Lecture 15 - Regulation of transcription II Flashcards
What kind of roles do proteins in eukaryotes regulate transcription.
As in prokaryotes regulatory proteins (transcription factors) recognise specific DNA sequences.
They are often modular and can have additional domains that:
* Aid oligomerization
* Activate or repress transcription
* Interact with other regulators
They often recruit other proteins that help to regulate transcription that do not have DNA-binding activity themselves (co-activators and co-repressors).
How does histone modification regulate transcription?
The histone proteins that comprise the octamer core of the nucleosome each have N-terminal tails that can be covalently modified in various ways.
Histone acetylation
Histone acetylation is caried out by histone acetyl transferases (HATs). Deacetylation is carried out by histone deacetylases (HDACs)
Modification of lysine residues:
* Hypoacetylation - strong internuclosomal interactions: histone tails constrain wrapping of DNA on nucleosome surface.
* Hyperacetylation - weak internuclosomal interactions: histone tails do not constrain DNA, which is accessible to transcription factors. Acetyl groups can also directly recruit proteins via bromodomain proteins.
Nucleosome remodelling complexes
Nucleosome remodelling complexes are binding sites for transcription factors, they can be inaccessible as they are wrapped around nucleosomes.
Chromatin remodelling complexes (e.g. SWI/SNF) use ATP to move the histone octamer. They can be recruited either sequence specifically or by histone modification.
DNA methylation and transcriptional control
In the DNA of some eukaryotes (e.g. mammals) cytosine residues are methylated at CpG sites.
Transcriptionally active genes - lower levels of DNA methylation
Methylation - affects chromatin structure and transcription. The pattern of methylation can change in conditions such as cancer, aging and fragile X syndrome.
Methyl groups on either DNA or histone tails can recruit methyl-binding proteins which serve to recruit other proteins that modify chromatin. This affects gene expression.
What is the role of the mediator complex?
RNA polymerase II requires the presence of the general transcription factors (e.g. TFIID) to bind to the promotor.
It also requires the Mediator complex, which consists of approximately 20 proteins is 1 MDa in size.
(Discovered in yeast)
How do bacteria alter gene expression in responce to their external environment.
Bacteria can alter gene expression in response to their external environment.
Eukaryotic cells do the same thing but use activators much more extensively
Examples of eternal cues include nutrient availability, stress, hormones and cytokines.
Describe ELK recruitement of mediator complex in proliferation.
Three genes GAL1, GAL7 and GAL10 encode enzymes that function in a pathway to metabolise galactose.
In the absence of galactose there is no transcription
If galactose is present and glucose is absent there is rapid transcription and glucose exerts catabolite repression.
Analogous to the bacterial lac operon but although GAL1, GAL& and GAL10 are located near to each other - they do not represent an operon.
GAL4 - regulatory protein binds to UASG (upstream activator sequence galactose)
* Gal4 activates transcription by binding to the UASG sequence
* In the absence of galactose, Fal80 binds to Gal4, preventing transcription.
When galactose is present, Gal3 binds to Gal80, preventing Gal80, preventing Gal80 binding to Gal4, and allowing Gal4 to recruit SAGA and Mediator, which activates transcription.
Discuss nuclear receptor protiens.
Humans have >30 nuclear receptor proteins that bind to particular signalling molecules (hormones)
1. Ligand binding leads to a conformational change that allows them to drive transcription.
2. In some cases binding of the ligand allows translocation to the nucleus e.g. the glucocorticoid receptor.
Describe transcriptional repression in nutrient sensing yeast.
Ume6 responds to nutritional cues in yeast can activate or repress transcription
When there is enough N and C in the cell, Ume6 bind DNA and recruits co-repressors (Sin3, Rpd3, Isw2)
* Rpd3 is a histone deacetylase
* Isw2 is a nucleosome remodelling enzyme
Ume6 is phosphorylated in the absence of N and C, Sin3 and Rpd3 dissociate, and a co-activator, Ime1 is recruited.
What is proximal promotor pausing
Promotor proximal pausing
In many genes RNA polymerase II stalls after 35-50 bp have been transcribed - called proximal promotor pausing and promoted by negative elongation factors (e.g. NELF and DSIF)
Relief of this pausing allows transcriptional elongation to proceed - this allows the cell to respond rapidly to change.
An example of this is the expression of the gene that encodes the Drosophila Hsp70 protein, a chaperone that protects cells form high temperatures.
Describe hsp70 transcription.
In the absence of heat stress, transcription factor GAGA binds and recruits NURF
NURF (nucleosome remodelling factor) alters the structure of chromatin exposing the control elements
However negative elongation factors (NELF and DSIF) prevent the phosphorylation of the Rpb1 C terminal domain.
If the temperature rises suddenly Hsf protein forms a trimer
The trimer binds to the HSE sequence
It interacts with Mediator to recruit a Kinase and the CTD is then phosphorylated, relieving pausing.
