condensing of chromatin into the nucleosome makes it difficult for transcription factors to access the DNA. Chromatin structure can be loosened to allow for better access to DNA

Question 13

What is euchromatin?

Answer 13

Euchromatin is a loosely packed form of chromatin composed of structures such as 30nm fibres and looped regions.
DNA is more accessible in this form of chromatin and so gene expression is active in euchromatin

Question 14

What is heterochromatin?

Answer 14

A highly condensed form of chromatin. It is associated with silent or non-expressed areas of the genome

Question 15

Why must nucleosomes be disassembled and reassembled during transcription? How does this occur?

Answer 15

In the standard nucleosome, TFs and RNA polymerase cannot bind to the DNA. For this reason, they must be disassembled and reassembled. This requires chromatin remodelling complexes and histone chaperones

Question 16

What are histone modifications?

Answer 16

Histone modifications are key in regulating chromatin structure. They can alter the physical properties of chromatin, making DNA more accessible to TFs.

Question 17

Name some of the several types of histone modifications. Which are the main ones?

Answer 17

1. Acetylation
2. Methylation
3. Ubiquitination
4. Phosphorylation
5. Sumolyation
   Acetylation and methylation are the main histone modifications

Question 18

Explain how histone acetylation works?

Answer 18

Histone acetylation involves
- the addition of an acetyl group to from acetyl coenzyme A to specific lysine residues on histones
- the process is catalysed by acetyltransferases
- acetylation removes the positive charge from lysine residues which leads to lower affinity of the DNA-Histone complex and promotes a more relaxed chromatin structure
Acetylated lysine residues create binding sites for protein containing bromodomains. These proteins recognise and bind to acetylated histones, further facilitating transcription

Question 19

What type of mechanism is DNA methylation?

Answer 19

DNA methylation is one of several epigenetic mechanisms that can be used to regulate gene expression

Question 20

How does DNA methylation work to regulate gene expression and chromatin structure?

Answer 20

• Methylation of the 5’ position of cytosine.
• this methylation happen at CpG islands in promoter and enhancer regions
• methyl groups added to CpG sites, attract proteins called methyl-binding domain proteins (MBDs)
• these MBDs recruit other proteins involved in chromatin modelling and transcriptional repression
• the presence of methyl groups interferes with the binding of TFs, preventing transcription.

Question 21

What catalyses DNA methylation? What is the function of each?

Answer 21

DNA methylation is catalysed by DNA methyltransferases Dnmt1 and Dnmt2. Dnmt1 maintains methylation of DNA after replication while Dnmt2 initiates de novo methylation.

Question 22

Give an example where DNA methylation altered gene expression? What is this phenomenon called? What happens to the silenced chromosome?

Answer 22

This is shown by the inactivation of the X chromosome in females.
- early in embryonic development, one of the two X chromosomes in females is randomly and permanently deactivated due to DNA methylation
This phenomenon is called X-inactivation.
The silenced chromosome is condensed into a structure called a Barr body where is is maintained in a silent state.